4.8.0

Improve performance of `IndexPairBonds` assignment

.eslintignore

@@ -1,3 +1,4 @@
 node_modules/*
 build/*
+docs/site/*
 lib/*

CHANGELOG.md

@@ -5,7 +5,144 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
-## [v4.2.0] - 2023-04-05
+## [v4.8.0] - 2024-10-27
+
+- Add SSAO support for transparent geometry
+- Fix SSAO color not updating
+- Improve blending of overlapping outlines from transparent & opaque geometries
+- Default to `blended` transparency on iOS due to `wboit` not being supported.
+- Fix direct-volume with fog off (and on with `dpoit`) and transparent background on (#1286)
+- Fix missing pre-multiplied alpha for `blended` & `wboit` with no fog (#1284)
+- Fix backfaces visible using blended transparency on impostors (#1285)
+- Fix StructureElement.Loci.isSubset() only considers common units (#1292)
+- Fix `Scene.opacityAverage` calculation never 1
+- Fix bloom in illumination mode
+- Fix `findPredecessorIndex` bug when repeating values
+- MolViewSpec: Support for transparency and custom properties
+- MolViewSpec: MVP Support for geometrical primitives (mesh, lines, line, label, distance measurement)
+- Mesoscale Explorer: Add support for 4-character PDB IDs (e.g., 8ZZC) in PDB-Dev loader
+- Fix Sequence View in Safari 18
+- Improve performance of `IndexPairBonds` assignment when operator keys are available
+- ModelArchive QualityAssessment extension:
+    - Add support for ma_qa_metric_local_pairwise mmCIF category
+    - Add PAE plot component
+- Add new AlphaFoldDB-PAE example app
+- Add support for LAMMPS data and dump formats
+- Remove extra anti-aliasing from text shader (fixes #1208 & #1306)
+
+## [v4.7.1] - 2024-09-30
+
+- Improve `resolutionMode` (#1279)
+    - Add `auto` that picks `scaled` for mobile devices and `native` elsewhere
+    - Add `resolution-mode` Viewer GET param
+    - Add `PluginConfig.General.ResolutionMode` config item
+
+## [v4.7.0] - 2024-09-29
+
+- Add illumination mode
+    - Path-traced SSGI
+    - Automatic thickness (estimate)
+        - Base thickness as max(backface depth) - min(frontface depth)
+        - Per object density factor to adjust thickness
+    - Progressively trace samples to keep viewport interactive
+    - Toggle on/off by pressing "G"
+    - `illumination` Viewer GET param
+- Enables dXrayShaded define when rendering depth
+- Fix handling of PDB files that have chains with same id separated by TER record (#1245)
+- Sequence Panel: Improve visuals of unmodeled sequence positions (#1248)
+- Fix no-compression xtc parser (#1258)
+- Mol2 Reader: Fix mol2 status_bit read error (#1251)
+- Fix shadows with multiple lights
+- Fix impostor sphere interior normal when using orthographic projection
+- Add `resolutionMode` parameter to `Canvas3DContext`
+    - `scaled`, divides by `devicePixelRatio`
+    - `native`, no changes
+- Add `CustomProperty.Context.errorContext` to support reporting errors during loading of custom properties (#1254)
+    - Use in MolViewSpec extension
+- Mesoscale Explorer: fix color & style issues
+- Remove use of deprecated SASS explicit color functions
+- Allow "Components" section to display nested components created by "Apply Action > Selection".
+
+## [v4.6.0] - 2024-08-28
+
+- Add round-caps option on tubular alpha helices
+- Fix missing Sequence UI update on state object removal (#1219)
+- Improved prmtop format support (CTITLE, %COMMENT)
+- Avoid calculating bonds for water units when `ignoreHydrogens` is on
+- Add `Water` trait to `Unit`
+- Improve entity-id coloring for structures with multiple models from the same source (#1221)
+- Wrap screenshot & image generation in a `Task`
+- AlphaFold DB: Add BinaryCIF support when fetching data
+- PDB-Dev: Add support for 4-character PDB IDs (e.g., 8ZZC)
+- Fix polymer-gap visual coloring with cartoon theme
+- Add formal-charge color theme (#328)
+- Add more coloring options to cartoon theme
+- Use `CompressionStream` Browser API when available
+- Add `pdbx_structure_determination_methodology` mmcif field and `Model` helpers
+- Fix cartoon representation not updated when secondary structure changes
+- Add Zhang-Skolnick secondary-structure assignment method which handles coarse-grained models (#49)
+- Calculate bonds for coarse-grained models
+- VolumeServer: Add `health-check` endpoint + `healthCheckPath` config prop to report service health
+- ModelServer: Add `health-check` endpoint + `healthCheckPath` config prop to report service health
+
+## [v4.5.0] - 2024-07-28
+
+- Separated postprocessing passes
+- Take into account explicit hydrogens when computing hydrogen bonds
+- Fix DoF with pixel ratios =! 1
+- Fix DoF missing transparent depth
+- Fix trackball pinch zoom and add pan
+- Fix aromatic link rendering when `adjustCylinderLength` is true
+- Change trackball animate spin speed unit to radians per second
+- Fix `mol-plugin-ui/skin/base/components/misc.scss` syntax to be in line with latest Sass syntax
+- Handle missing theme updates
+    - Fix trajectory-index color-theme not always updated (#896)
+    - Fix bond cylinders not updated on size-theme change with `adjustCylinderLength` enabled (#1215)
+- Use `OES_texture_float_linear` for SSAO when available
+
+## [v4.4.1] - 2024-06-30
+
+- Clean `solidInterior` transparent cylinders
+- Create a transformer to deflate compressed data
+- Adjust Quick Styles panel button labels
+- Improve camera interpolation code (interpolate camera rotation instead of just position)
+- Mesoscale Explorer
+    - Add `illustrative` coloring option
+    - Press 'C' to toggle between center and zoom & center on click
+    - Add entities selection description
+    - Clicking a leaf node in the right panel tree will center each instance in turn
+    - Add measurement controls to right panel
+    - Mouse left click on label with snapshot key will load snapshot
+    - Mouse hover over label with protein name highlight entities with the same name
+    - Custom ViewportSnapshotDescription with custom MarkdowAnchor
+        - \# other snapshots with a given key \[...](#key)
+        - i highlight a protein with a given NAME \[...](iNAME)
+        - g highlight a group with a given group type and group name \[...](ggrouptype.groupname)
+        - h URLs with a given link \[...](http...)
+    - Snapshot description panel window size and text can be resized and hidden with new icons
+    - Add styles controls to right panel
+    - Add viewport settings to left panel
+    - Add app info component to left panel with interactive tour and doc link
+- Fixes SSAO edge artifacts (#1122)
+    - Add `reuseOcclusion` parameter to multi-sample pass
+    - Add `blurDepthBias` parameter to occlusion pass
+    - Handle near clip in SSAO blur
+- Support reading score from B-factor in pLDDT color theme
+- Add Cel-shading support
+    - `celShaded` geometry parameter
+    - `celSteps` renderer parameter
+- Add the ability to customize the Snapshot Description component via `PluginUISpec.components.viewport.snapshotDescription`
+- Add `doNotDisposeCanvas3DContext` option to `PluginContext.dispose`
+- Remove support for density data from edmaps.rcsb.org
+
+## [v4.3.0] - 2024-05-26
+
+- Fix State Snapshots export animation (#1140)
+- Add depth of field (dof) postprocessing effect
+- Add `SbNcbrTunnels` extension for for visualizing tunnels in molecular structures from ChannelsDB (more info in [tunnels.md](./docs/docs/extensions/tunnels.md))
+- Fix edge case in minimizing RMSD transform computation
+
+## [v4.2.0] - 2024-05-04
 
 - Add emissive material support
 - Add bloom post-processing
@@ -23,7 +160,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix SSAO artifacts (@corredD, #1082)
 - Fix bumpiness artifacts (#1107, #1084)
 
-## [v4.1.0] - 2023-03-31
+## [v4.1.0] - 2024-03-31
 
 - Add `VolumeTransform` to translate/rotate a volume like in a structure superposition
 - Fix BinaryCIF encoder edge cases caused by re-encoding an existing BinaryCIF file
@@ -34,13 +171,13 @@ Note that since we don't clearly distinguish between a public and private interf
     - This can give results similar to pymol's surface_ramp_above_mode=1
 - Add `rotation` parameter to skybox background
 
-## [v4.0.1] - 2023-02-19
+## [v4.0.1] - 2024-02-19
 
 - Fix BinaryCIF decoder edge cases. Fixes mmCIF model export from data provided by ModelServer.
 - MolViewSpec extension: support for MVSX file format
 - Revert "require WEBGL_depth_texture extension" & "remove renderbuffer use"
 
-## [v4.0.0] - 2023-02-04
+## [v4.0.0] - 2024-02-04
 
 - Add Mesoscale Explorer app for investigating large systems
 - [Breaking] Remove `cellpack` extension (superseded by Mesoscale Explorer app)
@@ -76,7 +213,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add stochastic/dithered transparency to fade overlapping LODs in and out
 - Add "Automatic Detail" preset that shows surface/cartoon/ball & stick based on camera distance
 
-## [v3.45.0] - 2023-02-03
+## [v3.45.0] - 2024-02-03
 
 - Add color interpolation to impostor cylinders
 - MolViewSpec components are applicable only when the model has been loaded from MolViewSpec
@@ -90,7 +227,7 @@ Note that since we don't clearly distinguish between a public and private interf
   - Support `disableInteractiveUpdates` to only trigger updates once the control loses focus
 - Move dependencies related to the headless context from optional deps to optional peer deps
 
-## [v3.44.0] - 2023-01-06
+## [v3.44.0] - 2024-01-06
 
 - Add new `cartoon` visuals to support atomic nucleotide base with sugar
 - Add `thicknessFactor` to `cartoon` representation for scaling nucleotide block/ring/atomic-fill visuals

data/cif-field-names/mmcif-field-names.csv

@@ -107,6 +107,7 @@ entity.id
 entity.type
 entity.src_method
 entity.pdbx_description
+entity.pdbx_parent_entity_id
 entity.formula_weight
 entity.pdbx_number_of_molecules
 entity.details
@@ -262,6 +263,7 @@ software.version
 struct.entry_id
 struct.title
 struct.pdbx_descriptor
+struct.pdbx_structure_determination_methodology
 
 struct_asym.id
 struct_asym.pdbx_blank_PDB_chainid_flag
@@ -366,18 +368,43 @@ struct_site.details
 
 struct_site_gen.id
 struct_site_gen.site_id
-struct_site_gen.pdbx_num_res
-struct_site_gen.label_comp_id
+struct_site_gen.auth_asym_id
+struct_site_gen.auth_atom_id
+struct_site_gen.auth_comp_id
+struct_site_gen.auth_seq_id
+struct_site_gen.details
+struct_site_gen.label_alt_id
 struct_site_gen.label_asym_id
+struct_site_gen.label_atom_id
+struct_site_gen.label_comp_id
 struct_site_gen.label_seq_id
 struct_site_gen.pdbx_auth_ins_code
-struct_site_gen.auth_comp_id
-struct_site_gen.auth_asym_id
-struct_site_gen.auth_seq_id
-struct_site_gen.label_atom_id
-struct_site_gen.label_alt_id
+struct_site_gen.pdbx_num_res
 struct_site_gen.symmetry
-struct_site_gen.details
+
+struct_site_keywords.site_id
+struct_site_keywords.text
+
+struct_mon_prot_cis.pdbx_id
+struct_mon_prot_cis.auth_asym_id
+struct_mon_prot_cis.auth_comp_id
+struct_mon_prot_cis.auth_seq_id
+struct_mon_prot_cis.label_alt_id
+struct_mon_prot_cis.label_asym_id
+struct_mon_prot_cis.label_comp_id
+struct_mon_prot_cis.label_seq_id
+struct_mon_prot_cis.pdbx_PDB_ins_code
+struct_mon_prot_cis.pdbx_PDB_ins_code_2
+struct_mon_prot_cis.pdbx_PDB_model_num
+struct_mon_prot_cis.pdbx_auth_asym_id_2
+struct_mon_prot_cis.pdbx_auth_comp_id_2
+struct_mon_prot_cis.pdbx_auth_ins_code
+struct_mon_prot_cis.pdbx_auth_ins_code_2
+struct_mon_prot_cis.pdbx_auth_seq_id_2
+struct_mon_prot_cis.pdbx_label_asym_id_2
+struct_mon_prot_cis.pdbx_label_comp_id_2
+struct_mon_prot_cis.pdbx_label_seq_id_2
+struct_mon_prot_cis.pdbx_omega_angle
 
 symmetry.entry_id
 symmetry.cell_setting
@@ -849,6 +876,17 @@ ma_qa_metric_local.metric_value
 ma_qa_metric_local.model_id
 ma_qa_metric_local.ordinal_id
 
+ma_qa_metric_local_pairwise.ordinal_id
+ma_qa_metric_local_pairwise.model_id
+ma_qa_metric_local_pairwise.label_asym_id_1
+ma_qa_metric_local_pairwise.label_comp_id_1
+ma_qa_metric_local_pairwise.label_seq_id_1
+ma_qa_metric_local_pairwise.label_asym_id_2
+ma_qa_metric_local_pairwise.label_comp_id_2
+ma_qa_metric_local_pairwise.label_seq_id_2
+ma_qa_metric_local_pairwise.metric_id
+ma_qa_metric_local_pairwise.metric_value
+
 ma_software_group.group_id
 ma_software_group.ordinal_id
 ma_software_group.software_id

docs/docs/extensions/tunnels.md

@@ -0,0 +1,118 @@
+# Tunnel Visualization Extension
+This documentation outlines the usage of the Mol* extension for visualizing tunnels in molecular structures. The extension integrates with Mol* to render 3D representations of tunnels using specified data sources and properties.
+
+The extension is a key component in ChannelsDB (https://channelsdb2.biodata.ceitec.cz/), enabling users to visualize tunnels within molecules directly from the database. While it is used with ChannelsDB, users can also input their own data or connect to different databases, ensuring versatility across various research environments.
+
+## Data Types
+The primary data types involved in tunnel visualization are:
+
+### Tunnel
+A Tunnel object contains the actual tunnel data necessary for visualization. It consists of:
+
+- `data`: An array of `Profile` objects that describe the tunnel at various points.
+- `props`: Properties such as the tunnel's type, ID, and optional labels or descriptions.
+
+### Profile
+A `Profile` object in a `Tunnel` holds detailed geometric and physical properties of a tunnel at specific points along its length. These properties include:
+
+- `Charge`: The electric charge at a specific point in the tunnel.
+- `Radius`: The overall radius of the tunnel at this point.
+- `FreeRadius`: The radius of the tunnel not obstructed by any molecular elements.
+- `T`: Temperature factor or a similar property related to the point.
+- `Distance`: Distance along the tunnel's path from the start.
+- `X`, `Y`, `Z`: Coordinates of the point in 3D space.
+
+These profiles are crucial for understanding the physical and chemical environment inside the tunnel, allowing for detailed analysis and visualization.
+
+Example:
+```json
+"Profile": [
+    {
+        "Radius": 1.49,
+        "FreeRadius": 1.49,
+        "T": 0,
+        "Distance": 0,
+        "X": -19.152,
+        "Y": -22.654,
+        "Z": -13.034,
+        "Charge": 0
+    },
+    {
+        "Radius": 1.524,
+        "FreeRadius": 1.524,
+        "T": 0.00625,
+        "Distance": 0.087,
+        "X": -19.162,
+        "Y": -22.596,
+        "Z": -12.969,
+        "Charge": 0
+    },
+    {
+        "Radius": 1.56,
+        "FreeRadius": 1.56,
+        "T": 0.0125,
+        "Distance": 0.174,
+        "X": -19.171,
+        "Y": -22.539,
+        "Z": -12.905,
+        "Charge": 0
+    }
+]
+```
+## Transformers Usage
+The extension uses several transformations to process and visualize tunnel data:
+
+### Tunnels Data Transformer
+- `Purpose`: Converts a collection of Tunnel data into a state object.
+- `Usage`:
+    ```typescript
+    update.toRoot().apply(TunnelsFromRawData, { data: tunnels });
+    ```
+
+### Tunnel Data Provider
+- `Purpose`: Converts single Tunnel data into a state object for individual processing.
+- `Usage`:
+    ```typescript
+    update.toRoot().apply(TunnelFromRawData, {
+        data: {
+            data: tunnel.Profile,
+            props: { id: tunnel.Id, type: tunnel.Type }
+        }
+    });
+    ```
+
+### Tunnel Shape Provider
+- `Purpose`: Provides the shapes for rendering the tunnel based on WebGL context and shape parameters.
+- `Usage`:
+    ```typescript
+    update.apply(TunnelShapeProvider, {
+        webgl,
+    }).apply(StateTransforms.Representation.ShapeRepresentation3D);
+    ```
+
+## Visualization Examples
+To help users understand how to use these transformations in practice, include detailed examples:
+
+### Visualizing Multiple Tunnels
+This example ([runVisualizeTunnels](../../../src/extensions/sb-ncbr/tunnels/examples.ts#L19)) demonstrates how to visualize multiple tunnels from a fetched dataset.
+```typescript
+update.toRoot()
+        .apply(TunnelsFromRawData, { data: tunnels })
+        .apply(SelectTunnel)
+        .apply(TunnelShapeProvider, { webgl })
+        .apply(StateTransforms.Representation.ShapeRepresentation3D);
+```
+
+### Visualizing a Single Tunnel
+This example ([runVisualizeTunnel](../../../src/extensions/sb-ncbr/tunnels/examples.ts#L46)) shows how to visualize a single tunnel.
+```typescript
+update.toRoot()
+        .apply(TunnelFromRawData, {
+            data: {
+                data: tunnel.Profile,
+                props: { id: tunnel.Id, type: tunnel.Type }
+            }
+        })
+        .apply(TunnelShapeProvider, { webgl })
+        .apply(StateTransforms.Representation.ShapeRepresentation3D);
+```

docs/docs/misc/exporting-components.md

@@ -0,0 +1,59 @@
+# Exporting components
+
+Export components data can be useful to reproduce the same view in a different visualization software.
+To do that, one would need to loop over all components, extract its selection (for example by using atom indices) and its representations (type, coloring and sizing).
+
+### Getting assets / molecular files
+
+```js
+for (const { asset, file } of plugin.managers.asset.assets) {
+  const isFile = asset.asset.kind === 'url'
+  console.log(asset.asset.id)
+  console.log(isFile)
+  const data = await file.arrayBuffer()
+}
+```
+
+### Getting components per structure
+
+```js
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
+//...
+
+const componentManager = plugin.managers.structure.component;
+for (const structure of componentManager.currentStructures) {
+  if (!structure.properties) {
+      continue;
+  }
+  const cell = plugin.state.data.select(structure.properties.cell.transform.ref)[0];
+  if (!cell || !cell.obj) {
+    continue;
+  }
+  const structureData = (cell.obj as PSO.Molecule.Structure).data;
+  for (const component of structure.components) {
+    if (!component.cell.obj) {
+      continue;
+    }
+    // For each component in each structure, display the content of the selection
+    Structure.eachAtomicHierarchyElement(component.cell.obj.data, {
+      atom: location => console.log(location.element)
+    });
+    for (const rep of component.representations) {
+      // For each representation of the component, display its type
+      console.log(rep.cell?.transform?.params?.type?.name)
+
+      // Also display the color for each atom
+      const colorThemeName = rep.cell.transform.params?.colorTheme.name;
+      const colorThemeParams = rep.cell.transform.params?.colorTheme.params;
+      const theme = plugin.representation.structure.themes.colorThemeRegistry.create(
+        colorThemeName || '',
+        { structure: structureData },
+        colorThemeParams
+      ) as ColorTheme<typeof colorThemeParams>;
+      Structure.eachAtomicHierarchyElement(component.cell.obj.data, {
+        atom: loc => console.log(theme.color(loc, false))
+      });
+    }
+  }
+}
+```

docs/docs/misc/interesting-pdb-entries.md

@@ -22,7 +22,7 @@
 * Discontinuous chains, i.e. gaps in the sequence (3sn6)
 * Lots of sheets (1cbs)
 * DNA (2np2, 1d66)
-* C-alpha only (2rcj)
+* C-alpha only (2RCJ, 6ZIG, 5AJ2)
 * Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
 * Close backbone atoms but not linked (e.g. 4HIV)
 * Non-standard residues

docs/docs/plugin/custom-library.md

@@ -0,0 +1,193 @@
+# Building a Custom Library
+
+This page goes over creating a custom Mol\* based library usable inside a `<script>` tag in an HTML page.
+
+## Setup
+
+- Create a new npm/yarn package
+- Install `molstar` and `esbuild` packages
+
+```
+mkdir molstar-lib
+cd molstar-lib
+npm init
+npm install molstar
+npm install esbuild --save-dev
+```
+
+## Example Library Code
+
+Create new file `src/index.ts` (or `.js` if you don't want to use TypeScript):
+
+```ts
+import { DefaultPluginSpec, PluginSpec } from 'molstar/lib/mol-plugin/spec';
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+
+export async function initViewer(element: string | HTMLDivElement, options?: { spec?: PluginSpec }) {
+    const parent = typeof element === 'string' ? document.getElementById(element)! as HTMLDivElement : element;
+    const canvas = document.createElement('canvas') as HTMLCanvasElement;
+    parent.appendChild(canvas);
+
+    const spec = options?.spec ?? DefaultPluginSpec();
+
+    const plugin = new PluginContext(spec);
+    await plugin.init();
+
+    plugin.initViewer(canvas, parent);
+
+    return plugin;
+}
+
+export async function loadStructure(
+    plugin: PluginContext,
+    url: string,
+    options?: { format?: string, isBinary?: boolean }
+) {
+    const data = await plugin.builders.data.download(
+        { url, isBinary: options?.isBinary }
+    );
+    const trajectory = await plugin.builders.structure.parseTrajectory(
+        data,
+        options?.format ?? 'mmcif' as any
+    );
+    const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    return preset;
+}
+```
+
+## Building the Library
+
+Add new commands to the `scripts` section of the `package.json` file
+
+```json
+"scripts": {
+  "build": "esbuild src/index.ts --bundle --outfile=./build/js/index.js --global-name=molstarLib",
+  "watch": "esbuild src/index.ts --bundle --outfile=./build/js/index.js --global-name=molstarLib --watch"
+}
+```
+
+and run the command `npm run build` (or `watch` for interactive development experience). This will create `build/js/index.js` file which can be imported with a `<script>` tag and the exported functions called view the `molstarLib` prefix (you can customize this parameter).
+
+## Using the Library
+
+Create file `build/index.html`:
+
+```html
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Library Example</title>
+    </head>
+    <style>
+        #viewer {
+            position: absolute;
+            width: 800px;
+            height: 600px;
+        }
+    </style>
+    <script type="text/javascript" src="./js/index.js"></script>
+    <body>
+        <div id="viewer"></div>
+        <script type="text/javascript">
+            async function init() {1
+                const plugin = await molstarLib.initViewer("viewer");
+                await molstarLib.loadStructure(
+                    plugin,
+                    "https://models.rcsb.org/4hhb.bcif",
+                    { isBinary: true }
+                );
+            }
+            init();
+        </script>
+    </body>
+</html>
+```
+
+After opening `index.html` in a browser, you should see 
+
+![lib-example](lib-example.png)
+
+## Using Mol* React UI
+
+The above example does not make use of the default Mol\* React UI and any UI components are therefore the author's responsibility. The below examples show how to (re)use the Mol\* React UI.
+
+- Create `src/ui.tsx`:
+```tsx
+import React from 'react';
+import { createRoot } from 'react-dom/client';
+
+import { DefaultPluginUISpec, PluginUISpec } from 'molstar/lib/mol-plugin-ui/spec';
+import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
+import { Plugin } from 'molstar/lib/mol-plugin-ui/plugin';
+
+export async function initViewerUI(element: string | HTMLDivElement, options?: { spec?: PluginUISpec }) {
+    const parent = typeof element === 'string' ? document.getElementById(element)! as HTMLDivElement : element;
+    const spec = { ...DefaultPluginUISpec(), ...options?.spec };
+    const plugin = new PluginUIContext(spec);
+    await plugin.init();
+
+    createRoot(parent).render(<Plugin plugin={plugin} />)
+
+    return plugin;
+}
+
+export async function loadStructure(plugin: PluginUIContext, url: string, options?: { format?: string, isBinary?: boolean }) {
+    const data = await plugin.builders.data.download({ url, isBinary: options?.isBinary });
+    const trajectory = await plugin.builders.structure.parseTrajectory(data, options?.format ?? 'mmcif' as any);
+    await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+}
+```
+- Create `src/style.scss`:
+```scss
+@import '../node_modules/molstar/lib/mol-plugin-ui/skin/light.scss';
+```
+- Create `build/ui.html`:
+```html
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* UI Library Example</title>
+    </head>
+    <link rel="stylesheet" type="text/css" href="css/style.css" />
+    <style>
+        #viewer {
+            position: absolute;
+            inset: 0;
+        }
+    </style>
+    <script type="text/javascript" src="./js/ui.js"></script>
+    <body>
+        <div id="viewer"></div>
+        <script type="text/javascript">
+            async function init() {
+                const plugin = await molstarLib.initViewerUI("viewer", {
+                    spec: {
+                        layout: {
+                            initial: {
+                                isExpanded: true,
+                                showControls: true,
+                            },
+                        },
+                    }
+                });
+                await molstarLib.loadStructure(plugin, "https://models.rcsb.org/4hhb.bcif", { isBinary: true });
+            }
+            init();
+        </script>
+    </body>
+</html>
+```
+
+- Install `sass`: `npm install sass -save-dev` (or use [`esbuild` plugin](https://www.npmjs.com/package/esbuild-sass-plugin) and `import` the scss file in `ui.tsx`)
+- Add scripts to `package.json`:
+```json
+"build-ui": "esbuild src/ui.tsx --bundle --outfile=./build/js/ui.js --global-name=molstarLib",
+"css": "sass src/style.scss ./build/css/style.css"
+```
+- Run `npm run build-ui` and `npm run css` (skip if using `esbuild-sass-plugin`)
+- Opening `build/ui.html`:
+![ui-example](ui-example.png)

docs/mkdocs.yml

@@ -32,6 +32,7 @@ nav:
   - Plugin:
     - Creating Instance: 'plugin/instance.md'
     - Examples: plugin/examples.md
+    - Custom Library: 'plugin/custom-library.md'
     - Selections: 'plugin/selections.md'
     - Viewer State: 'plugin/viewer-state.md'
     - Data State: 'plugin/data-state.md'
@@ -53,6 +54,8 @@ nav:
   - Extensions:
     - MolViewSpec: 'extensions/mvs/index.md'
     - wwPDB StructConn: 'extensions/struct-conn.md'
+    - Tunnels: 'extensions/tunnels.md'
   - Misc:
     - Interesting PDB entries: misc/interesting-pdb-entries.md
-repo_url: https://github.com/molstar/docs
+    - Exporting component data: exporting-components.md
+repo_url: https://github.com/molstar/docs

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "4.2.0",
+  "version": "4.8.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -106,67 +106,73 @@
     "Yakov Pechersky <ffxen158@gmail.com>",
     "Christian Dominguez <christian.99dominguez@gmail.com>",
     "Cai Huiyu <szmun.caihy@gmail.com>",
-    "Ryan DiRisio <rjdiris@gmail.com>"
+    "Ryan DiRisio <rjdiris@gmail.com>",
+    "Dušan Veľký <dvelky@mail.muni.cz>",
+    "Neli Fonseca <neli@ebi.ac.uk>",
+    "Paul Pillot <paul.pillot@tandemai.com>",
+    "Herman Bergwerf <post@hbergwerf.nl>",
+    "Eric E <etongfu@outlook.com>",
+    "Xavier Martinez <xavier.martinez.xm@gmail.com"
   ],
   "license": "MIT",
   "devDependencies": {
     "@types/cors": "^2.8.17",
     "@types/gl": "^6.0.5",
+    "@types/jest": "^29.5.14",
     "@types/pngjs": "^6.0.5",
-    "@types/jest": "^29.5.12",
-    "@types/react": "^18.3.1",
-    "@types/react-dom": "^18.3.0",
-    "@typescript-eslint/eslint-plugin": "^7.8.0",
-    "@typescript-eslint/parser": "^7.8.0",
+    "@types/react": "^18.3.12",
+    "@types/react-dom": "^18.3.1",
+    "@typescript-eslint/eslint-plugin": "^7.18.0",
+    "@typescript-eslint/parser": "^7.18.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^8.2.2",
-    "cpx2": "^7.0.1",
-    "crypto-browserify": "^3.12.0",
-    "css-loader": "^7.1.1",
-    "eslint": "^8.57.0",
+    "concurrently": "^9.0.1",
+    "cpx2": "^8.0.0",
+    "crypto-browserify": "^3.12.1",
+    "css-loader": "^7.1.2",
+    "eslint": "^8.57.1",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^11.2.0",
     "http-server": "^14.1.1",
     "jest": "^29.7.0",
     "jpeg-js": "^0.4.4",
-    "mini-css-extract-plugin": "^2.9.0",
+    "mini-css-extract-plugin": "^2.9.1",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
     "react": "^18.3.1",
     "react-dom": "^18.3.1",
-    "sass": "^1.76.0",
-    "sass-loader": "^14.2.1",
-    "simple-git": "^3.24.0",
+    "sass": "^1.80.4",
+    "sass-loader": "^16.0.2",
+    "simple-git": "^3.27.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^4.0.0",
-    "ts-jest": "^29.1.2",
-    "typescript": "^5.4.5",
-    "webpack": "^5.91.0",
+    "ts-jest": "^29.2.5",
+    "typescript": "^5.6.3",
+    "webpack": "^5.95.0",
     "webpack-cli": "^5.1.4"
   },
   "dependencies": {
-    "@types/argparse": "^2.0.16",
+    "@types/argparse": "^2.0.17",
     "@types/benchmark": "^2.1.5",
     "@types/compression": "1.7.5",
     "@types/express": "^4.17.21",
-    "@types/node": "^18.19.31",
+    "@types/node": "^18.19.59",
     "@types/node-fetch": "^2.6.11",
-    "@types/swagger-ui-dist": "3.30.4",
+    "@types/swagger-ui-dist": "3.30.5",
     "argparse": "^2.0.1",
-    "body-parser": "^1.20.2",
+    "body-parser": "^1.20.3",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
-    "express": "^4.19.2",
+    "express": "^4.21.1",
     "h264-mp4-encoder": "^1.0.12",
     "immer": "^10.1.1",
-    "immutable": "^4.3.5",
+    "immutable": "^4.3.7",
     "io-ts": "^2.2.21",
     "node-fetch": "^2.7.0",
     "react-markdown": "^9.0.1",
     "rxjs": "^7.8.1",
-    "swagger-ui-dist": "^5.17.2",
-    "tslib": "^2.6.2",
+    "swagger-ui-dist": "^5.17.14",
+    "tslib": "^2.8.0",
     "util.promisify": "^1.1.2",
     "xhr2": "^0.2.1"
   },

scripts/deploy.js

@@ -42,7 +42,7 @@ function copyViewer() {
 function copyMe() {
     console.log('\n###', 'copy me files');
     const meBuildPath = path.resolve(buildDir, '../build/mesoscale-explorer/');
-    const meDeployPath = path.resolve(localPath, 'me/');
+    const meDeployPath = path.resolve(localPath, 'me/viewer/');
     fse.copySync(meBuildPath, meDeployPath, { overwrite: true });
     addAnalytics(path.resolve(meDeployPath, 'index.html'));
 }

src/apps/docking-viewer/viewport.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -44,15 +44,6 @@ function occlusionStyle(plugin: PluginContext) {
         },
         postprocessing: {
             ...plugin.canvas3d!.props.postprocessing,
-            occlusion: { name: 'on', params: {
-                blurKernelSize: 15,
-                multiScale: { name: 'off', params: {} },
-                radius: 5,
-                bias: 0.8,
-                samples: 32,
-                resolutionScale: 1,
-                color: Color(0x000000),
-            } },
             outline: { name: 'on', params: {
                 scale: 1.0,
                 threshold: 0.33,

src/apps/mesoscale-explorer/app.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -30,6 +30,7 @@ import { Asset } from '../../mol-util/assets';
 import { AnimateCameraSpin } from '../../mol-plugin-state/animation/built-in/camera-spin';
 import { AnimateCameraRock } from '../../mol-plugin-state/animation/built-in/camera-rock';
 import { AnimateStateSnapshots } from '../../mol-plugin-state/animation/built-in/state-snapshots';
+import { MesoViewportSnapshotDescription } from './ui/entities';
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode, setTimingMode, consoleStats } from '../../mol-util/debug';
@@ -46,7 +47,9 @@ export type ExampleEntry = {
 export type MesoscaleExplorerState = {
     examples?: ExampleEntry[],
     graphicsMode: GraphicsMode,
+    illumination: boolean,
     stateRef?: string,
+    driver?: any,
     stateCache: { [k: string]: any },
 }
 
@@ -76,6 +79,8 @@ const DefaultMesoscaleExplorerOptions = {
     preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
     allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
     powerPreference: PluginConfig.General.PowerPreference.defaultValue,
+    resolutionMode: PluginConfig.General.ResolutionMode.defaultValue,
+    illumination: false,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -90,7 +95,8 @@ const DefaultMesoscaleExplorerOptions = {
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default' as SaccharideCompIdMapType,
 
-    graphicsMode: 'quality' as GraphicsMode
+    graphicsMode: 'quality' as GraphicsMode,
+    driver: undefined
 };
 type MesoscaleExplorerOptions = typeof DefaultMesoscaleExplorerOptions;
 
@@ -170,6 +176,9 @@ export class MesoscaleExplorer {
                     right: RightPanel,
                 },
                 remoteState: 'none',
+                viewport: {
+                    snapshotDescription: MesoViewportSnapshotDescription,
+                }
             },
             config: [
                 [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
@@ -179,6 +188,7 @@ export class MesoscaleExplorer {
                 [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
                 [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
                 [PluginConfig.General.PowerPreference, o.powerPreference],
+                [PluginConfig.General.ResolutionMode, o.resolutionMode],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
@@ -207,7 +217,12 @@ export class MesoscaleExplorer {
             onBeforeUIRender: async plugin => {
                 let examples: MesoscaleExplorerState['examples'] = undefined;
                 try {
-                    examples = await plugin.fetch({ url: './examples/list.json', type: 'json' }).run();
+                    examples = await plugin.fetch({ url: '../examples/list.json', type: 'json' }).run();
+                    // extend the array with file tour.json if it exists
+                    const tour = await plugin.fetch({ url: '../examples/tour.json', type: 'json' }).run();
+                    if (tour) {
+                        examples = examples?.concat(tour);
+                    }
                 } catch (e) {
                     console.log(e);
                 }
@@ -215,6 +230,8 @@ export class MesoscaleExplorer {
                 (plugin.customState as MesoscaleExplorerState) = {
                     examples,
                     graphicsMode: o.graphicsMode,
+                    illumination: o.illumination,
+                    driver: o.driver,
                     stateCache: {},
                 };
 

src/apps/mesoscale-explorer/behavior/camera.ts

@@ -11,10 +11,12 @@ import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observ
 import { Binding } from '../../../mol-util/binding';
 import { PluginCommands } from '../../../mol-plugin/commands';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { StructureElement } from '../../../mol-model/structure';
 
 const B = ButtonsType;
 const M = ModifiersKeys;
 const Trigger = Binding.Trigger;
+const Key = Binding.TriggerKey;
 
 const DefaultMesoFocusLociBindings = {
     clickCenter: Binding([
@@ -23,13 +25,14 @@ const DefaultMesoFocusLociBindings = {
     clickCenterFocus: Binding([
         Trigger(B.Flag.Secondary, M.create()),
     ], 'Camera center and focus', 'Click element using ${triggers}'),
+    keyCenterOnly: Binding([Key('C')], 'Center Only Toggle', 'Press ${triggers}'),
 };
-const MesoFocusLociParams = {
+
+export const MesoFocusLociParams = {
     minRadius: PD.Numeric(8, { min: 1, max: 50, step: 1 }),
     extraRadius: PD.Numeric(4, { min: 1, max: 50, step: 1 }, { description: 'Value added to the bounding-sphere radius of the Loci' }),
     durationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'Camera transition duration' }),
     centerOnly: PD.Boolean(true, { description: 'Keep current camera distance' }),
-
     bindings: PD.Value(DefaultMesoFocusLociBindings, { isHidden: true }),
 };
 type MesoFocusLociProps = PD.Values<typeof MesoFocusLociParams>
@@ -47,25 +50,45 @@ export const MesoFocusLoci = PluginBehavior.create<MesoFocusLociProps>({
                 const sphere = Loci.getBoundingSphere(loci) || Sphere3D();
 
                 const { clickCenter, clickCenterFocus } = this.params.bindings;
-                const { durationMs, extraRadius, minRadius } = this.params;
+                const { durationMs, extraRadius, minRadius, centerOnly } = this.params;
                 const radius = Math.max(sphere.radius + extraRadius, minRadius);
 
                 if (Binding.match(clickCenter, button, modifiers)) {
+                    // left mouse button
                     if (Loci.isEmpty(current.loci)) {
                         PluginCommands.Camera.Reset(this.ctx, { });
                         return;
                     }
-
-                    const snapshot = canvas3d.camera.getCenter(sphere.center);
-                    canvas3d.requestCameraReset({ durationMs, snapshot });
+                    if (StructureElement.Loci.is(current.loci)) {
+                        if (centerOnly) {
+                            const snapshot = canvas3d.camera.getCenter(sphere.center);
+                            canvas3d.requestCameraReset({ durationMs, snapshot });
+                        } else {
+                            this.ctx.managers.camera.focusSphere(sphere, this.params);
+                        }
+                    }
                 } else if (Binding.match(clickCenterFocus, button, modifiers)) {
+                    // right mouse button
                     if (Loci.isEmpty(current.loci)) {
                         PluginCommands.Camera.Reset(this.ctx, { });
                         return;
                     }
+                    if (centerOnly) {
+                        const snapshot = canvas3d.camera.getCenter(sphere.center, radius);
+                        canvas3d.requestCameraReset({ durationMs, snapshot });
+                    } else {
+                        this.ctx.managers.camera.focusSphere(sphere, this.params);
+                    }
+                }
+            });
 
-                    const snapshot = canvas3d.camera.getCenter(sphere.center, radius);
-                    canvas3d.requestCameraReset({ durationMs, snapshot });
+            this.subscribeObservable(this.ctx.behaviors.interaction.key, ({ code, key, modifiers }) => {
+                if (!this.ctx.canvas3d) return;
+                const b = { ...DefaultMesoFocusLociBindings, ...this.params.bindings };
+                const { centerOnly } = this.params;
+
+                if (Binding.matchKey(b.keyCenterOnly, code, modifiers, key)) {
+                    this.params.centerOnly = !centerOnly;
                 }
             });
         }

src/apps/mesoscale-explorer/behavior/select.ts

@@ -16,12 +16,16 @@ import { StateTreeSpine } from '../../../mol-state/tree/spine';
 import { Representation } from '../../../mol-repr/representation';
 import { MarkerAction } from '../../../mol-util/marker-action';
 import { PluginContext } from '../../../mol-plugin/context';
+import { MesoscaleState, expandAllGroups, getCellDescription, getEveryEntity } from '../data/state';
 
 const B = ButtonsType;
 const M = ModifiersKeys;
 const Trigger = Binding.Trigger;
 
 const DefaultMesoSelectLociBindings = {
+    click: Binding([
+        Trigger(B.Flag.Primary, M.create())
+    ], 'Click', 'Click element using ${triggers}'),
     clickToggleSelect: Binding([
         Trigger(B.Flag.Primary, M.create({ shift: true })),
         Trigger(B.Flag.Primary, M.create({ control: true })),
@@ -63,15 +67,36 @@ export const MesoSelectLoci = PluginBehavior.create<MesoSelectLociProps>({
             this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
                 if (!this.ctx.canvas3d || this.ctx.isBusy) return;
 
-                const { clickToggleSelect } = this.params.bindings;
+                const { click, clickToggleSelect } = this.params.bindings;
                 if (Binding.match(clickToggleSelect, button, modifiers)) {
                     if (Loci.isEmpty(current.loci)) {
                         this.ctx.managers.interactivity.lociSelects.deselectAll();
                         return;
                     }
-
                     const loci = Loci.normalize(current.loci, modifiers.control ? 'entity' : 'chain');
                     this.ctx.managers.interactivity.lociSelects.toggle({ loci }, false);
+                    if (StructureElement.Loci.is(current.loci)) {
+                        const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                        const d = getCellDescription(cell!);
+                        MesoscaleState.set(this.ctx, { focusInfo: `${d}` });
+                    }
+                }
+                if (Binding.match(click, button, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) {
+                        MesoscaleState.set(this.ctx, { focusInfo: '', filter: '' });
+                        return;
+                    }
+                    const snapshotKey = current.repr?.props?.snapshotKey?.trim() ?? '';
+                    if (snapshotKey) {
+                        this.ctx.managers.snapshot.applyKey(snapshotKey);
+                    } else {
+                        if (StructureElement.Loci.is(current.loci)) {
+                            const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
+                            const d = getCellDescription(cell!);
+                            MesoscaleState.set(this.ctx, { focusInfo: `${d}`, filter: `${cell?.obj?.label}` });
+                            expandAllGroups(this.ctx);
+                        }
+                    }
                 }
             });
             this.ctx.managers.interactivity.lociSelects.addProvider(this.lociMarkProvider);
@@ -87,22 +112,41 @@ export const MesoSelectLoci = PluginBehavior.create<MesoSelectLociProps>({
                         this.ctx.managers.interactivity.lociHighlights.clearHighlights();
                         return;
                     }
-
-                    if (modifiers.control) {
-                        this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EveryLoci }, false);
-                    } else {
-                        const loci = Loci.normalize(current.loci, 'chain');
-                        this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci }, false);
+                    if (StructureElement.Loci.is(current.loci)) {
+                        if (modifiers.control) {
+                            this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EveryLoci }, false);
+                        } else {
+                            const loci = Loci.normalize(current.loci, 'chain');
+                            this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci }, false);
+                        }
                     }
                 }
 
                 if (Loci.isEmpty(current.loci)) {
                     this.ctx.behaviors.labels.highlight.next({ labels: [] });
+                    this.ctx.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
                 } else {
                     const labels: string[] = [];
                     if (StructureElement.Loci.is(current.loci)) {
                         const cell = this.ctx.helpers.substructureParent.get(current.loci.structure);
-                        labels.push(cell?.obj?.label || 'Unknown');
+                        const d = getCellDescription(cell!);
+                        labels.push(d);
+                    } else {
+                        const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
+                        if (loci.kind === 'group-loci') {
+                            if ('shape' in current.loci && current.loci.shape.geometry.kind === 'text') {
+                                const qname = current.repr?.props.customText;
+                                // highlight protein with same name
+                                const entities = getEveryEntity(this.ctx, qname);
+                                for (const r of entities) {
+                                    const repr = r.obj?.data.repr;
+                                    if (repr) {
+                                        this.ctx.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+                                    }
+                                }
+                            }
+                            labels.push(loci.shape.getLabel(0, 0));
+                        }
                     }
                     this.ctx.behaviors.labels.highlight.next({ labels });
                 }

src/apps/mesoscale-explorer/data/cellpack/model.ts

@@ -161,15 +161,12 @@ const CellpackStructure = PluginStateTransform.BuiltIn({
 
             const unitsByEntity = getUnitsByEntity(parent);
             const units = unitsByEntity.get(idx) || [];
-            // if (!unitsByEntity.get(idx)) {
-            //     console.log(entities.data.pdbx_description.value(idx));
-            // }
+
             const structure = Structure.create(units);
-
-            const description = entities.data.pdbx_description.value(idx)[0] || 'model';
-            const label = description.split('.').at(-1) || a.label;
-
-            return new PSO.Molecule.Structure(structure, { label, description: `${a.description}` });
+            const description_label = entities.data.pdbx_description.value(idx)[0] || 'model';
+            const label = description_label.split('.').at(-1) || a.label;
+            const description = entities.data.pdbx_parent_entity_id.value(idx) || label;
+            return new PSO.Molecule.Structure(structure, { label, description: description }); // `${a.description}`
         });
     },
     dispose({ b }) {

src/apps/mesoscale-explorer/data/cellpack/preset.ts

@@ -96,12 +96,12 @@ export async function createCellpackHierarchy(plugin: PluginContext, trajectory:
 
     const compRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:comp:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `comp:`, label: 'compartment', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: 'comp:', label: 'compartment', color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
 
     const funcRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:func:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `func:`, label: 'function', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: 'func:', label: 'function', color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
 
     if (entities._rowCount > 1) {
@@ -159,7 +159,7 @@ export async function createCellpackHierarchy(plugin: PluginContext, trajectory:
                     parent.cell!.state.isCollapsed = false;
                     const group = await state.build()
                         .to(parent)
-                        .applyOrUpdateTagged(`group:comp:${n}`, MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `comp:${p}`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                        .apply(MesoscaleGroup, { ...groupParams, root: parent === compRoot, index: colorIdx, tag: `comp:${n}`, label, color: { type: 'generate', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:comp:${n}`, `comp:${p}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
                         .commit({ revertOnError: true });
                     compGroups.set(n, group);
                 }
@@ -171,7 +171,7 @@ export async function createCellpackHierarchy(plugin: PluginContext, trajectory:
                 const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : ColorNames.white;
                 const group = await state.build()
                     .to(funcRoot)
-                    .applyOrUpdateTagged(`group:func:${f}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'func:', state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                    .apply(MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `func:${f}`, label: f, color: { type: 'custom', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:func:${f}`, 'func:'], state: { isCollapsed: true, isHidden: groupParams.hidden } })
                     .commit({ revertOnError: true });
                 funcGroups.set(f, group);
             }

src/apps/mesoscale-explorer/data/generic/model.ts

@@ -76,6 +76,7 @@ const StructureFromGeneric = PluginStateTransform.BuiltIn({
     params: {
         instances: PD.Value<GenericInstances<Asset>>(EmptyInstances),
         label: PD.Optional(PD.Text('')),
+        description: PD.Optional(PD.Text('')),
         cellSize: PD.Numeric(500, { min: 0, max: 10000, step: 100 }),
     }
 })({
@@ -111,7 +112,7 @@ const StructureFromGeneric = PluginStateTransform.BuiltIn({
                 structure = assembler.getStructure();
             }
 
-            const props = { label, description: Structure.elementDescription(structure) };
+            const props = { label, description: params.description || Structure.elementDescription(structure) };
             return new SO.Molecule.Structure(structure, props);
         });
     },

src/apps/mesoscale-explorer/data/generic/preset.ts

@@ -11,7 +11,7 @@ import { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/
 import { Color } from '../../../../mol-util/color';
 import { utf8Read } from '../../../../mol-io/common/utf8';
 import { Mat3, Quat, Vec3 } from '../../../../mol-math/linear-algebra';
-import { GraphicsMode, MesoscaleGroup, MesoscaleState, getGraphicsModeProps, getMesoscaleGroupParams, updateColors } from '../state';
+import { GraphicsMode, MesoscaleGroup, MesoscaleState, getGraphicsModeProps, getMesoscaleGroupParams } from '../state';
 import { ColorNames } from '../../../../mol-util/color/names';
 import { ShapeRepresentation3D, StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation';
 import { ParseCif, ParsePly, ReadFile } from '../../../../mol-plugin-state/transforms/data';
@@ -124,7 +124,7 @@ export async function createGenericHierarchy(plugin: PluginContext, file: Asset.
     async function addGroup(g: GenericGroup, cell: StateObjectSelector, parent: string) {
         const group = await state.build()
             .to(cell)
-            .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
+            .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `${g.root}:${g.id}`, label: g.label || g.id, description: g.description, color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`], state: { isCollapsed: true, isHidden: groupParams.hidden } })
             .commit();
 
         if (g.children) {
@@ -137,7 +137,7 @@ export async function createGenericHierarchy(plugin: PluginContext, file: Asset.
     for (const r of manifest.roots) {
         const root = await state.build()
             .toRoot()
-            .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
+            .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `${r.id}:`, label: r.label || r.id, description: r.description, color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })
             .commit();
 
         if (r.children) {
@@ -193,11 +193,12 @@ export async function createGenericHierarchy(plugin: PluginContext, file: Asset.
                 const file = Asset.File(new File([t], ent.file));
 
                 const color = ColorNames.skyblue;
-                const label = ent.label || ent.file.split('.')[0];
+
                 const sizeFactor = ent.sizeFactor || 1;
                 const tags = ent.groups.map(({ id, root }) => `${root}:${id}`);
                 const instances = ent.instances && getAssetInstances(ent.instances);
-
+                const description = ent.description;
+                const label = ent.label || ent.file.split('.')[0];
                 build = build
                     .toRoot()
                     .apply(ReadFile, { file, label, isBinary });
@@ -233,7 +234,7 @@ export async function createGenericHierarchy(plugin: PluginContext, file: Asset.
 
                     build = build
                         .apply(ModelFromTrajectory, { modelIndex: 0 })
-                        .apply(StructureFromGeneric, { instances, label })
+                        .apply(StructureFromGeneric, { instances, label, description })
                         .apply(StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode, clipVariant), { tags });
                 } else if (['ply'].includes(info.ext)) {
                     if (['ply'].includes(info.ext)) {
@@ -249,10 +250,6 @@ export async function createGenericHierarchy(plugin: PluginContext, file: Asset.
                 }
             }
             await build.commit();
-
-            const rootId = `${manifest.roots[0].id}:`;
-            const values = { type: 'group-generate', value: ColorNames.white, lightness: 0, alpha: 1 };
-            await updateColors(plugin, values, rootId, '');
         } catch (e) {
             console.error(e);
             plugin.log.error(e);

src/apps/mesoscale-explorer/data/mmcif/model.ts

@@ -186,9 +186,10 @@ const MmcifStructure = PluginStateTransform.BuiltIn({
             } else {
                 structure = Structure.create(units);
             }
-
+            // could also use _struct_ref.pdbx_db_accession to point to uniprot with _struct_ref.db_name == UNP
             const label = entities.data.pdbx_description.value(idx).join(', ') || 'model';
-            return new PSO.Molecule.Structure(structure, { label, description: `${a.description}` });
+            const description = `*Entity id* ${entities.data.id.value(idx)} *src_method* ${entities.data.src_method.value(idx)} *type* ${entities.data.type.value(idx)}`;
+            return new PSO.Molecule.Structure(structure, { label, description: description });
         });
     },
     update({ newParams, oldParams }) {

src/apps/mesoscale-explorer/data/mmcif/preset.ts

@@ -114,7 +114,7 @@ export async function createMmcifHierarchy(plugin: PluginContext, trajectory: St
 
     const entRoot = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'custom', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: 'ent:', label: 'entity', color: { type: 'custom', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit();
 
     const getEntityType = (i: number) => {
@@ -148,7 +148,7 @@ export async function createMmcifHierarchy(plugin: PluginContext, trajectory: St
             const color = colorIdx !== undefined ? baseEntColors[colorIdx] : ColorNames.white;
             const group = await state.build()
                 .to(entRoot)
-                .applyOrUpdateTagged(`group:ent:${t}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+                .applyOrUpdateTagged(`group:ent:${t}`, MesoscaleGroup, { ...groupParams, index: colorIdx, tag: `ent:${t}`, label: t, color: { type: 'generate', illustrative: false, value: color, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
                 .commit({ revertOnError: true });
             entGroups.set(t, group);
         }

src/apps/mesoscale-explorer/data/petworld/model.ts

@@ -39,8 +39,10 @@ const StructureFromPetworld = PluginStateTransform.BuiltIn({
 
             const { frame } = s.model.sourceData.data;
             const pdbx_model = frame.categories.pdbx_model.getField('name')!;
+            const pdbx_description = frame.categories.pdbx_model.getField('description')!;
+            const description = pdbx_description ? pdbx_description.str(params.modelIndex) : Structure.elementDescription(s);
             const label = pdbx_model.str(params.modelIndex);
-            const props = { label, description: Structure.elementDescription(s) };
+            const props = { label, description: description };
             return new SO.Molecule.Structure(s, props);
         });
     },

src/apps/mesoscale-explorer/data/petworld/preset.ts

@@ -97,12 +97,12 @@ export async function createPetworldHierarchy(plugin: PluginContext, trajectory:
 
     const group = await state.build()
         .toRoot()
-        .applyOrUpdateTagged('group:ent:', MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: 'group:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })
+        .apply(MesoscaleGroup, { ...groupParams, root: true, index: -1, tag: `ent:`, label: 'entity', color: { type: 'generate', illustrative: false, value: ColorNames.white, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: ['group:ent:'], state: { isCollapsed: false, isHidden: groupParams.hidden } })
         .commit({ revertOnError: true });
 
     await state.build()
         .to(group)
-        .applyOrUpdateTagged(`group:ent:mem`, MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', value: ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })
+        .apply(MesoscaleGroup, { ...groupParams, index: undefined, tag: `ent:mem`, label: 'Membrane', color: { type: 'uniform', illustrative: false, value: ColorNames.lightgrey, variability: 20, shift: 0, lightness: 0, alpha: 1, emissive: 0 } }, { tags: ['group:ent:mem', 'ent:', '__no_group_color__'], state: { isCollapsed: true, isHidden: groupParams.hidden } })
         .commit();
 
     const colors = getDistinctBaseColors(other.length, 0);
@@ -115,13 +115,13 @@ export async function createPetworldHierarchy(plugin: PluginContext, trajectory:
                 build = build
                     .to(cell)
                     .apply(StructureFromPetworld, membrane[i])
-                    .apply(StructureRepresentation3D, getSpacefillParams(ColorNames.lightgrey, graphicsMode), { tags: [`ent:mem`] });
+                    .apply(StructureRepresentation3D, getSpacefillParams(ColorNames.lightgrey, graphicsMode), { tags: ['ent:mem', '__no_group_color__'] });
             }
             for (let i = 0, il = other.length; i < il; ++i) {
                 build = build
                     .to(cell)
                     .apply(StructureFromPetworld, other[i])
-                    .apply(StructureRepresentation3D, getSpacefillParams(colors[i], graphicsMode), { tags: [`ent:`] });
+                    .apply(StructureRepresentation3D, getSpacefillParams(colors[i], graphicsMode), { tags: ['ent:'] });
             }
             await build.commit();
         } catch (e) {

src/apps/mesoscale-explorer/data/state.ts

@@ -24,6 +24,7 @@ import { SpacefillRepresentationProvider } from '../../../mol-repr/structure/rep
 import { assertUnreachable } from '../../../mol-util/type-helpers';
 import { MesoscaleExplorerState } from '../app';
 import { saturate } from '../../../mol-math/interpolate';
+import { Material } from '../../../mol-util/material';
 
 function getHueRange(hue: number, variability: number) {
     let min = hue - variability;
@@ -106,6 +107,7 @@ export function getDistinctBaseColors(count: number, shift: number, props?: Part
 
 export const ColorParams = {
     type: PD.Select('generate', PD.arrayToOptions(['generate', 'uniform', 'custom'])),
+    illustrative: PD.Boolean(false, { description: 'Illustrative style', hideIf: p => p.type === 'custom' }),
     value: PD.Color(Color(0xFFFFFF), { hideIf: p => p.type === 'custom' }),
     variability: PD.Numeric(20, { min: 1, max: 180, step: 1 }, { hideIf: p => p.type !== 'generate' }),
     shift: PD.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
@@ -119,6 +121,7 @@ export const ColorValueParam = PD.Color(Color(0xFFFFFF));
 
 export const RootParams = {
     type: PD.Select('custom', PD.arrayToOptions(['group-generate', 'group-uniform', 'generate', 'uniform', 'custom'])),
+    illustrative: PD.Boolean(false, { description: 'Illustrative style', hideIf: p => p.type === 'custom' }),
     value: PD.Color(Color(0xFFFFFF), { hideIf: p => p.type !== 'uniform' }),
     variability: PD.Numeric(20, { min: 1, max: 180, step: 1 }, { hideIf: p => p.type !== 'group-generate' }),
     shift: PD.Numeric(0, { min: 0, max: 100, step: 1 }, { hideIf: p => !p.type.includes('generate') }),
@@ -132,6 +135,10 @@ export const LightnessParams = {
 };
 export const DimLightness = 6;
 
+export const IllustrativeParams = {
+    illustrative: PD.Boolean(false, { description: 'Illustrative style' }),
+};
+
 export const OpacityParams = {
     alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
 };
@@ -140,11 +147,24 @@ export const EmissiveParams = {
     emissive: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }),
 };
 
+export const celShaded = {
+    celShaded: PD.Boolean(false, { description: 'Cel Shading light for stylized rendering of representations' })
+};
+
+export type celShadedProps = PD.Values<typeof celShaded>;
+
+
 export const PatternParams = {
     frequency: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
     amplitude: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
 };
 
+export const StyleParams = {
+    ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representations' }),
+    materialStyle: Material.getParam(),
+    celShaded: PD.Boolean(false, { description: 'Cel Shading light for stylized rendering of representations' }),
+};
+
 export const LodParams = {
     lodLevels: Spheres.Params.lodLevels,
     cellSize: Spheres.Params.cellSize,
@@ -250,6 +270,7 @@ export const MesoscaleGroupParams = {
     index: PD.Value<number>(-1, { isHidden: true }),
     tag: PD.Value<string>('', { isHidden: true }),
     label: PD.Value<string>('', { isHidden: true }),
+    description: PD.Value<string>('', { isHidden: true }),
     hidden: PD.Boolean(false),
     color: PD.Group(RootParams),
     lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
@@ -271,7 +292,7 @@ export const MesoscaleGroup = PluginStateTransform.BuiltIn({
 })({
     apply({ a, params }, plugin: PluginContext) {
         return Task.create('Apply Mesoscale Group', async () => {
-            return new MesoscaleGroupObject({}, { label: params.label });
+            return new MesoscaleGroupObject({}, { label: params.label, description: params.description });
         });
     },
 });
@@ -318,10 +339,10 @@ export function getLodLevels(graphicsMode: Exclude<GraphicsMode, 'custom'>): Lod
             ];
         case 'ultra':
             return [
-                { minDistance: 1, maxDistance: 2000, overlap: 0, stride: 1, scaleBias: 1 },
-                { minDistance: 2000, maxDistance: 8000, overlap: 0, stride: 10, scaleBias: 3 },
-                { minDistance: 8000, maxDistance: 20000, overlap: 0, stride: 50, scaleBias: 2.5 },
-                { minDistance: 20000, maxDistance: 10000000, overlap: 0, stride: 200, scaleBias: 2 },
+                { minDistance: 1, maxDistance: 5000, overlap: 0, stride: 1, scaleBias: 1 },
+                { minDistance: 5000, maxDistance: 10000, overlap: 0, stride: 10, scaleBias: 3 },
+                { minDistance: 10000, maxDistance: 30000, overlap: 0, stride: 50, scaleBias: 2.5 },
+                { minDistance: 30000, maxDistance: 10000000, overlap: 0, stride: 200, scaleBias: 2 },
             ];
         default:
             assertUnreachable(graphicsMode);
@@ -360,7 +381,10 @@ export const MesoscaleStateParams = {
     filter: PD.Value<string>('', { isHidden: true }),
     graphics: PD.Select('quality', PD.arrayToOptions(['ultra', 'quality', 'balanced', 'performance', 'custom'] as GraphicsMode[])),
     description: PD.Value<string>('', { isHidden: true }),
+    focusInfo: PD.Value<string>('', { isHidden: true }),
     link: PD.Value<string>('', { isHidden: true }),
+    textSizeDescription: PD.Numeric(14, { min: 1, max: 100, step: 1 }, { isHidden: true }),
+    index: PD.Value<number>(-1, { isHidden: true })
 };
 
 export class MesoscaleStateObject extends PSO.Create<MesoscaleState>({ name: 'Mesoscale State', typeClass: 'Object' }) { }
@@ -482,6 +506,7 @@ function getFilterMatcher(filter: string) {
 }
 
 export function getFilteredEntities(plugin: PluginContext, tag: string, filter: string) {
+    if (!filter) return getEntities(plugin, tag);
     const matcher = getFilterMatcher(filter);
     return getEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
 }
@@ -499,22 +524,72 @@ export function getAllEntities(plugin: PluginContext, tag?: string) {
 }
 
 export function getAllFilteredEntities(plugin: PluginContext, tag: string, filter: string) {
+    if (!filter) return getAllEntities(plugin, tag);
     const matcher = getFilterMatcher(filter);
     return getAllEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
 }
 
+export function getEveryEntity(plugin: PluginContext, filter?: string, tag?: string) {
+    if (filter) {
+        const matcher = getFilterMatcher(filter);
+        return getAllEntities(plugin, tag).filter(c => getEntityLabel(plugin, c).match(matcher) !== null);
+    } else {
+        return getAllEntities(plugin, tag);
+    }
+}
+
 export function getEntityLabel(plugin: PluginContext, cell: StateObjectCell) {
     return StateObjectRef.resolve(plugin.state.data, cell.transform.parent)?.obj?.label || 'Entity';
 }
 
-//
+export function getCellDescription(cell: StateObjectCell) {
+    // markdown style for description
+    return '**' + cell?.obj?.label + '**\n\n' + cell?.obj?.description;
+}
+
+export function getEntityDescription(plugin: PluginContext, cell: StateObjectCell) {
+    const s = StateObjectRef.resolve(plugin.state.data, cell.transform.parent);
+    const d = getCellDescription(s!);
+    return d;
+}
+
+export async function updateStyle(plugin: PluginContext, options: { ignoreLight: boolean, material: Material, celShaded: boolean, illustrative: boolean }) {
+    const update = plugin.state.data.build();
+    const { ignoreLight, material, celShaded, illustrative } = options;
+
+    const entities = getAllEntities(plugin);
+
+    for (let j = 0; j < entities.length; ++j) {
+        update.to(entities[j]).update(old => {
+            if (old.type) {
+                const value = old.colorTheme.name === 'illustrative'
+                    ? old.colorTheme.params.style.params.value
+                    : old.colorTheme.params.value;
+                const lightness = old.colorTheme.name === 'illustrative'
+                    ? old.colorTheme.params.style.params.lightness
+                    : old.colorTheme.params.lightness;
+                if (illustrative) {
+                    old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value, lightness } } } };
+                } else {
+                    old.colorTheme = { name: 'uniform', params: { value, lightness } };
+                }
+                old.type.params.ignoreLight = ignoreLight;
+                old.type.params.material = material;
+                old.type.params.celShaded = celShaded;
+            }
+        });
+    }
+
+    await update.commit();
+};
 
 export async function updateColors(plugin: PluginContext, values: PD.Values, tag: string, filter: string) {
     const update = plugin.state.data.build();
-    const { type, value, shift, lightness, alpha, emissive } = values;
-
+    const { type, illustrative, value, shift, lightness, alpha, emissive } = values;
     if (type === 'group-generate' || type === 'group-uniform') {
-        const groups = getAllLeafGroups(plugin, tag);
+        const leafGroups = getAllLeafGroups(plugin, tag);
+        const rootLeafGroups = getRoots(plugin).filter(g => g.params?.values.tag === tag && getEntities(plugin, g.params?.values.tag).length > 0);
+        const groups = [...leafGroups, ...rootLeafGroups];
         const baseColors = getDistinctBaseColors(groups.length, shift);
 
         for (let i = 0; i < groups.length; ++i) {
@@ -531,8 +606,11 @@ export async function updateColors(plugin: PluginContext, values: PD.Values, tag
                 const c = type === 'group-generate' ? groupColors[j] : baseColors[i];
                 update.to(entities[j]).update(old => {
                     if (old.type) {
-                        old.colorTheme.params.value = c;
-                        old.colorTheme.params.lightness = lightness;
+                        if (illustrative) {
+                            old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value: c, lightness: lightness } } } };
+                        } else {
+                            old.colorTheme = { name: 'uniform', params: { value: c, lightness: lightness } };
+                        }
                         old.type.params.alpha = alpha;
                         old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
                         old.type.params.emissive = emissive;
@@ -548,6 +626,7 @@ export async function updateColors(plugin: PluginContext, values: PD.Values, tag
 
             update.to(g.transform.ref).update(old => {
                 old.color.type = type === 'group-generate' ? 'generate' : 'uniform';
+                old.color.illustrative = illustrative;
                 old.color.value = baseColors[i];
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
@@ -566,8 +645,11 @@ export async function updateColors(plugin: PluginContext, values: PD.Values, tag
             const c = type === 'generate' ? groupColors[j] : value;
             update.to(entities[j]).update(old => {
                 if (old.type) {
-                    old.colorTheme.params.value = c;
-                    old.colorTheme.params.lightness = lightness;
+                    if (illustrative) {
+                        old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value: c, lightness: lightness } } } };
+                    } else {
+                        old.colorTheme = { name: 'uniform', params: { value: c, lightness: lightness } };
+                    }
                     old.type.params.alpha = alpha;
                     old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
                     old.type.params.emissive = emissive;
@@ -585,6 +667,7 @@ export async function updateColors(plugin: PluginContext, values: PD.Values, tag
         for (const o of others) {
             update.to(o).update(old => {
                 old.color.type = type === 'generate' ? 'custom' : 'uniform';
+                old.color.illustrative = illustrative;
                 old.color.value = value;
                 old.color.lightness = lightness;
                 old.color.alpha = alpha;
@@ -603,3 +686,4 @@ export function expandAllGroups(plugin: PluginContext) {
         }
     }
 };
+

src/apps/mesoscale-explorer/embedded.html

@@ -0,0 +1,79 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+    <style>
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+        html, body {
+            width: 100%;
+            height: 100%;
+            display: flex;
+            flex-direction: column;
+            align-items: center;
+            justify-content: flex-start;
+            overflow: hidden;
+        }
+        #controls {
+            display: flex;
+            justify-content: center;
+            width: 800px;
+            margin-bottom: 10px;
+            z-index: 1;
+        }
+        button {
+            margin: 5px;
+            padding: 10px 20px;
+            font-size: 14px;
+            cursor: pointer;
+        }
+        #viewer-container {
+            width: 100%;
+            height: 600px;
+            border: 1px solid #ccc;
+            position: relative;
+        }
+    </style>
+    <link rel="stylesheet" type="text/css" href="./molstar.css" />
+</head>
+<body>
+    <div id="controls">
+        <button onclick="loadExample('cellpack-hiv1')">Load HIV-1 Example</button>
+        <button onclick="loadExample('machineryoflife-tour')">Load Machinery of Life Tour</button>
+        <button onclick="loadExample('petworld-synvesicle')">Load Synaptic Vesicle Example</button>
+    </div>
+    <div id="viewer-container">
+        <div id="meso-viewer" style="position: relative; width: 100%; height: 400px;"></div>
+    </div>
+
+    <script src="./molstar.js"></script>
+    <script type="text/javascript">
+        let mesoExplorer;
+
+        function loadExample(example) {
+            if (mesoExplorer) {
+                mesoExplorer.loadExample(example);
+            }
+        }
+
+        molstar.MesoscaleExplorer.create('meso-viewer', {
+            layoutShowControls: false,
+            viewportShowExpand: false,
+	        layoutIsExpanded: false,
+            powerPreference: 'high-performance',
+            graphicsMode: 'quality'
+        }).then(me => {
+            mesoExplorer = me;
+            me.loadExample('cellpack-hiv1');  // Load the default example on page load
+
+            window.addEventListener('unload', () => {
+                me.dispose();
+            });
+        });
+    </script>
+</body>
+</html>

src/apps/mesoscale-explorer/index.html

@@ -4,6 +4,7 @@
         <meta charset="utf-8" />
         <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
         <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <link rel="stylesheet" href="../extras/driver.css"/>
         <title>Mol* Mesoscale Explorer</title>
         <style>
             * {
@@ -38,8 +39,11 @@
     </head>
     <body>
         <div id="app"></div>
+        <script src="../extras/driver.js.iife.js"></script>
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
+            const driver = window.driver ? window.driver.js.driver() : undefined;
+
             function getParam(name, regex) {
                 var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
                 return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
@@ -56,6 +60,8 @@
             var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
             var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
             var graphicsMode = getParam('graphics-mode', '[^&]+').trim().toLowerCase();
+            var illumination = getParam('illumination', '[^&]+').trim() === '1';
+            var resolutionMode = getParam('resolution-mode', '[^&]+').trim().toLowerCase();
 
             molstar.MesoscaleExplorer.create('app', {
                 layoutShowControls: !hideControls,
@@ -64,6 +70,9 @@
                 allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
                 powerPreference: powerPreference || 'high-performance',
                 graphicsMode: graphicsMode || 'quality',
+                illumination: illumination,
+                resolutionMode: resolutionMode || 'auto',
+                driver: driver
             }).then(me => {
                 var example = getParam('example', '[^&]+').trim();
                 if (example) {
@@ -89,7 +98,6 @@
                     me.loadPdbDev(pdbdev);
                     return;
                 }
-
                 window.addEventListener('unload', () => {
                     // to aid GC
                     me.dispose();
@@ -98,4 +106,4 @@
         </script>
         <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
-</html>
+</html>

src/apps/mesoscale-explorer/style.scss

@@ -1,3 +1,5 @@
+@use "sass:color";
+
 $default-background:         #2D3E50;
 $font-color:                 #EDF1F2;
 $hover-font-color:           #3B9AD9;
@@ -16,14 +18,15 @@ $log-error:            #FD354B;
 $logo-background: rgba(0,0,0,0.75);
 
 @function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
+    @return color.adjust($color, $lightness: -$amount, $space: hsl);
 }
 
 @function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+    @return color.adjust($color, $lightness: $amount, $space: hsl);
 }
 
 @import 'mol-plugin-ui/skin/base/base';
+@import 'mol-plugin-ui/skin/base/variables';
 
 a {
     color: $font-color;
@@ -31,3 +34,35 @@ a {
         color: $hover-font-color;
     }
 }
+
+
+.msp-snapshot-description-me {
+    background: color.change($default-background, $alpha: 0.5, $space: rgb);
+
+    position: absolute;
+    height: 50vh; // 50% of the viewport height
+    left: 0;
+    top: $control-spacing + $row-height;
+    padding: (0.66 * $control-spacing) $control-spacing;
+
+    resize: both; /* Allows resizing in both directions */
+    overflow: auto; /* Adjust as needed */
+
+    a {
+        text-decoration: underline;
+        cursor: pointer;
+        color: $font-color;
+    }
+
+    ul, ol {
+        padding-left: $control-spacing + 4px;
+    }
+
+    &.hidden {
+        display: none;
+    }
+
+    &.shown {
+        display: block; // or 'flex', 'grid', etc. depending on your layout
+    }
+}

src/apps/mesoscale-explorer/ui/entities.tsx

@@ -4,9 +4,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { PluginUIComponent } from '../../../mol-plugin-ui/base';
+import { PluginReactContext, PluginUIComponent } from '../../../mol-plugin-ui/base';
 import { Button, ControlGroup, IconButton } from '../../../mol-plugin-ui/controls/common';
-import { ArrowDropDownSvg, ArrowRightSvg, CloseSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg, ContentCutSvg, BrushSvg, SearchSvg } from '../../../mol-plugin-ui/controls/icons';
+import { ArrowDropDownSvg, ArrowRightSvg, CloseSvg, VisibilityOffOutlinedSvg, VisibilityOutlinedSvg, ContentCutSvg, BrushSvg, SearchSvg, TooltipTextSvg, TooltipTextOutlineSvg, PlusBoxSvg, MinusBoxSvg } from '../../../mol-plugin-ui/controls/icons';
 import { PluginCommands } from '../../../mol-plugin/commands';
 import { State, StateObjectCell, StateSelection, StateTransformer } from '../../../mol-state';
 import { ParameterControls, ParameterMappingControl, ParamOnChange, SelectControl } from '../../../mol-plugin-ui/controls/parameters';
@@ -18,14 +18,17 @@ import { CombinedColorControl } from '../../../mol-plugin-ui/controls/color';
 import { MarkerAction } from '../../../mol-util/marker-action';
 import { EveryLoci, Loci } from '../../../mol-model/loci';
 import { deepEqual } from '../../../mol-util';
-import { ColorValueParam, ColorParams, ColorProps, DimLightness, LightnessParams, LodParams, MesoscaleGroup, MesoscaleGroupProps, OpacityParams, SimpleClipParams, SimpleClipProps, createClipMapping, getClipObjects, getDistinctGroupColors, RootParams, MesoscaleState, getRoots, getAllGroups, getAllLeafGroups, getFilteredEntities, getAllFilteredEntities, getGroups, getEntities, getAllEntities, getEntityLabel, updateColors, getGraphicsModeProps, GraphicsMode, MesoscaleStateParams, setGraphicsCanvas3DProps, PatternParams, expandAllGroups, EmissiveParams } from '../data/state';
-import React from 'react';
+import { ColorValueParam, ColorParams, ColorProps, DimLightness, LightnessParams, LodParams, MesoscaleGroup, MesoscaleGroupProps, OpacityParams, SimpleClipParams, SimpleClipProps, createClipMapping, getClipObjects, getDistinctGroupColors, RootParams, MesoscaleState, getRoots, getAllGroups, getAllLeafGroups, getFilteredEntities, getAllFilteredEntities, getGroups, getEntities, getAllEntities, getEntityLabel, updateColors, getGraphicsModeProps, GraphicsMode, MesoscaleStateParams, setGraphicsCanvas3DProps, PatternParams, expandAllGroups, EmissiveParams, IllustrativeParams, getCellDescription, getEntityDescription, getEveryEntity } from '../data/state';
+import React, { useState } from 'react';
 import { MesoscaleExplorerState } from '../app';
 import { StructureElement } from '../../../mol-model/structure/structure/element';
 import { PluginStateObject as PSO } from '../../../mol-plugin-state/objects';
 import { Structure } from '../../../mol-model/structure';
 import { PluginContext } from '../../../mol-plugin/context';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { MesoFocusLoci } from '../behavior/camera';
+import Markdown from 'react-markdown';
+import { combineLatest } from 'rxjs';
 
 function centerLoci(plugin: PluginContext, loci: Loci, durationMs = 250) {
     const { canvas3d } = plugin;
@@ -60,6 +63,7 @@ export class ModelInfo extends PluginUIComponent<{}, { isDisabled: boolean }> {
         if (!state.description && !state.link) return;
 
         return {
+            selectionDescription: state.focusInfo,
             description: state.description,
             link: state.link,
         };
@@ -68,7 +72,7 @@ export class ModelInfo extends PluginUIComponent<{}, { isDisabled: boolean }> {
     render() {
         const info = this.info;
         return info && <>
-            <div className='msp-help-text'>
+            <div id='modelinfo' className='msp-help-text'>
                 <div>{info.description}</div>
                 <div><a href={info.link} target='_blank'>Source</a></div>
             </div>
@@ -101,17 +105,20 @@ export class SelectionInfo extends PluginUIComponent<{}, { isDisabled: boolean }
     }
 
     get info() {
-        const info: { label: string, key: string }[] = [];
+        const infos: { label: string, key: string, description?: string }[] = [];
         this.plugin.managers.structure.selection.entries.forEach((e, k) => {
             if (StructureElement.Loci.is(e.selection) && !StructureElement.Loci.isEmpty(e.selection)) {
                 const cell = this.plugin.helpers.substructureParent.get(e.selection.structure);
-                info.push({
+                const { entities } = e.selection.structure.model;
+                const description = entities.data.pdbx_description.value(0)[0] || 'model';
+                infos.push({
+                    description: description,
                     label: cell?.obj?.label || 'Unknown',
                     key: k,
                 });
             }
         });
-        return info;
+        return infos;
     }
 
     find(label: string) {
@@ -133,31 +140,40 @@ export class SelectionInfo extends PluginUIComponent<{}, { isDisabled: boolean }
 
         const loci = Structure.toStructureElementLoci(e.selection.structure);
         centerLoci(this.plugin, loci);
+        const cell = this.plugin.helpers.substructureParent.get(loci.structure);
+        const d = getCellDescription(cell!); // '### ' + cell?.obj?.label + '\n\n' + cell?.obj?.description;
+        MesoscaleState.set(this.plugin, { focusInfo: `${d}` });
     }
 
     get selection() {
         const info = this.info;
+        const help_selection = <><div>Use <i>ctrl+left</i> to select entities, either on the 3D canvas or in the tree below</div><div>Use <i>shift+left</i> to select individual chain on the 3D canvas</div></>;
         if (!info.length) return <>
-            <div className='msp-help-text'>
-                <div>Use <i>ctrl+left click</i> to select entities, either on the 3D canvas or in the tree below</div>
+            <div id='seleinfo' className='msp-help-text'>
+                {help_selection}
             </div>
         </>;
-
         return <>
-            {info.map((entry, index) => {
-                const label = <Button className={`msp-btn-tree-label`} noOverflow disabled={this.state.isDisabled}
-                    onClick={() => this.center(entry.key)}
-                >
-                    <span title={entry.label}>{entry.label}</span>
-                </Button>;
-                const find = <IconButton svg={SearchSvg} toggleState={false} disabled={this.state.isDisabled} small onClick={() => this.find(entry.label)} />;
-                const remove = <IconButton svg={CloseSvg} toggleState={false} disabled={this.state.isDisabled} onClick={() => this.remove(entry.key)} />;
-                return <div key={index} className={`msp-flex-row`} style={{ margin: `1px 5px 1px ${1 * 10 + 5}px` }}>
-                    {label}
-                    {find}
-                    {remove}
-                </div>;
-            })}
+            <div id='seleinfo'>
+                {info.map((entry, index) => {
+                    const label = <Button className={`msp-btn-tree-label`} noOverflow disabled={this.state.isDisabled}
+                        onClick={() => this.center(entry.key)}
+                    >
+                        <span title={entry.label}>
+                            {entry.label}
+                        </span>
+                    </Button>;
+                    const find = <IconButton svg={SearchSvg} toggleState={false} disabled={this.state.isDisabled} small onClick={() => this.find(entry.label)} />;
+                    const remove = <IconButton svg={CloseSvg} toggleState={false} disabled={this.state.isDisabled} onClick={() => this.remove(entry.key)} />;
+                    return <>
+                        <div key={index} className={`msp-flex-row`} style={{ margin: `1px 5px 1px ${1 * 10 + 5}px` }}>
+                            {label}
+                            {find}
+                            {remove}
+                        </div>
+                    </>;
+                })};
+            </div>
         </>;
     }
 
@@ -216,7 +232,7 @@ export class SelectionInfo extends PluginUIComponent<{}, { isDisabled: boolean }
 
     renderStyle() {
         const style = this.style || '';
-        return <div style={{ margin: '5px', marginBottom: '10px' }}>
+        return <div id='selestyle' style={{ margin: '5px', marginBottom: '10px' }}>
             <SelectControl name={'Style'} param={SelectionStyleParam} value={style} onChange={(e) => { this.setStyle(e.value); }} />
         </div>;
     }
@@ -229,6 +245,192 @@ export class SelectionInfo extends PluginUIComponent<{}, { isDisabled: boolean }
     }
 }
 
+export function MesoMarkdownAnchor({ href, children, element }: { href?: string, children?: any, element?: any }) {
+    const plugin = React.useContext(PluginReactContext);
+    if (!href) return element;
+    // Decode the href to handle encoded spaces and other characters
+    const decodedHref = href ? decodeURIComponent(href) : '';
+    const handleHover = (e: React.MouseEvent<HTMLAnchorElement, MouseEvent>) => {
+        e.preventDefault();
+        if (decodedHref.startsWith('i')) {
+            plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+            const query_names = decodedHref.substring(1).split(',');
+            for (const query_name of query_names) {
+                const entities = getEveryEntity(plugin, query_name);
+                for (const r of entities) {
+                    const repr = r.obj?.data.repr;
+                    if (repr) {
+                        plugin.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+                    }
+                }
+            }
+        } else if (decodedHref.startsWith('g')) {
+            plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+            const qindex = decodedHref.indexOf('.');
+            const query = decodedHref.substring(1, qindex) + ':';
+            const query_names = decodedHref.substring(qindex + 1).split(',');
+            for (const query_name of query_names) {
+                const e = getAllEntities(plugin, query + query_name);
+                for (const r of e) {
+                    const repr = r.obj?.data.repr;
+                    if (repr) {
+                        plugin.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+                    }
+                }
+            }
+        }
+    };
+    const handleLeave = (e: React.MouseEvent<HTMLAnchorElement, MouseEvent>) => {
+        // Implement your hover off logic here
+        // Example: Perform an action if the href starts with 'h'
+        if (decodedHref.startsWith('i') || decodedHref.startsWith('g')) {
+            // Example hover off action
+            e.preventDefault();
+            plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+        }
+    };
+    const handleClick = (e: React.MouseEvent<HTMLAnchorElement, MouseEvent>) => {
+        e.preventDefault();
+        if (href.startsWith('#')) {
+            plugin.managers.snapshot.applyKey(decodedHref.substring(1));
+        } else if (decodedHref.startsWith('i')) {
+            plugin.managers.interactivity.lociSelects.deselectAll();
+            plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+            const query_names = decodedHref.substring(1).split(',');
+            for (const query_name of query_names) {
+                const entities = getFilteredEntities(plugin, '', query_name);
+                for (const r of entities) {
+                    const repr = r.obj?.data.repr;
+                    if (repr) {
+                        plugin.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+                    }
+                    const cell = r as StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D> | undefined;
+                    if (!(cell?.obj?.data.sourceData instanceof Structure)) {
+                        return;
+                    }
+                    const loci = Structure.toStructureElementLoci(cell.obj.data.sourceData);
+                    plugin.managers.interactivity.lociSelects.toggle({ loci }, false);
+                }
+            }
+        } else if (decodedHref.startsWith('g')) {
+            plugin.managers.interactivity.lociSelects.deselectAll();
+            plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
+            const qindex = decodedHref.indexOf('.');
+            const query = decodedHref.substring(1, qindex) + ':';
+            const query_names = decodedHref.substring(qindex + 1).split(',');
+            for (const query_name of query_names) {
+                const entities = getAllEntities(plugin, query + query_name);
+                for (const r of entities) {
+                    const repr = r.obj?.data.repr;
+                    if (repr) {
+                        plugin.canvas3d?.mark({ repr, loci: EveryLoci }, MarkerAction.Highlight);
+                    }
+                    const cell = r as StateObjectCell<PSO.Molecule.Structure.Representation3D | PSO.Shape.Representation3D> | undefined;
+                    if (!(cell?.obj?.data.sourceData instanceof Structure)) return;
+                    const loci = Structure.toStructureElementLoci(cell.obj.data.sourceData);
+                    plugin.managers.interactivity.lociSelects.toggle({ loci }, false);
+                }
+            }
+        } else {
+            // open the link in a new tab
+            window.open(decodedHref, '_blank');
+        }
+    };
+
+    if (decodedHref[0] === '#') {
+        return <a href={decodedHref[0]} onMouseOver={handleHover} onClick={handleClick}>{children}</a>;
+    }
+    if (decodedHref[0] === 'i' || decodedHref[0] === 'g') {
+        return <a href={decodedHref[0]} onMouseLeave={handleLeave} onMouseOver={handleHover} onClick={handleClick}>{children}</a>;
+    }
+    if (decodedHref[0] === 'h') {
+        return <a href={decodedHref[0]} onClick={handleClick} rel='noopener noreferrer'>{children}</a>;
+    }
+    return element;
+}
+
+export function MesoViewportSnapshotDescription() {
+    let tSize = 14;
+    const plugin = React.useContext(PluginReactContext);
+    if (MesoscaleState.has(plugin)) {
+        const state = MesoscaleState.get(plugin);
+        tSize = state.textSizeDescription;
+    }
+    const [_, setV] = React.useState(0);
+    const [isShown, setIsShown] = useState(true);
+    const [textSize, setTextSize] = useState(tSize);
+    const toggleVisibility = () => {
+        setIsShown(!isShown);
+    };
+
+    const increaseTextSize = () => {
+        setTextSize(prevSize => Math.min(prevSize + 2, 50)); // Increase the text size by 2px, but not above 50px
+    };
+
+    const decreaseTextSize = () => {
+        setTextSize(prevSize => Math.max(prevSize - 2, 2)); // Decrease the text size by 2px, but not below 2px
+    };
+
+
+    React.useEffect(() => {
+        const sub = plugin.managers.snapshot.events.changed.subscribe(() => setV(v => v + 1));
+        return () => sub.unsubscribe();
+    }, [plugin]);
+
+    const current = plugin.managers.snapshot.state.current;
+    if (!current) return null;
+
+    const e = plugin.managers.snapshot.getEntry(current)!;
+    if (!e?.description?.trim()) return null;
+    if (MesoscaleState.has(plugin)) {
+        MesoscaleState.set(plugin, { textSizeDescription: textSize });
+    }
+    const showInfo = <IconButton svg={isShown ? TooltipTextSvg : TooltipTextOutlineSvg} flex='20px' onClick={toggleVisibility} title={isShown ? 'Hide Description' : 'Show Description'}/>;
+    const increasePoliceSize = <IconButton svg={PlusBoxSvg} flex='20px' onClick={increaseTextSize} title='Bigger Text' />;
+    const decreasePoliceSize = <IconButton svg={MinusBoxSvg} flex='20px' onClick={decreaseTextSize} title='Smaller Text' />;
+    return (
+        <>
+            <div id='snapinfoctrl' className="msp-state-snapshot-viewport-controls" style={{ marginRight: '30px' }}>
+                {showInfo}{increasePoliceSize}{decreasePoliceSize}
+            </div>
+            <div id='snapinfo' className={`msp-snapshot-description-me ${isShown ? 'shown' : 'hidden'}`} style={{ fontSize: `${textSize}px` }}>
+                {<Markdown skipHtml={false} components={{ a: MesoMarkdownAnchor }}>{e.description}</Markdown>}
+            </div>
+        </>
+    );
+}
+
+export class FocusInfo extends PluginUIComponent<{}, { isDisabled: boolean }> {
+    componentDidMount() {
+        this.subscribe(combineLatest([
+            this.plugin.state.data.behaviors.isUpdating,
+            this.plugin.managers.structure.selection.events.changed
+        ]), ([isUpdating]) => {
+            if (!isUpdating) this.forceUpdate();
+        });
+    }
+
+    get info() {
+        let focusInfo = '';
+        if (MesoscaleState.has(this.plugin)) {
+            const state = MesoscaleState.get(this.plugin);
+            if (state.focusInfo) focusInfo = state.focusInfo;
+        }
+        return focusInfo;
+    }
+
+    render() {
+        const focusInfo = this.info;
+        const description = (focusInfo !== '') ? <Markdown skipHtml components={{ a: MesoMarkdownAnchor }}>{focusInfo}</Markdown> : '';
+        return <>
+            <div id='focusinfo' className='msp-help-text'>
+                {description}
+            </div>
+        </>;
+    }
+}
+
+
 export class EntityControls extends PluginUIComponent<{}, { isDisabled: boolean }> {
     filterRef = React.createRef<HTMLInputElement>();
     prevFilter = '';
@@ -336,7 +538,7 @@ export class EntityControls extends PluginUIComponent<{}, { isDisabled: boolean
 
     renderGraphics() {
         const graphics = this.graphics;
-        return <div style={{ margin: '5px', marginBottom: '10px' }}>
+        return <div id='graphicsquality' style={{ margin: '5px', marginBottom: '10px' }}>
             <SelectControl name={'Graphics'} param={MesoscaleStateParams.graphics} value={`${graphics}`} onChange={(e) => { this.setGraphics(e.value); }} />
         </div>;
     }
@@ -363,7 +565,7 @@ export class EntityControls extends PluginUIComponent<{}, { isDisabled: boolean
 
         return <>
             {this.renderGraphics()}
-            <div className={`msp-flex-row msp-control-row`} style={{ margin: '5px', marginBottom: '10px' }}>
+            <div id='searchtree' className={`msp-flex-row msp-control-row`} style={{ margin: '5px', marginBottom: '10px' }}>
                 <input type='text' ref={this.filterRef}
                     value={filter}
                     placeholder='Search'
@@ -373,10 +575,12 @@ export class EntityControls extends PluginUIComponent<{}, { isDisabled: boolean
                 />
                 <IconButton svg={CloseSvg} toggleState={false} disabled={disabled} onClick={() => this.setFilter('')} />
             </div>
-            {options.length > 1 && <div style={{ margin: '5px', marginBottom: '10px' }}>
+            {options.length > 1 && <div id='grouptree' style={{ margin: '5px', marginBottom: '10px' }}>
                 <SelectControl name={'Group By'} param={groupParam} value={`${groupBy}`} onChange={(e) => { this.setGroupBy(parseInt(e.value)); }} />
             </div>}
-            <GroupNode filter={filter} cell={root} depth={0} />
+            <div id='tree' style={{ position: 'relative', overflowY: 'auto', borderBottom: '1px  solid #000', maxHeight: '600px' }}>
+                <GroupNode filter={filter} cell={root} depth={0} />
+            </div>
         </>;
     }
 }
@@ -435,6 +639,12 @@ export class GroupNode extends Node<{ filter: string }, { isCollapsed: boolean,
         this.setState({ action: this.state.action === 'root' ? undefined : 'root' });
     };
 
+    showInfo = (e: React.MouseEvent<HTMLElement>) => {
+        e.preventDefault();
+        const d = getCellDescription(this.cell); // '### ' + this.cell?.obj?.label + '\n\n' + this.cell?.obj?.description;
+        MesoscaleState.set(this.plugin, { focusInfo: `${d}` });
+    };
+
     highlight = (e: React.MouseEvent<HTMLElement>) => {
         e.preventDefault();
         this.plugin.canvas3d?.mark({ loci: EveryLoci }, MarkerAction.RemoveHighlight);
@@ -493,7 +703,7 @@ export class GroupNode extends Node<{ filter: string }, { isCollapsed: boolean,
 
     updateColor = (values: ColorProps) => {
         const update = this.plugin.state.data.build();
-        const { value, type, lightness, alpha, emissive } = values;
+        const { value, illustrative, type, lightness, alpha, emissive } = values;
 
         const entities = this.filteredEntities;
 
@@ -507,8 +717,11 @@ export class GroupNode extends Node<{ filter: string }, { isCollapsed: boolean,
             const c = type === 'generate' ? groupColors[i] : value;
             update.to(entities[i]).update(old => {
                 if (old.type) {
-                    old.colorTheme.params.value = c;
-                    old.colorTheme.params.lightness = lightness;
+                    if (illustrative) {
+                        old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value: c, lightness } } } };
+                    } else {
+                        old.colorTheme = { name: 'uniform', params: { value: c, lightness } };
+                    }
                     old.type.params.alpha = alpha;
                     old.type.params.xrayShaded = alpha < 1 ? 'inverted' : false;
                     old.type.params.emissive = emissive;
@@ -655,6 +868,7 @@ export class GroupNode extends Node<{ filter: string }, { isCollapsed: boolean,
         const label = <Button className={`msp-btn-tree-label`} noOverflow disabled={disabled}
             onMouseEnter={this.highlight}
             onMouseLeave={this.clearHighlight}
+            onClick={this.showInfo}
         >
             <span title={groupLabel}>{groupLabel}</span>
         </Button>;
@@ -774,18 +988,63 @@ export class EntityNode extends Node<{}, { action?: 'color' | 'clip', isDisabled
         if (e.ctrlKey) {
             this.toggleSelect(e);
         } else {
-            this.center(e);
+            const d = getEntityDescription(this.plugin, this.cell);
+            if (this.cell?.obj?.data.sourceData.state.models.length !== 0) {
+                const repr = this.cell?.obj?.data.repr;
+                if (repr) {
+                    // for fiber need to think how to handle.
+                    const aloci = repr.getAllLoci()[0];
+                    const locis = Loci.normalize(aloci, 'chainInstances') as StructureElement.Loci;
+                    const nChain = aloci.structure.state.unitSymmetryGroups.length;
+                    let index = MesoscaleState.get(this.plugin).index + 1;
+                    if (index * nChain >= locis.elements.length) index = 0;
+                    const elems = locis.elements.slice(index * nChain, ((index + 1) * nChain)); // end index is not included
+                    const loci = StructureElement.Loci(aloci.structure, elems);
+                    const sphere = Loci.getBoundingSphere(loci) || Sphere3D();
+                    const state = this.plugin.state.behaviors;
+                    const selections = state.select(StateSelection.Generators.ofTransformer(MesoFocusLoci));
+                    const params = selections.length === 1 ? selections[0].obj?.data.params : undefined;
+                    if (!params.centerOnly) {
+                        this.plugin.managers.camera.focusSphere(sphere, params);
+                    } else {
+                        const snapshot = this.plugin.canvas3d?.camera.getCenter(sphere.center);
+                        this.plugin.canvas3d?.requestCameraReset({ durationMs: params.durationMs, snapshot });
+                    }
+                    MesoscaleState.set(this.plugin, { index: index, focusInfo: `${d}` });
+                }
+            } else {
+                this.center(e);
+                MesoscaleState.set(this.plugin, { focusInfo: `${d}` });
+            }
         }
     };
 
     get colorValue(): Color | undefined {
-        return this.cell.transform.params?.colorTheme?.params.value ?? this.cell.transform.params?.coloring?.params.color;
+        if (this.cell.transform.params?.colorTheme?.params.value) {
+            return this.cell.transform.params?.colorTheme?.params.value;
+        } else if (this.cell.transform.params?.colorTheme?.name === 'illustrative') {
+            return this.cell.transform.params?.colorTheme?.params.style.params.value;
+        } else {
+            return this.cell.transform.params?.colorTheme?.params.value ?? this.cell.transform.params?.coloring?.params.color;
+        }
+    }
+
+    get illustrativeValue(): { illustrative: boolean } | undefined {
+        return {
+            illustrative: (this.cell.transform.params?.colorTheme?.name === 'illustrative')
+        };
     }
 
     get lightnessValue(): { lightness: number } | undefined {
-        return {
-            lightness: this.cell.transform.params?.colorTheme?.params.lightness ?? this.cell.transform.params?.coloring?.params.lightness ?? 0
-        };
+        if (this.cell.transform.params?.colorTheme?.name === 'illustrative') {
+            return {
+                lightness: this.cell.transform.params?.colorTheme?.params.style.params.lightness ?? 0
+            };
+        } else {
+            return {
+                lightness: this.cell.transform.params?.colorTheme?.params.lightness ?? this.cell.transform.params?.coloring?.params.lightness ?? 0
+            };
+        }
     }
 
     get opacityValue(): { alpha: number } | undefined {
@@ -838,7 +1097,11 @@ export class EntityNode extends Node<{}, { action?: 'color' | 'clip', isDisabled
         }
         update.to(this.ref).update(old => {
             if (old.colorTheme) {
-                old.colorTheme.params.value = value;
+                if (old.colorTheme.name === 'illustrative') {
+                    old.colorTheme.params.style.params.value = value;
+                } else {
+                    old.colorTheme.params.value = value;
+                }
             } else if (old.coloring) {
                 old.coloring.params.color = value;
             }
@@ -846,10 +1109,26 @@ export class EntityNode extends Node<{}, { action?: 'color' | 'clip', isDisabled
         update.commit();
     };
 
+    updateIllustrative = (values: PD.Values) => {
+        return this.plugin.build().to(this.ref).update(old => {
+            if (old.colorTheme) {
+                if (old.colorTheme.name !== 'illustrative' && values.illustrative) {
+                    old.colorTheme = { name: 'illustrative', params: { style: { name: 'uniform', params: { value: old.colorTheme.params.value, lightness: old.colorTheme.params.lightness } } } };
+                } else if (old.colorTheme.name === 'illustrative' && !values.illustrative) {
+                    old.colorTheme = { name: 'uniform', params: { value: old.colorTheme.params.style.params.value, lightness: old.colorTheme.params.style.params.lightness } };
+                }
+            }
+        }).commit();
+    };
+
     updateLightness = (values: PD.Values) => {
         return this.plugin.build().to(this.ref).update(old => {
             if (old.colorTheme) {
-                old.colorTheme.params.lightness = values.lightness;
+                if (old.colorTheme.name === 'illustrative') {
+                    old.colorTheme.params.style.params.lightness = values.lightness;
+                } else {
+                    old.colorTheme.params.lightness = values.lightness;
+                }
             } else if (old.coloring) {
                 old.coloring.params.lightness = values.lightness;
             }
@@ -924,6 +1203,7 @@ export class EntityNode extends Node<{}, { action?: 'color' | 'clip', isDisabled
         const depth = this.props.depth;
         const colorValue = this.colorValue;
         const lightnessValue = this.lightnessValue;
+        const illustrativeValue = this.illustrativeValue;
         const opacityValue = this.opacityValue;
         const emissiveValue = this.emissiveValue;
         const lodValue = this.lodValue;
@@ -953,6 +1233,7 @@ export class EntityNode extends Node<{}, { action?: 'color' | 'clip', isDisabled
                 <ControlGroup header='Color' initialExpanded={true} hideExpander={true} hideOffset={true} onHeaderClick={this.toggleColor}
                     topRightIcon={CloseSvg} noTopMargin childrenClassName='msp-viewport-controls-panel-controls'>
                     <CombinedColorControl param={ColorValueParam} value={colorValue ?? Color(0xFFFFFF)} onChange={this.updateColor} name='color' hideNameRow />
+                    <ParameterControls params={IllustrativeParams} values={illustrativeValue} onChangeValues={this.updateIllustrative} />
                     <ParameterControls params={LightnessParams} values={lightnessValue} onChangeValues={this.updateLightness} />
                     <ParameterControls params={OpacityParams} values={opacityValue} onChangeValues={this.updateOpacity} />
                     <ParameterControls params={EmissiveParams} values={emissiveValue} onChangeValues={this.updateEmissive} />

src/apps/mesoscale-explorer/ui/panels.tsx

@@ -5,20 +5,63 @@
  */
 
 import { Mp4EncoderUI } from '../../../extensions/mp4-export/ui';
-import { PluginUIComponent } from '../../../mol-plugin-ui/base';
+import { CollapsableControls, CollapsableState, PluginUIComponent } from '../../../mol-plugin-ui/base';
 import { SectionHeader } from '../../../mol-plugin-ui/controls/common';
+import { ParameterControls } from '../../../mol-plugin-ui/controls/parameters';
+import { PluginCommands } from '../../../mol-plugin/commands';
+import { StructureMeasurementsControls } from '../../../mol-plugin-ui/structure/measurements';
 import { MesoscaleExplorerState } from '../app';
 import { MesoscaleState } from '../data/state';
-import { EntityControls, ModelInfo, SelectionInfo } from './entities';
-import { LoaderControls, ExampleControls, SessionControls, SnapshotControls, DatabaseControls } from './states';
+import { EntityControls, FocusInfo, ModelInfo, SelectionInfo } from './entities';
+import { LoaderControls, ExampleControls, SessionControls, SnapshotControls, DatabaseControls, MesoQuickStylesControls, ExplorerInfo } from './states';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { TuneSvg } from '../../../mol-plugin-ui/controls/icons';
+import { RendererParams } from '../../../mol-gl/renderer';
+import { TrackballControlsParams } from '../../../mol-canvas3d/controls/trackball';
 
 const Spacer = () => <div style={{ height: '2em' }} />;
 
+const ViewportParams = {
+    renderer: PD.Group(RendererParams),
+    trackball: PD.Group(TrackballControlsParams),
+};
+
+class ViewportSettingsUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState {
+        return {
+            header: 'Viewport Settings',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: TuneSvg }
+        };
+    }
+
+    protected renderControls(): JSX.Element | null {
+        return <>
+            {this.plugin.canvas3d && this.plugin.canvas3dContext && <>
+                <ParameterControls params={ViewportParams} values={this.plugin.canvas3d.props} onChange={this.setSettings} />
+            </>}
+        </>;
+    }
+
+    private setSettings = (p: { param: PD.Base<any>, name: string, value: any }) => {
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { [p.name]: p.value } });
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
+        this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
+    }
+}
+
 export class LeftPanel extends PluginUIComponent {
     render() {
         const customState = this.plugin.customState as MesoscaleExplorerState;
 
         return <div className='msp-scrollable-container'>
+            {customState.driver && <>
+                <ExplorerInfo />
+                <Spacer />
+            </>}
             <SectionHeader title='Database' />
             <DatabaseControls />
             <Spacer />
@@ -42,6 +85,7 @@ export class LeftPanel extends PluginUIComponent {
             <Spacer />
 
             <Mp4EncoderUI />
+            <ViewportSettingsUI />
         </div>;
     }
 }
@@ -59,6 +103,13 @@ export class RightPanel extends PluginUIComponent<{}, { isDisabled: boolean }> {
         );
     }
 
+    get hasFocusInfo() {
+        return (
+            MesoscaleState.has(this.plugin) &&
+            !!(MesoscaleState.get(this.plugin).focusInfo !== '')
+        );
+    }
+
     componentDidMount() {
         this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
             this.setState({ isDisabled: v });
@@ -89,10 +140,18 @@ export class RightPanel extends PluginUIComponent<{}, { isDisabled: boolean }> {
                 <SectionHeader title='Selection' />
                 <SelectionInfo />
                 <Spacer />
+                <StructureMeasurementsControls initiallyCollapsed={true}/>
             </>
-
+            <MesoQuickStylesControls />
+            <Spacer />
             <SectionHeader title='Entities' />
             <EntityControls />
+            <Spacer />
+            {this.hasFocusInfo && <>
+                <SectionHeader title='Focus Info' />
+                <FocusInfo />
+                <Spacer />
+            </>}
         </div>;
     }
-}
+}

src/apps/mesoscale-explorer/ui/states.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -7,9 +7,9 @@
 import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 import { MmcifProvider } from '../../../mol-plugin-state/formats/trajectory';
 import { PluginStateObject } from '../../../mol-plugin-state/objects';
-import { PluginUIComponent } from '../../../mol-plugin-ui/base';
-import { Button, ExpandGroup } from '../../../mol-plugin-ui/controls/common';
-import { GetAppSvg, Icon, OpenInBrowserSvg } from '../../../mol-plugin-ui/controls/icons';
+import { Button, ExpandGroup, IconButton } from '../../../mol-plugin-ui/controls/common';
+import { GetAppSvg, HelpOutlineSvg, MagicWandSvg, TourSvg, Icon, OpenInBrowserSvg } from '../../../mol-plugin-ui/controls/icons';
+import { CollapsableControls, PluginUIComponent } from '../../../mol-plugin-ui/base';
 import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
 import { LocalStateSnapshotList, LocalStateSnapshotParams, LocalStateSnapshots } from '../../../mol-plugin-ui/state/snapshots';
 import { PluginCommands } from '../../../mol-plugin/commands';
@@ -24,9 +24,13 @@ import { createCellpackHierarchy } from '../data/cellpack/preset';
 import { createGenericHierarchy } from '../data/generic/preset';
 import { createMmcifHierarchy } from '../data/mmcif/preset';
 import { createPetworldHierarchy } from '../data/petworld/preset';
-import { MesoscaleState, MesoscaleStateObject, setGraphicsCanvas3DProps } from '../data/state';
+import { MesoscaleState, MesoscaleStateObject, setGraphicsCanvas3DProps, updateStyle } from '../data/state';
+import { isTimingMode } from '../../../mol-util/debug';
+import { now } from '../../../mol-util/now';
 
 function adjustPluginProps(ctx: PluginContext) {
+    const customState = ctx.customState as MesoscaleExplorerState;
+
     ctx.managers.interactivity.setProps({ granularity: 'chain' });
     ctx.canvas3d?.setProps({
         multiSample: { mode: 'off' },
@@ -77,14 +81,15 @@ function adjustPluginProps(ctx: PluginContext) {
                     radius: 5,
                     bias: 1,
                     blurKernelSize: 11,
+                    blurDepthBias: 0.5,
                     resolutionScale: 1,
                     color: Color(0x000000),
+                    transparentThreshold: 0.4,
                 }
             },
             shadow: {
                 name: 'on',
                 params: {
-                    bias: 0.6,
                     maxDistance: 80,
                     steps: 3,
                     tolerance: 1.0,
@@ -98,8 +103,13 @@ function adjustPluginProps(ctx: PluginContext) {
                     color: Color(0x000000),
                     includeTransparent: false,
                 }
-            }
-        }
+            },
+        },
+        illumination: {
+            enabled: customState.illumination,
+            firstStepSize: 0.1,
+            rayDistance: 1024,
+        },
     });
 
     const { graphics } = MesoscaleState.get(ctx);
@@ -162,14 +172,36 @@ export async function loadExampleEntry(ctx: PluginContext, entry: ExampleEntry)
 }
 
 export async function loadUrl(ctx: PluginContext, url: string, type: 'molx' | 'molj' | 'cif' | 'bcif') {
+    let startTime = 0;
+    if (isTimingMode) {
+        startTime = now();
+    }
     if (type === 'molx' || type === 'molj') {
+        const customState = ctx.customState as MesoscaleExplorerState;
+        delete customState.stateRef;
+        customState.stateCache = {};
+        ctx.managers.asset.clear();
+
+        await PluginCommands.State.Snapshots.Clear(ctx);
         await PluginCommands.State.Snapshots.OpenUrl(ctx, { url, type });
+
+        const cell = ctx.state.data.selectQ(q => q.ofType(MesoscaleStateObject))[0];
+        if (!cell) throw new Error('Missing MesoscaleState');
+
+        customState.stateRef = cell.transform.ref;
+        customState.graphicsMode = cell.obj?.data.graphics || customState.graphicsMode;
     } else {
         await reset(ctx);
         const isBinary = type === 'bcif';
         const data = await ctx.builders.data.download({ url, isBinary });
         await createHierarchy(ctx, data.ref);
     }
+    if (isTimingMode) {
+        const endTime = now();
+        // Calculate the elapsed time
+        const timeTaken = endTime - startTime;
+        console.log(`Model loaded in ${timeTaken} milliseconds`);
+    }
 }
 
 export async function loadPdb(ctx: PluginContext, id: string) {
@@ -181,8 +213,14 @@ export async function loadPdb(ctx: PluginContext, id: string) {
 
 export async function loadPdbDev(ctx: PluginContext, id: string) {
     await reset(ctx);
-    const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
-    const url = `https://pdb-dev.wwpdb.org/bcif/${nId.toUpperCase()}.bcif`;
+    let url: string;
+    // 4 character PDB id, TODO: support extended PDB ID
+    if (id.match(/^[1-9][A-Z0-9]{3}$/i) !== null) {
+        url = `https://pdb-dev.wwpdb.org/bcif/${id.toLowerCase()}.bcif`;
+    } else {
+        const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
+        url = `https://pdb-dev.wwpdb.org/bcif/${nId.toUpperCase()}.bcif`;
+    }
     const data = await ctx.builders.data.download({ url, isBinary: true });
     await createHierarchy(ctx, data.ref);
 }
@@ -269,7 +307,7 @@ export class DatabaseControls extends PluginUIComponent {
     }
 
     render() {
-        return <div style={{ margin: '5px' }}>
+        return <div id='database' style={{ margin: '5px' }}>
             <ApplyActionControl state={this.plugin.state.data} action={LoadDatabase} nodeRef={this.plugin.state.data.tree.root.ref} applyLabel={'Load'} hideHeader />
         </div>;
     }
@@ -281,7 +319,7 @@ export class LoaderControls extends PluginUIComponent {
     }
 
     render() {
-        return <div style={{ margin: '5px' }}>
+        return <div id='loader' style={{ margin: '5px' }}>
             <ApplyActionControl state={this.plugin.state.data} action={LoadModel} nodeRef={this.plugin.state.data.tree.root.ref} applyLabel={'Load'} hideHeader />
         </div>;
     }
@@ -293,7 +331,7 @@ export class ExampleControls extends PluginUIComponent {
     }
 
     render() {
-        return <div style={{ margin: '5px' }}>
+        return <div id='example' style={{ margin: '5px' }}>
             <ApplyActionControl state={this.plugin.state.data} action={LoadExample} nodeRef={this.plugin.state.data.tree.root.ref} applyLabel={'Load'} hideHeader />
         </div>;
     }
@@ -330,7 +368,7 @@ export class SessionControls extends PluginUIComponent {
     };
 
     render() {
-        return <div style={{ margin: '5px' }}>
+        return <div id='session' style={{ margin: '5px' }}>
             <div className='msp-flex-row'>
                 <Button icon={GetAppSvg} onClick={this.downloadToFileZip} title='Download the state.'>
                     Download
@@ -346,14 +384,14 @@ export class SessionControls extends PluginUIComponent {
 export class SnapshotControls extends PluginUIComponent<{}> {
     render() {
         return <div style={{ margin: '5px' }}>
-            <div style={{ marginBottom: '10px' }}>
+            <div id='snaplist' style={{ marginBottom: '10px' }}>
                 <LocalStateSnapshotList />
             </div>
-            <div style={{ marginBottom: '10px' }}>
+            <div id='snap' style={{ marginBottom: '10px' }}>
                 <LocalStateSnapshots />
             </div>
 
-            <div style={{ marginBottom: '10px' }}>
+            <div id='snapoption' style={{ marginBottom: '10px' }}>
                 <ExpandGroup header='Snapshot Options' initiallyExpanded={false}>
                     <LocalStateSnapshotParams />
                 </ExpandGroup>
@@ -361,3 +399,336 @@ export class SnapshotControls extends PluginUIComponent<{}> {
         </div>;
     }
 }
+
+export class ExplorerInfo extends PluginUIComponent<{}, { isDisabled: boolean, showHelp: boolean }> {
+    state = {
+        isDisabled: false,
+        showHelp: false
+    };
+
+    componentDidMount() {
+        this.subscribe(this.plugin.state.data.behaviors.isUpdating, v => {
+            this.setState({ isDisabled: v });
+        });
+
+        this.subscribe(this.plugin.state.events.cell.stateUpdated, e => {
+            if (!this.state.isDisabled && MesoscaleState.has(this.plugin) && MesoscaleState.ref(this.plugin) === e.ref) {
+                this.forceUpdate();
+            }
+        });
+    }
+
+    setupDriver = () => {
+        // setup the tour of the interface
+        const driver = (this.plugin.customState as MesoscaleExplorerState).driver;
+        if (!driver) return;
+
+        driver.setSteps([
+            // Left panel
+            { element: '#explorerinfo', popover: { title: 'Explorer Header Info', description: 'This section displays the explorer header with version information, documentation access, and tour navigation. Use the right and left arrow keys to navigate the tour.', side: 'left', align: 'start' } },
+            { element: '#database', popover: { title: 'Import from PDB', description: 'Load structures directly from PDB and PDB-DEV databases.', side: 'bottom', align: 'start' } },
+            { element: '#loader', popover: { title: 'Import from File', description: 'Load local files (.molx, .molj, .zip, .cif, .bcif) using this option.', side: 'bottom', align: 'start' } },
+            { element: '#example', popover: { title: 'Example Models and Tours', description: 'Select from a range of example models and tours provided.', side: 'left', align: 'start' } },
+            { element: '#session', popover: { title: 'Session Management', description: 'Download the current session in .molx format.', side: 'top', align: 'start' } },
+            { element: '#snaplist', popover: { title: 'Snapshot List', description: 'View and manage the list of snapshots. You can reorder them and edit their titles, keys, and descriptions. Snapshot states cannot be edited.', side: 'right', align: 'start' } },
+            { element: '#snap', popover: { title: 'Add Snapshot', description: 'Save the current state (e.g., camera position, color, visibility, etc.) in a snapshot with an optional title, key, and description.', side: 'right', align: 'start' } },
+            { element: '#snapoption', popover: { title: 'Snapshot Options', description: 'These options are saved in the snapshot. Set them before adding a snapshot to see their effect during animation playback.', side: 'right', align: 'start' } },
+            { element: '#exportanimation', popover: { title: 'Export Animation', description: 'Create movies or scenes with rocking, rotating, or snapshots animations.', side: 'right', align: 'start' } },
+            { element: '#viewportsettings', popover: { title: 'Viewport Settings', description: 'Advanced settings for the renderer and trackball.', side: 'right', align: 'start' } },
+            // Viewport
+            { element: '#snapinfo', popover: { title: 'Snapshot Description', description: 'Save the current state (e.g., camera position, color, visibility, etc.) in a snapshot with an optional title, key, and description.', side: 'right', align: 'start' } },
+            { element: '#snapinfoctrl', popover: { title: 'Snapshot Description Control', description: 'Control the visibility and text size of the snapshot description widget.', side: 'right', align: 'start' } },
+            // Right panel
+            { element: '#modelinfo', popover: { title: 'Model Information', description: 'Summary information about the model, if available.', side: 'right', align: 'start' } },
+            { element: '#selestyle', popover: { title: 'Selection Style', description: 'Choose the rendering style for entity selection accessed via Shift/Ctrl mouse. Options include: Color & Outline, Color, Outline.', side: 'right', align: 'start' } },
+            { element: '#seleinfo', popover: { title: 'Selection List', description: 'View the current list of selected entities.', side: 'right', align: 'start' } },
+            { element: '#measurements', popover: { title: 'Measurements', description: 'Use this widget to create labels, measure distances, angles, dihedral orientations, and planes for the selected entities.', side: 'right', align: 'start' } },
+            { element: '#quickstyles', popover: { title: 'Quick Styles', description: 'Change between a selection of style presets.', side: 'right', align: 'start' } },
+            { element: '#graphicsquality', popover: { title: 'Graphics Quality', description: 'Adjust the overall graphics quality. Lower quality improves performance. Options are: Ultra, Quality (Default), Balanced, Performance, Custom. Custom settings use the Culling & LOD values set in the Tree.', side: 'right', align: 'start' } },
+            { element: '#searchtree', popover: { title: 'Search', description: 'Filter the entity tree based on your queries.', side: 'right', align: 'start' } },
+            { element: '#grouptree', popover: { title: 'Group By', description: 'Change the grouping of the hierarchy tree, e.g., group by instance or by compartment.', side: 'right', align: 'start' } },
+            { element: '#tree', popover: { title: 'Tree Hierarchy', description: 'View the hierarchical tree of entity types in the model.', side: 'right', align: 'start' } },
+            { element: '#focusinfo', popover: { title: 'Selection Description', description: 'Detailed information about the current selection, if present in the loaded file.', side: 'right', align: 'start' } },
+            { popover: { title: 'Happy Exploring!', description: 'That’s all! Go ahead and start exploring or creating mesoscale tours.' } }
+        ]);
+        driver.refresh();
+    };
+
+    openHelp = () => {
+        // open a new page with the documentation
+        window.open('https://molstar.org/me-docs/', '_blank');
+    };
+
+    toggleHelp = () => {
+        const driver = (this.plugin.customState as MesoscaleExplorerState).driver;
+        if (!driver || !driver.hasNextStep()) {
+            this.setupDriver();
+        }
+        this.setState({ showHelp: !this.state.showHelp }, () => {
+            if (this.state.showHelp && driver) {
+                driver.drive(); // start at 0
+            }
+        });
+    };
+
+    render() {
+        const driver = (this.plugin.customState as MesoscaleExplorerState).driver;
+        if (!driver) return;
+
+        const help = <IconButton svg={HelpOutlineSvg} toggleState={false} small onClick={this.openHelp} title='Open the Documentation' />;
+        const tour = <IconButton svg={TourSvg} toggleState={false} small onClick={this.toggleHelp} title='Start the interactive tour' />;
+        return <>
+            <div id='explorerinfo' style={{ display: 'flex', alignItems: 'center', padding: '4px 0 4px 8px' }} className='msp-help-text'>
+                <h2 style={{ flexGrow: 1 }}>Mol* Mesoscale Explorer</h2>
+                {tour}{help}
+            </div>
+        </>;
+    }
+}
+
+
+export class MesoQuickStylesControls extends CollapsableControls {
+    defaultState() {
+        return {
+            isCollapsed: true,
+            header: 'Quick Styles',
+            brand: { accent: 'gray' as const, svg: MagicWandSvg }
+        };
+    }
+
+    renderControls() {
+        return <>
+            <MesoQuickStyles />
+        </>;
+    }
+}
+
+export class MesoQuickStyles extends PluginUIComponent {
+    async default() {
+        if (!this.plugin.canvas3d) return;
+        const p = this.plugin.canvas3d.props;
+        this.plugin.canvas3d.setProps({
+            renderer: {
+                exposure: 1.1,
+            },
+            postprocessing: {
+                ...p.postprocessing,
+                shadow: {
+                    name: 'on',
+                    params: {
+                        maxDistance: 80,
+                        steps: 3,
+                        tolerance: 1.0,
+                    }
+                },
+                outline: {
+                    name: 'on',
+                    params: {
+                        scale: 1,
+                        threshold: 0.15,
+                        color: Color(0x000000),
+                        includeTransparent: false,
+                    }
+                },
+                dof: { name: 'off', params: {} },
+            }
+        });
+        await updateStyle(this.plugin, {
+            ignoreLight: true,
+            material: { metalness: 0, roughness: 1.0, bumpiness: 0 },
+            celShaded: false,
+            illustrative: false,
+        });
+    }
+
+    async celshading() {
+        if (!this.plugin.canvas3d) return;
+        const p = this.plugin.canvas3d.props;
+        this.plugin.canvas3d.setProps({
+            renderer: {
+                exposure: 1.5,
+            },
+            postprocessing: {
+                ...p.postprocessing,
+                shadow: {
+                    name: 'on',
+                    params: {
+                        maxDistance: 256,
+                        steps: 64,
+                        tolerance: 1.0,
+                    }
+                },
+                outline: { name: 'off', params: {} },
+                dof: { name: 'off', params: {} },
+            }
+        });
+        await updateStyle(this.plugin, {
+            ignoreLight: false,
+            material: { metalness: 0, roughness: 1.0, bumpiness: 0 },
+            celShaded: true,
+            illustrative: false,
+        });
+    }
+
+    async shinyDof() {
+        if (!this.plugin.canvas3d) return;
+        const p = this.plugin.canvas3d.props;
+        this.plugin.canvas3d.setProps({
+            renderer: {
+                exposure: 1.1,
+            },
+            postprocessing: {
+                ...p.postprocessing,
+                shadow: {
+                    name: 'on',
+                    params: {
+                        maxDistance: 256,
+                        steps: 64,
+                        tolerance: 1.0,
+                    }
+                },
+                outline: { name: 'off', params: {} },
+                dof: {
+                    name: 'on',
+                    params: {
+                        blurSize: 9,
+                        blurSpread: 1.0,
+                        inFocus: 0.0,
+                        PPM: 200.0,
+                        center: 'camera-target',
+                        mode: 'sphere',
+                    }
+                }
+            }
+        });
+        await updateStyle(this.plugin, {
+            ignoreLight: false,
+            material: { metalness: 0, roughness: 0.2, bumpiness: 0 },
+            celShaded: false,
+            illustrative: false,
+        });
+    }
+
+    async illustrative() {
+        if (!this.plugin.canvas3d) return;
+        const p = this.plugin.canvas3d.props;
+        this.plugin.canvas3d.setProps({
+            renderer: {
+                exposure: 1.5,
+            },
+            postprocessing: {
+                ...p.postprocessing,
+                shadow: {
+                    name: 'on',
+                    params: {
+                        maxDistance: 256,
+                        steps: 64,
+                        tolerance: 1.0,
+                    }
+                },
+                outline: {
+                    name: 'on',
+                    params: {
+                        scale: 1,
+                        threshold: 0.15,
+                        color: Color(0x000000),
+                        includeTransparent: false,
+                    }
+                },
+                dof: { name: 'off', params: {} },
+            }
+        });
+        await updateStyle(this.plugin, {
+            ignoreLight: true,
+            material: { metalness: 0, roughness: 1.0, bumpiness: 0 },
+            celShaded: false,
+            illustrative: true,
+        });
+    }
+
+    async shiny() {
+        if (!this.plugin.canvas3d) return;
+        const p = this.plugin.canvas3d.props;
+        this.plugin.canvas3d.setProps({
+            renderer: {
+                exposure: 1.5,
+            },
+            postprocessing: {
+                ...p.postprocessing,
+                shadow: { name: 'off', params: {} },
+                outline: { name: 'off', params: {} },
+                dof: { name: 'off', params: {} },
+            }
+        });
+        await updateStyle(this.plugin, {
+            ignoreLight: false,
+            material: { metalness: 0, roughness: 0.2, bumpiness: 0 },
+            celShaded: false,
+            illustrative: false,
+        });
+    }
+
+    async stylized() {
+        if (!this.plugin.canvas3d) return;
+        const p = this.plugin.canvas3d.props;
+        this.plugin.canvas3d.setProps({
+            renderer: {
+                exposure: 1.1,
+            },
+            postprocessing: {
+                ...p.postprocessing,
+                shadow: {
+                    name: 'on',
+                    params: {
+                        maxDistance: 256,
+                        steps: 64,
+                        tolerance: 1.0,
+                    }
+                },
+                outline: {
+                    name: 'on',
+                    params: {
+                        scale: 1,
+                        threshold: 0.15,
+                        color: Color(0x000000),
+                        includeTransparent: false,
+                    }
+                },
+                dof: { name: 'off', params: {} },
+            }
+        });
+        await updateStyle(this.plugin, {
+            ignoreLight: false,
+            material: { metalness: 0, roughness: 0.2, bumpiness: 0 },
+            celShaded: false,
+            illustrative: true,
+        });
+    }
+
+    render() {
+        return <>
+            <div className='msp-flex-row'>
+                <Button noOverflow title='Applies default representation preset and sets outline and occlusion effects to default' onClick={() => this.default()} style={{ width: 'auto' }}>
+                    Default
+                </Button>
+                <Button noOverflow title='Applies celShading' onClick={() => this.celshading()} style={{ width: 'auto' }}>
+                    Cel-shaded
+                </Button>
+                <Button noOverflow title='Applies illustrative colors preset' onClick={() => this.illustrative()} style={{ width: 'auto' }}>
+                    Illustrative
+                </Button>
+            </div>
+            <div className='msp-flex-row'>
+                <Button noOverflow title='Apply shiny material to default' onClick={() => this.shiny()} style={{ width: 'auto' }}>
+                    Shiny
+                </Button>
+                <Button noOverflow title='Enable shiny material, outline, and illustrative colors' onClick={() => this.stylized()} style={{ width: 'auto' }}>
+                    Shiny-Illustrative
+                </Button>
+                <Button noOverflow title='Enable DOF and shiny material' onClick={() => this.shinyDof()} style={{ width: 'auto' }}>
+                    Shiny-DOF
+                </Button>
+            </div>
+        </>;
+    }
+}

src/apps/viewer/app.ts

@@ -3,6 +3,8 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Neli Fonseca <neli@ebi.ac.uk>
+ * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
@@ -10,18 +12,18 @@ import { Backgrounds } from '../../extensions/backgrounds';
 import { DnatcoNtCs } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
 import { GeometryExport } from '../../extensions/geo-export';
-import { MAQualityAssessment, QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
+import { MAQualityAssessment, MAQualityAssessmentConfig, QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
 import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { MolViewSpec } from '../../extensions/mvs/behavior';
 import { loadMVSX } from '../../extensions/mvs/components/formats';
-import { loadMVS } from '../../extensions/mvs/load';
+import { loadMVS, MolstarLoadingExtension } from '../../extensions/mvs/load';
 import { MVSData } from '../../extensions/mvs/mvs-data';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBValidationReport } from '../../extensions/rcsb';
 import { AssemblySymmetry, AssemblySymmetryConfig } from '../../extensions/assembly-symmetry';
-import { SbNcbrPartialCharges, SbNcbrPartialChargesPreset, SbNcbrPartialChargesPropertyProvider } from '../../extensions/sb-ncbr';
+import { SbNcbrPartialCharges, SbNcbrPartialChargesPreset, SbNcbrPartialChargesPropertyProvider, SbNcbrTunnels } from '../../extensions/sb-ncbr';
 import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
 import { wwPDBChemicalComponentDictionary } from '../../extensions/wwpdb/ccd/behavior';
 import { wwPDBStructConnExtensionFunctions } from '../../extensions/wwpdb/struct-conn';
@@ -46,7 +48,7 @@ import { createPluginUI } from '../../mol-plugin-ui';
 import { renderReact18 } from '../../mol-plugin-ui/react18';
 import { DefaultPluginUISpec, PluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { PluginConfig } from '../../mol-plugin/config';
+import { PluginConfig, PluginConfigItem } from '../../mol-plugin/config';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 import { PluginSpec } from '../../mol-plugin/spec';
 import { PluginState } from '../../mol-plugin/state';
@@ -81,6 +83,7 @@ export const ExtensionMap = {
     'sb-ncbr-partial-charges': PluginSpec.Behavior(SbNcbrPartialCharges),
     'wwpdb-chemical-component-dictionary': PluginSpec.Behavior(wwPDBChemicalComponentDictionary),
     'mvs': PluginSpec.Behavior(MolViewSpec),
+    'tunnels': PluginSpec.Behavior(SbNcbrTunnels),
 };
 
 const DefaultViewerOptions = {
@@ -103,6 +106,8 @@ const DefaultViewerOptions = {
     preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
     allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
     powerPreference: PluginConfig.General.PowerPreference.defaultValue,
+    resolutionMode: PluginConfig.General.ResolutionMode.defaultValue,
+    illumination: false,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -120,6 +125,8 @@ const DefaultViewerOptions = {
     rcsbAssemblySymmetryDefaultServerType: AssemblySymmetryConfig.DefaultServerType.defaultValue,
     rcsbAssemblySymmetryDefaultServerUrl: AssemblySymmetryConfig.DefaultServerUrl.defaultValue,
     rcsbAssemblySymmetryApplyColors: AssemblySymmetryConfig.ApplyColors.defaultValue,
+
+    config: [] as [PluginConfigItem, any][],
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 
@@ -180,6 +187,7 @@ export class Viewer {
                 [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
                 [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
                 [PluginConfig.General.PowerPreference, o.powerPreference],
+                [PluginConfig.General.ResolutionMode, o.resolutionMode],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
@@ -198,6 +206,7 @@ export class Viewer {
                 [AssemblySymmetryConfig.DefaultServerType, o.rcsbAssemblySymmetryDefaultServerType],
                 [AssemblySymmetryConfig.DefaultServerUrl, o.rcsbAssemblySymmetryDefaultServerUrl],
                 [AssemblySymmetryConfig.ApplyColors, o.rcsbAssemblySymmetryApplyColors],
+                ...(o.config ?? []),
             ]
         };
 
@@ -215,6 +224,7 @@ export class Viewer {
                 plugin.builders.structure.representation.registerPreset(ViewerAutoPreset);
             }
         });
+        plugin.canvas3d?.setProps({ illumination: { enabled: o.illumination } });
         return new Viewer(plugin);
     }
 
@@ -316,7 +326,10 @@ export class Viewer {
             source: {
                 name: 'alphafolddb' as const,
                 params: {
-                    id: afdb,
+                    provider: {
+                        id: afdb,
+                        encoding: 'bcif'
+                    },
                     options: {
                         ...params.source.params.options,
                         representation: 'preset-structure-representation-ma-quality-assessment-plddt'
@@ -422,6 +435,34 @@ export class Viewer {
         });
     }
 
+    loadFullResolutionEMDBMap(emdbId: string, options: { isoValue: Volume.IsoValue, color?: Color }) {
+        const plugin = this.plugin;
+        const numericId = parseInt(emdbId.toUpperCase().replace('EMD-', ''));
+        const url = `https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-${numericId}/map/emd_${numericId}.map.gz`;
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.build().toRoot()
+                .apply(StateTransforms.Data.Download, { url, isBinary: true, label: emdbId }, { state: { isGhost: true } })
+                .apply(StateTransforms.Data.DeflateData)
+                .commit();
+
+            const parsed = await plugin.dataFormats.get('ccp4')!.parse(plugin, data, { entryId: emdbId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!firstVolume?.isOk) throw new Error('Failed to parse any volume.');
+
+            const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[0] ?? parsed.volume;
+            await plugin.build()
+                .to(volume)
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
+                    type: 'isosurface',
+                    typeParams: { alpha: 1, isoValue: options.isoValue },
+                    color: 'uniform',
+                    colorParams: { value: options.color ?? Color(0x33BB33) }
+                }))
+                .commit();
+        });
+    }
+
     /**
      * @example
      *  viewer.loadTrajectory({
@@ -470,7 +511,7 @@ export class Viewer {
         return { model, coords, preset };
     }
 
-    async loadMvsFromUrl(url: string, format: 'mvsj' | 'mvsx', options?: { replaceExisting?: boolean, keepCamera?: boolean }) {
+    async loadMvsFromUrl(url: string, format: 'mvsj' | 'mvsx', options?: { replaceExisting?: boolean, keepCamera?: boolean, extensions?: MolstarLoadingExtension<any>[] }) {
         if (format === 'mvsj') {
             const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'string' }));
             const mvsData = MVSData.fromMVSJ(data);
@@ -489,7 +530,7 @@ export class Viewer {
     /** Load MolViewSpec from `data`.
      * If `format` is 'mvsj', `data` must be a string or a Uint8Array containing a UTF8-encoded string.
      * If `format` is 'mvsx', `data` must be a Uint8Array or a string containing base64-encoded binary data prefixed with 'base64,'. */
-    async loadMvsData(data: string | Uint8Array, format: 'mvsj' | 'mvsx', options?: { replaceExisting?: boolean, keepCamera?: boolean }) {
+    async loadMvsData(data: string | Uint8Array, format: 'mvsj' | 'mvsx', options?: { replaceExisting?: boolean, keepCamera?: boolean, extensions?: MolstarLoadingExtension<any>[] }) {
         if (typeof data === 'string' && data.startsWith('base64')) {
             data = Uint8Array.from(atob(data.substring(7)), c => c.charCodeAt(0)); // Decode base64 string to Uint8Array
         }
@@ -578,4 +619,9 @@ export const ViewerAutoPreset = StructureRepresentationPresetProvider({
 export const PluginExtensions = {
     wwPDBStructConn: wwPDBStructConnExtensionFunctions,
     mvs: { MVSData, loadMVS },
+    modelArchive: {
+        qualityAssessment: {
+            config: MAQualityAssessmentConfig
+        }
+    }
 };

src/apps/viewer/index.html

@@ -63,6 +63,8 @@
             var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
             var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
             var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
+            var illumination = getParam('illumination', '[^&]+').trim() === '1';
+            var resolutionMode = getParam('resolution-mode', '[^&]+').trim().toLowerCase();
 
             // console.log('Available extensions: ', Object.keys(molstar.ExtensionMap));
 
@@ -83,6 +85,8 @@
                 preferWebgl1: preferWebgl1,
                 allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
                 powerPreference: powerPreference || 'high-performance',
+                illumination: illumination,
+                resolutionMode: resolutionMode || 'auto'
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();
                 if (snapshotId) viewer.setRemoteSnapshot(snapshotId);

src/cli/cifschema/util/cif-dic.ts

@@ -234,13 +234,19 @@ const FORCE_INT_FIELDS = [
     '_atom_site.id',
     '_atom_site.auth_seq_id',
     '_atom_site_anisotrop.id',
+    '_atom_site_anisotrop.pdbx_auth_seq_id',
     '_pdbx_struct_mod_residue.auth_seq_id',
+    '_pdbx_unobs_or_zero_occ_residues.auth_seq_id',
     '_struct_conf.beg_auth_seq_id',
     '_struct_conf.end_auth_seq_id',
     '_struct_conn.ptnr1_auth_seq_id',
     '_struct_conn.ptnr2_auth_seq_id',
     '_struct_sheet_range.beg_auth_seq_id',
     '_struct_sheet_range.end_auth_seq_id',
+    '_struct_site.pdbx_auth_seq_id',
+    '_struct_site_gen.auth_seq_id',
+    '_struct_mon_prot_cis.auth_seq_id',
+    '_struct_mon_prot_cis.pdbx_auth_seq_id_2',
 ];
 
 /**

src/cli/lipid-params/index.ts

@@ -13,8 +13,8 @@ import { UniqueArray } from '../../mol-data/generic';
 
 const LIPIDS_DIR = path.resolve(__dirname, '../../../../build/lipids/');
 
-const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
-const MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
+const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids_v3.itp');
+const MARTINI_LIPIDS_URL = 'https://cgmartini-library.s3.ca-central-1.amazonaws.com/1_Downloads/ff_parameters/martini3/martini_v3.0.0_phospholipids_v1.itp';
 
 async function ensureAvailable(path: string, url: string) {
     if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
@@ -32,6 +32,7 @@ async function ensureAvailable(path: string, url: string) {
 async function ensureLipidsAvailable() { await ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL); }
 
 const extraLipids = ['DMPC'];
+const v2lipids = ['DAPC', 'DBPC', 'DFPC', 'DGPC', 'DIPC', 'DLPC', 'DNPC', 'DOPC', 'DPPC', 'DRPC', 'DTPC', 'DVPC', 'DXPC', 'DYPC', 'LPPC', 'PAPC', 'PEPC', 'PGPC', 'PIPC', 'POPC', 'PRPC', 'PUPC', 'DAPE', 'DBPE', 'DFPE', 'DGPE', 'DIPE', 'DLPE', 'DNPE', 'DOPE', 'DPPE', 'DRPE', 'DTPE', 'DUPE', 'DVPE', 'DXPE', 'DYPE', 'LPPE', 'PAPE', 'PGPE', 'PIPE', 'POPE', 'PQPE', 'PRPE', 'PUPE', 'DAPS', 'DBPS', 'DFPS', 'DGPS', 'DIPS', 'DLPS', 'DNPS', 'DOPS', 'DPPS', 'DRPS', 'DTPS', 'DUPS', 'DVPS', 'DXPS', 'DYPS', 'LPPS', 'PAPS', 'PGPS', 'PIPS', 'POPS', 'PQPS', 'PRPS', 'PUPS', 'DAPG', 'DBPG', 'DFPG', 'DGPG', 'DIPG', 'DLPG', 'DNPG', 'DOPG', 'DPPG', 'DRPG', 'DTPG', 'DVPG', 'DXPG', 'DYPG', 'LPPG', 'PAPG', 'PGPG', 'PIPG', 'POPG', 'PRPG', 'DAPA', 'DBPA', 'DFPA', 'DGPA', 'DIPA', 'DLPA', 'DNPA', 'DOPA', 'DPPA', 'DRPA', 'DTPA', 'DVPA', 'DXPA', 'DYPA', 'LPPA', 'PAPA', 'PGPA', 'PIPA', 'POPA', 'PRPA', 'PUPA', 'DPP', 'DPPI', 'PAPI', 'PIPI', 'POP', 'POPI', 'PUPI', 'PVP', 'PVPI', 'PADG', 'PIDG', 'PODG', 'PUDG', 'PVDG', 'APC', 'CPC', 'IPC', 'LPC', 'OPC', 'PPC', 'TPC', 'UPC', 'VPC', 'BNSM', 'DBSM', 'DPSM', 'DXSM', 'PGSM', 'PNSM', 'POSM', 'PVSM', 'XNSM', 'DPCE', 'DXCE', 'PNCE', 'XNCE'];
 
 async function run(out: string) {
     await ensureLipidsAvailable();
@@ -50,11 +51,15 @@ async function run(out: string) {
         UniqueArray.add(lipids, v, v);
     }
 
+    for (const v of v2lipids) {
+        UniqueArray.add(lipids, v, v);
+    }
+
     const lipidNames = JSON.stringify(lipids.array);
 
     if (out) {
         const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
  *

src/cli/mvs/mvs-render.ts

@@ -46,6 +46,7 @@ interface Args {
     output: string[],
     size: { width: number, height: number },
     molj: boolean,
+    no_extensions: boolean,
 }
 
 /** Return parsed command line arguments for `main` */
@@ -55,6 +56,7 @@ function parseArguments(): Args {
     parser.add_argument('-o', '--output', { required: true, nargs: '+', help: 'File path(s) for output files (one output path for each input file). Output format is inferred from the file extension (.png or .jpg)' });
     parser.add_argument('-s', '--size', { help: `Output image resolution, {width}x{height}. Default: ${DEFAULT_SIZE}.`, default: DEFAULT_SIZE });
     parser.add_argument('-m', '--molj', { action: 'store_true', help: `Save Mol* state (.molj) in addition to rendered images (use the same output file paths but with .molj extension)` });
+    parser.add_argument('-n', '--no-extensions', { action: 'store_true', help: `Do not apply builtin MVS-loading extensions (not a part of standard MVS specification)` });
     const args = parser.parse_args();
     try {
         const parts = args.size.split('x');
@@ -92,7 +94,7 @@ async function main(args: Args): Promise<void> {
         } else {
             throw new Error(`Input file name must end with .mvsj or .mvsx: ${input}`);
         }
-        await loadMVS(plugin, mvsData, { sanityChecks: true, replaceExisting: true, sourceUrl: sourceUrl });
+        await loadMVS(plugin, mvsData, { sanityChecks: true, replaceExisting: true, sourceUrl: sourceUrl, extensions: args.no_extensions ? [] : undefined });
 
         fs.mkdirSync(path.dirname(output), { recursive: true });
         if (args.molj) {

src/examples/alphafolddb-pae/index.html

@@ -0,0 +1,58 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* AlphaFold DB Predicted Aligned Error Example</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+                font-family: sans-serif;
+            }
+            #app {
+                position: absolute;
+                top: 20px;
+                left: 20px;
+                width: 640px;
+                height: 480px;
+            }
+
+            #plot {
+                position: absolute;
+                left: 680px;
+                top: 20px;
+                width: 480px;
+                height: 480px;
+            }
+
+            #controls {
+                position: absolute;
+                left: 20px;
+                top: 520px;
+                font-family: sans-serif;
+                font-size: smaller;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <script type="text/javascript" src="./index.js"></script>
+    </head>
+    <body>
+        <div id='controls'>
+            <input type='text' id='af-id' value='Q8W3K0' />
+            <button id='af-load'>Load</button>
+        </div>
+        <div id='app'></div>
+        <div id='plot'></div>
+        <script>
+            AlphaFoldPAEExample.init({ pluginContainerId: 'app', plotContainerId: 'plot' }).then(example => {
+                example.load('Q8W3K0')
+            });
+
+            function $(id) { return document.getElementById(id); }
+            $('af-load').onclick = () => AlphaFoldPAEExample.load($('af-id').value)
+        </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
+    </body>
+</html>

src/examples/alphafolddb-pae/index.tsx

@@ -0,0 +1,96 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+
+import { createRoot } from 'react-dom/client';
+import { Viewer } from '../../apps/viewer/app';
+import { MAPairwiseScorePlot } from '../../extensions/model-archive/quality-assessment/pairwise/ui';
+import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { Model, ResidueIndex } from '../../mol-model/structure';
+import './index.html';
+require('mol-plugin-ui/skin/light.scss');
+
+export class AlphaFoldPAEExample {
+    viewer: Viewer;
+    plotContainerId: string;
+
+
+    async init(options: { pluginContainerId: string, plotContainerId: string }) {
+        this.plotContainerId = options.plotContainerId;
+        this.viewer = await Viewer.create(options.pluginContainerId, {
+            layoutIsExpanded: false,
+            layoutShowControls: false,
+            layoutShowLeftPanel: false,
+            layoutShowLog: false,
+        });
+
+        return this;
+    }
+
+    async load(afId: string) {
+        const id = afId.trim().toUpperCase();
+
+        const plotRoot = createRoot(document.getElementById(this.plotContainerId)!);
+        plotRoot.render(<div>Loading...</div>);
+
+        await this.viewer.plugin.clear();
+        await this.viewer.loadAlphaFoldDb(id);
+
+        try {
+            const req = await fetch(`https://alphafold.ebi.ac.uk/files/AF-${id}-F1-predicted_aligned_error_v4.json`);
+            const json = await req.json();
+
+            const model = this.viewer.plugin.managers.structure.hierarchy.current.models[0]?.cell.obj?.data!;
+            const metric = pairwiseMetricFromAlphaFoldDbJson(model, json)!;
+
+            createRoot(document.getElementById(this.plotContainerId)!).render(
+                <div className='msp-plugin' style={{ background: 'white' }}>
+                    <MAPairwiseScorePlot plugin={this.viewer.plugin} pairwiseMetric={metric} model={model} />
+                </div>
+            );
+        } catch (err) {
+            plotRoot.render(<div>Error: {String(err)}</div>);
+        }
+    }
+}
+
+function pairwiseMetricFromAlphaFoldDbJson(model: Model, data: any): QualityAssessment.Pairwise | undefined {
+    if (!Array.isArray(data) || !data[0]?.predicted_aligned_error) return undefined;
+
+    const { residues, residueAtomSegments, atomSourceIndex } = model.atomicHierarchy;
+    const sortedResidueIndices = new Array(residues._rowCount).fill(0).map((_, i) => i);
+    sortedResidueIndices.sort((a, b) => {
+        const idxA = atomSourceIndex.value(residueAtomSegments.offsets[a]);
+        const idxB = atomSourceIndex.value(residueAtomSegments.offsets[b]);
+        return idxA - idxB;
+    });
+
+    const metricData = data[0].predicted_aligned_error as number[][];
+
+    const metric: QualityAssessment.Pairwise = {
+        id: 0,
+        name: 'AlphaFold DB PAE',
+        residueRange: [0 as ResidueIndex, (residues._rowCount - 1) as ResidueIndex],
+        valueRange: [0, data[0].max_predicted_aligned_error],
+        values: {}
+    };
+
+    for (let i = 0; i < metricData.length; i++) {
+        const rA = sortedResidueIndices[i];
+        if (typeof rA !== 'number') continue;
+        const row = metricData[i];
+        const xs: any = (metric.values[rA as ResidueIndex] = {});
+        for (let j = 0; j < row.length; j++) {
+            const rB = sortedResidueIndices[j];
+            if (typeof rB !== 'number') continue;
+            xs[rB] = row[j];
+        }
+    }
+
+    return metric;
+}
+
+(window as any).AlphaFoldPAEExample = new AlphaFoldPAEExample();

src/examples/lighting/index.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -33,8 +33,10 @@ const Canvas3DPresets = {
                         radius: 5,
                         bias: 0.8,
                         blurKernelSize: 15,
+                        blurDepthBias: 0.5,
                         resolutionScale: 1,
                         color: Color(0x000000),
+                        transparentThreshold: 0.4,
                     }
                 },
                 outline: {

src/extensions/alpha-orbitals/transforms.ts

@@ -182,7 +182,7 @@ export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
         return Task.create('Orbitals Representation 3D', async ctx => {
             const params = volumeParams(plugin, a, srcParams);
 
-            const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
+            const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext };
             const provider = plugin.representation.volume.registry.get(params.type.name);
             if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
             const props = params.type.params || {};

src/extensions/anvil/behavior.ts

@@ -118,7 +118,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
     },
     apply({ a, params }, plugin: PluginContext) {
         return Task.create('Membrane Orientation', async ctx => {
-            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, a.data);
             const repr = MembraneOrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => MembraneOrientationParams);
             await repr.createOrUpdate(params, a.data).runInContext(ctx);
             return new PluginStateObject.Shape.Representation3D({ repr, sourceData: a.data }, { label: 'Membrane Orientation' });
@@ -126,7 +126,7 @@ const MembraneOrientation3D = PluginStateTransform.BuiltIn({
     },
     update({ a, b, newParams }, plugin: PluginContext) {
         return Task.create('Membrane Orientation', async ctx => {
-            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, a.data);
             const props = { ...b.data.repr.props, ...newParams };
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
             b.data.sourceData = a.data;
@@ -155,7 +155,7 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
 
         if (!MembraneOrientationProvider.get(structure).value) {
             await plugin.runTask(Task.create('Membrane Orientation', async runtime => {
-                await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure);
+                await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, structure);
             }));
         }
 

src/extensions/assembly-symmetry/behavior.ts

@@ -82,7 +82,7 @@ export const InitAssemblySymmetry3D = StateAction.build({
     params: (a, plugin: PluginContext) => getConfiguredDefaultParams(plugin)
 })(({ a, ref, state, params }, plugin: PluginContext) => Task.create('Init Assembly Symmetry', async ctx => {
     try {
-        const propCtx = { runtime: ctx, assetManager: plugin.managers.asset };
+        const propCtx = { runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext };
         await AssemblySymmetryDataProvider.attach(propCtx, a.data, params);
         const assemblySymmetryData = AssemblySymmetryDataProvider.get(a.data).value;
         const symmetryIndex = assemblySymmetryData ? AssemblySymmetryData.firstNonC1(assemblySymmetryData) : -1;
@@ -118,7 +118,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
     },
     apply({ a, params }, plugin: PluginContext) {
         return Task.create('Assembly Symmetry', async ctx => {
-            await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, a.data);
             const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
             if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
                 return StateObject.Null;
@@ -131,7 +131,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
     },
     update({ a, b, newParams }, plugin: PluginContext) {
         return Task.create('Assembly Symmetry', async ctx => {
-            await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, a.data);
             const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
             if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
                 // this should NOT be StateTransformer.UpdateResult.Null
@@ -176,7 +176,7 @@ export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
 
         if (!AssemblySymmetryDataProvider.get(structure).value) {
             await plugin.runTask(Task.create('Assembly Symmetry', async runtime => {
-                const propCtx = { runtime, assetManager: plugin.managers.asset };
+                const propCtx = { runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext };
                 const propProps = { serverType: params.serverType, serverUrl: params.serverUrl };
                 await AssemblySymmetryDataProvider.attach(propCtx, structure, propProps);
                 const assemblySymmetryData = AssemblySymmetryDataProvider.get(structure).value;

src/extensions/dnatco/confal-pyramids/behavior.ts

@@ -30,7 +30,7 @@ export const ConfalPyramidsPreset = StructureRepresentationPresetProvider({
         if (!structureCell || !model) return {};
 
         await plugin.runTask(Task.create('Confal Pyramids', async runtime => {
-            await ConfalPyramidsProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+            await ConfalPyramidsProvider.attach({ runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, model);
         }));
 
         const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);

src/extensions/dnatco/ntc-tube/behavior.ts

@@ -30,7 +30,7 @@ export const NtCTubePreset = StructureRepresentationPresetProvider({
         if (!structureCell || !model) return {};
 
         await plugin.runTask(Task.create('NtC tube', async runtime => {
-            await NtCTubeProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+            await NtCTubeProvider.attach({ runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, model);
         }));
 
         const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);

src/extensions/model-archive/quality-assessment/behavior.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-24 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -17,6 +18,12 @@ import { cantorPairing } from '../../../mol-data/util';
 import { QmeanScoreColorThemeProvider } from './color/qmean';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
 import { StateObjectRef } from '../../../mol-state';
+import { MAPairwiseScorePlotPanel } from './pairwise/ui';
+import { PluginConfigItem } from '../../../mol-plugin/config';
+
+export const MAQualityAssessmentConfig = {
+    EnablePairwiseScorePlot: new PluginConfigItem('ma-quality-assessment-prop.enable-pairwise-score-plot', true),
+};
 
 export const MAQualityAssessment = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
     name: 'ma-quality-assessment-prop',
@@ -52,6 +59,10 @@ export const MAQualityAssessment = PluginBehavior.create<{ autoAttach: boolean,
 
             this.ctx.builders.structure.representation.registerPreset(QualityAssessmentPLDDTPreset);
             this.ctx.builders.structure.representation.registerPreset(QualityAssessmentQmeanPreset);
+
+            if (this.ctx.config.get(MAQualityAssessmentConfig.EnablePairwiseScorePlot)) {
+                this.ctx.customStructureControls.set('ma-quality-assessment-pairwise-plot', MAPairwiseScorePlotPanel as any);
+            }
         }
 
         update(p: { autoAttach: boolean, showTooltip: boolean }) {
@@ -76,6 +87,8 @@ export const MAQualityAssessment = PluginBehavior.create<{ autoAttach: boolean,
 
             this.ctx.builders.structure.representation.unregisterPreset(QualityAssessmentPLDDTPreset);
             this.ctx.builders.structure.representation.unregisterPreset(QualityAssessmentQmeanPreset);
+
+            this.ctx.customStructureControls.delete('ma-quality-assessment-pairwise-plot');
         }
     },
     params: () => ({

src/extensions/model-archive/quality-assessment/color/plddt.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Mandar Deshpande <mandar@ebi.ac.uk>
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
@@ -8,7 +8,7 @@
 
 import { QualityAssessment, QualityAssessmentProvider } from '../prop';
 import { Location } from '../../../../mol-model/location';
-import { Bond, StructureElement, Unit } from '../../../../mol-model/structure';
+import { Bond, Model, StructureElement, Unit } from '../../../../mol-model/structure';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { Color } from '../../../../mol-util/color';
@@ -41,8 +41,13 @@ export function PLDDTConfidenceColorTheme(ctx: ThemeDataContext, props: PD.Value
         const getColor = (location: StructureElement.Location): Color => {
             const { unit, element } = location;
             if (!Unit.isAtomic(unit)) return DefaultColor;
+
             const qualityAssessment = QualityAssessmentProvider.get(unit.model).value;
-            const score = qualityAssessment?.pLDDT?.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]) ?? -1;
+            let score = qualityAssessment?.pLDDT?.get(unit.model.atomicHierarchy.residueAtomSegments.index[element]);
+            if (typeof score !== 'number') {
+                score = unit.model.atomicConformation.B_iso_or_equiv.value(element);
+            }
+
             if (score < 0) {
                 return DefaultColor;
             } else if (score <= 50) {
@@ -74,7 +79,7 @@ export function PLDDTConfidenceColorTheme(ctx: ThemeDataContext, props: PD.Value
         preferSmoothing: true,
         color,
         props,
-        description: 'Assigns residue colors according to the pLDDT Confidence score.',
+        description: 'Assigns residue colors according to the pLDDT Confidence score. If no Model Archive quality assessment score is available, the B-factor value is used instead.',
         legend: ConfidenceColorLegend
     };
 }
@@ -86,7 +91,7 @@ export const PLDDTConfidenceColorThemeProvider: ColorTheme.Provider<PLDDTConfide
     factory: PLDDTConfidenceColorTheme,
     getParams: getPLDDTConfidenceColorThemeParams,
     defaultValues: PD.getDefaultValues(getPLDDTConfidenceColorThemeParams({})),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT')),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => QualityAssessment.isApplicable(m, 'pLDDT') || (m.atomicConformation.B_iso_or_equiv.isDefined && !Model.isExperimental(m))),
     ensureCustomProperties: {
         attach: async (ctx: CustomProperty.Context, data: ThemeDataContext) => {
             if (data.structure) {

src/extensions/model-archive/quality-assessment/pairwise/plot.ts

@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Model, ResidueIndex } from '../../../../mol-model/structure';
+import { AtomicHierarchy } from '../../../../mol-model/structure/model/properties/atomic';
+import { Color } from '../../../../mol-util/color';
+import { QualityAssessment } from '../prop';
+
+
+const DefaultMetricColorRange = [0x00441B, 0xF7FCF5] as [Color, Color];
+
+export type MAResidueRangeInfo = { startOffset: number, endOffset: number, label: string };
+
+function drawMetricPNG(model: Model, metric: QualityAssessment.Pairwise, colorRange: [Color, Color], noDataColor: Color) {
+    const [minResidueIndex, maxResidueIndex] = metric.residueRange;
+    const [minMetric, maxMetric] = metric.valueRange;
+    const [minColor, maxColor] = colorRange;
+    const range = maxResidueIndex - minResidueIndex + 1;
+    const valueRange = maxMetric - minMetric;
+    const values = metric.values;
+
+    const canvas = document.createElement('canvas');
+    canvas.width = range;
+    canvas.height = range;
+    const ctx = canvas.getContext('2d')!;
+    ctx.fillStyle = Color.toStyle(noDataColor);
+    ctx.fillRect(0, 0, canvas.width, canvas.height);
+
+    for (let rA = minResidueIndex; rA <= maxResidueIndex; rA++) {
+        const row = values[rA];
+        if (!row) continue;
+
+        for (let rB = minResidueIndex; rB <= maxResidueIndex; rB++) {
+            const value = row[rB];
+            if (typeof value !== 'number') continue;
+
+            const x = rA - minResidueIndex;
+            const y = rB - minResidueIndex;
+            const t = (value - minMetric) / valueRange;
+
+            const color = Color.interpolate(minColor, maxColor, t);
+            ctx.fillStyle = Color.toStyle(color);
+            ctx.fillRect(x, y, 1, 1);
+            ctx.fillRect(y, x, 1, 1);
+        }
+    }
+
+    const chains: MAResidueRangeInfo[] = [];
+    const hierarchy = model.atomicHierarchy;
+    const { label_asym_id } = hierarchy.chains;
+
+    let cI = AtomicHierarchy.residueChainIndex(hierarchy, minResidueIndex as ResidueIndex);
+    let currentChain: MAResidueRangeInfo = { startOffset: 0, endOffset: 1, label: label_asym_id.value(cI) };
+    chains.push(currentChain);
+
+    for (let i = 1; i < range; i++) {
+        cI = AtomicHierarchy.residueChainIndex(hierarchy, (minResidueIndex + i) as ResidueIndex);
+        const asym_id = label_asym_id.value(cI);
+        if (asym_id === currentChain.label) {
+            currentChain.endOffset = i + 1;
+        } else {
+            currentChain = { startOffset: i, endOffset: i + 1, label: asym_id };
+            chains.push(currentChain);
+        }
+    }
+
+    return {
+        model,
+        metric,
+        chains,
+        colorRange: [Color.toStyle(colorRange[0]), Color.toStyle(colorRange[1])] as const,
+        png: canvas.toDataURL('png')
+    };
+}
+
+export function maDrawPairwiseMetricPNG(model: Model, metric: QualityAssessment.Pairwise) {
+    return drawMetricPNG(model, metric, DefaultMetricColorRange, Color(0xE2E2E2));
+}
+
+export type MAPairwiseMetricDrawing = ReturnType<typeof drawMetricPNG>

src/extensions/model-archive/quality-assessment/pairwise/ui.tsx

@@ -0,0 +1,504 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { CSSProperties, Fragment, memo, ReactNode, useEffect, useRef } from 'react';
+import { BehaviorSubject, combineLatest, distinctUntilChanged, throttleTime } from 'rxjs';
+import { clamp } from '../../../../mol-math/interpolate';
+import { Model, ResidueIndex, StructureElement, StructureProperties, StructureQuery } from '../../../../mol-model/structure';
+import { AtomicHierarchy } from '../../../../mol-model/structure/model/properties/atomic';
+import { atoms } from '../../../../mol-model/structure/query/queries/generators';
+import { PluginStateObject } from '../../../../mol-plugin-state/objects';
+import { OverpaintStructureRepresentation3DFromBundle } from '../../../../mol-plugin-state/transforms/representation';
+import { CollapsableControls, CollapsableState } from '../../../../mol-plugin-ui/base';
+import { ScatterPlotSvg } from '../../../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../../../mol-plugin-ui/controls/parameters';
+import { useBehavior } from '../../../../mol-plugin-ui/hooks/use-behavior';
+import { PluginContext } from '../../../../mol-plugin/context';
+import { StateBuilder, StateTransform } from '../../../../mol-state';
+import { round } from '../../../../mol-util';
+import { Color } from '../../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { SingleAsyncQueue } from '../../../../mol-util/single-async-queue';
+import { QualityAssessment } from '../prop';
+import { maDrawPairwiseMetricPNG, MAPairwiseMetricDrawing } from './plot';
+
+type State = ReturnType<typeof getPropsAndValues>
+
+export class MAPairwiseScorePlotPanel extends CollapsableControls<{}, State> {
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Predicted Aligned Error',
+            isCollapsed: false,
+            isHidden: true,
+            brand: { accent: 'purple', svg: ScatterPlotSvg },
+            params: {} as any,
+            values: undefined as any,
+            dataSources: [],
+        };
+    }
+
+    toggleCollapsed() {
+        if (!this.state.isCollapsed) {
+            this.setState({ isCollapsed: true });
+        } else {
+            const state = getPropsAndValues(this.plugin, this.state.values);
+            this.setState({
+                ...state,
+                isCollapsed: false,
+                isHidden: state.params.data.options.length === 0 || state.params.model.options.length === 0
+            });
+        }
+    };
+
+    interactivity = new BehaviorSubject<PlotInteractivityState>({});
+    queue = new SingleAsyncQueue();
+
+    componentDidMount() {
+        this.subscribe(combineLatest([
+            this.plugin.state.data.events.changed,
+            this.plugin.behaviors.state.isAnimating
+        ]), ([_, anim]) => {
+            if (anim || this.state.isCollapsed) return;
+            const state = getPropsAndValues(this.plugin, this.state.values);
+            this.setState({
+                ...state,
+                isHidden: state.params.data.options.length === 0 || state.params.model.options.length === 0
+            });
+        });
+
+        this.subscribe(filterHighlightState(this.interactivity), state => {
+            highlightState(this.plugin, state);
+        });
+        this.subscribe(filterOverpaintState(this.interactivity), state => {
+            this.queue.enqueue(() => overpaintState(this.plugin, state));
+        });
+    }
+
+    protected renderControls(): JSX.Element | null {
+        const { params, values, dataSources } = this.state;
+        return <>
+            <ParameterControls params={params} values={values} onChangeValues={values => this.setState({ values })} />
+            <PlotWrapper plugin={this.plugin} values={values} dataSources={dataSources} interactivity={this.interactivity} />
+        </>;
+    }
+}
+
+export function MAPairwiseScorePlot({ plugin, model, pairwiseMetric }: { plugin: PluginContext, model: Model, pairwiseMetric: QualityAssessment.Pairwise }) {
+    const _interactivity = useRef<BehaviorSubject<PlotInteractivityState>>();
+    const interactivity = _interactivity.current ??= new BehaviorSubject<PlotInteractivityState>({});
+
+    useEffect(() => {
+        const queue = new SingleAsyncQueue();
+
+        const highlight = filterHighlightState(interactivity).subscribe(state => highlightState(plugin, state));
+        const paint = filterOverpaintState(interactivity).subscribe(state => queue.enqueue(() => overpaintState(plugin, state)));
+
+        return () => {
+            highlight.unsubscribe();
+            paint.unsubscribe();
+            queue.enqueue(() => overpaintState(plugin, interactivity.value));
+        };
+    }, [model, pairwiseMetric]);
+
+    return <MAPairwiseScorePlotBase model={model} pairwiseMetric={pairwiseMetric} interactivity={interactivity} />;
+}
+
+function filterHighlightState(state: BehaviorSubject<PlotInteractivityState>) {
+    return state.pipe(
+        throttleTime(16, undefined, { leading: true, trailing: true }),
+        distinctUntilChanged((a, b) => a.crosshairOffset === b.crosshairOffset)
+    );
+}
+
+function filterOverpaintState(state: BehaviorSubject<PlotInteractivityState>) {
+    return state.pipe(
+        throttleTime(66, undefined, { leading: true, trailing: true }),
+        distinctUntilChanged((a, b) => a.boxStart === b.boxStart && (a.mouseDown ? a.crosshairOffset : a.boxEnd) === (b.mouseDown ? b.crosshairOffset : b.boxEnd))
+    );
+}
+
+const PlotWrapper = memo(({ plugin, values, dataSources, interactivity }: { plugin: PluginContext, values: State['values'], dataSources: State['dataSources'], interactivity: BehaviorSubject<PlotInteractivityState> }) => {
+    const model: Model | undefined = plugin.managers.structure.hierarchy.current.models.find(m => m.cell.transform.ref === values.model)?.cell.obj?.data;
+    const src = dataSources.find(src => src.id === values.data);
+    const cif: PluginStateObject.Format.Cif | undefined = plugin.state.data.cells.get(src?.dataRef!)?.obj;
+    const block = cif?.data.blocks[src?.blockIndex!];
+
+    if (!model || !block || !src) return <div className='msp-description'>Data not available</div>;
+
+    const metric = QualityAssessment.pairwiseMetricFromModelArchiveCIF(model, block, src.metridId);
+    if (!metric) return <div className='msp-description'>Data not available</div>;
+
+    return <MAPairwiseScorePlotBase interactivity={interactivity} model={model} pairwiseMetric={metric} />;
+}, (prev, next) => prev.values.data === next.values.data && prev.values.model === next.values.model);
+
+function getPropsAndValues(plugin: PluginContext, current?: { model?: string, data?: string }) {
+    const models = plugin.managers.structure.hierarchy.current.models;
+    const cifs = plugin.state.data.selectQ(q => q.root.subtree().ofType(PluginStateObject.Format.Cif));
+
+    const dataSources: {
+        id: string,
+        label: string,
+        metridId: number,
+        dataRef: StateTransform.Ref,
+        blockIndex: number,
+    }[] = [];
+
+    for (const cif of cifs) {
+        if (!cif.obj?.data.blocks) continue;
+        let blockIndex = 0;
+        for (const block of cif.obj.data.blocks) {
+            for (const pae of QualityAssessment.findModelArchiveCIFPAEMetrics(block)) {
+                dataSources.push({
+                    id: `${cif.transform.ref}:${blockIndex}:${pae.id}`,
+                    metridId: pae.id,
+                    label: `${block.header}: ${pae.name}`,
+                    dataRef: cif.transform.ref,
+                    blockIndex,
+                });
+            }
+            blockIndex++;
+        }
+    }
+
+    const params = {
+        model: PD.Select(models[0]?.cell.transform.ref, models.map(m => [m.cell.transform.ref, m.cell.obj?.data.label!]), { isHidden: models.length <= 1 }),
+        data: PD.Select(dataSources[0]?.id, dataSources.map(o => [o.id, o.label]), { isHidden: dataSources.length <= 1 })
+    };
+
+    const values = {
+        model: params.model.options.find(o => o[0] === current?.model)?.[0] ?? params.model.options[0]?.[0],
+        data: params.data.options.find(o => o[0] === current?.data)?.[0] ?? params.data.options[0]?.[0],
+    };
+
+    return { params, values, dataSources };
+}
+
+const PlotSize = 1000;
+const PlotOffset = 120;
+
+const PlotColors = {
+    ScoredOverpaint: Color(0xFFA500),
+    ScoredLabel: Color(0xBC7100),
+    AlignedOverpaint: Color(0x1AFFBB),
+    AlignedLabel: Color(0x0F8E68),
+};
+
+interface PlotInteractivityState {
+    model?: Model;
+    drawing?: MAPairwiseMetricDrawing;
+    crosshairOffset?: [number, number];
+    inside?: boolean;
+    mouseDown?: boolean;
+    boxStart?: [number, number];
+    boxEnd?: [number, number];
+}
+
+export const MAPairwiseScorePlotBase = memo(({ model, pairwiseMetric, interactivity }: { model: Model, pairwiseMetric: QualityAssessment.Pairwise, interactivity: BehaviorSubject<PlotInteractivityState> }) => {
+    const interactivityRect = useRef<SVGRectElement>();
+    const drawing = maDrawPairwiseMetricPNG(model, pairwiseMetric);
+
+    useEffect(() => {
+        if (!drawing) {
+            interactivity.next({});
+            return;
+        }
+        interactivity.next({ model, drawing });
+        const moveEvent = (ev: MouseEvent) => {
+            const current = interactivity.value;
+            if (!current.inside && !current.mouseDown) return;
+
+            const offset = getPlotMouseOffsetBase(interactivityRect.current!, ev.clientX, ev.clientY);
+            interactivity.next({ ...current, crosshairOffset: offset });
+        };
+        const mouseUpEvent = (ev: MouseEvent) => {
+            if (!interactivity.value.mouseDown) return;
+            const offset = getPlotMouseOffsetBase(interactivityRect.current!, ev.clientX, ev.clientY);
+            interactivity.next({ ...interactivity.value, mouseDown: false, boxEnd: offset });
+        };
+        window.addEventListener('mousemove', moveEvent);
+        window.addEventListener('mouseup', mouseUpEvent);
+        return () => {
+            window.removeEventListener('mousemove', moveEvent);
+            window.removeEventListener('mouseup', mouseUpEvent);
+        };
+    }, [model, interactivity, drawing]);
+
+    if (!drawing) return <>Not available</>;
+
+
+    const { metric, colorRange, chains, png } = drawing;
+    const nResidues = metric.residueRange[1] - metric.residueRange[0];
+
+    const border = '#333';
+    const line = '#000';
+
+    const legendHeight = 80;
+    const legendOffsetY = PlotOffset + PlotSize + 50;
+
+    const viewBox = '0 0 1140 1270';
+
+    return <div style={{ margin: '8px 8px 0 8px', position: 'relative' }}>
+        <svg viewBox={viewBox} width='100%'>
+            <image x={PlotOffset + 1} y={PlotOffset + 1} width={PlotSize - 1} height={PlotSize - 1} href={png} />
+            <line x1={PlotOffset} x2={PlotOffset + PlotSize} y1={PlotOffset} y2={PlotOffset + PlotSize} style={{ stroke: line, strokeDasharray: '15,15' }} />
+            <linearGradient id='legend-gradient' x1={0} x2={1} y1={0} y2={0}>
+                <stop offset='0%' stopColor={colorRange[0]} />
+                <stop offset='100%' stopColor={colorRange[1]} />
+            </linearGradient>
+            <rect x={PlotOffset} y={legendOffsetY} width={PlotSize} height={legendHeight} style={{ fill: 'url(#legend-gradient)', strokeWidth: 1, stroke: border }} />
+            <text x={PlotOffset + 20} y={legendOffsetY + legendHeight - 22} style={{ fontSize: '45px', fill: 'white', fontWeight: 'bold' }}>{round(metric.valueRange[0], 2)} Å</text>
+            <text x={PlotOffset + PlotSize - 20} y={legendOffsetY + legendHeight - 22} style={{ fontSize: '45px', fill: 'black', fontWeight: 'bold' }} textAnchor='end'>{round(metric.valueRange[1], 2)} Å</text>
+            <text x={PlotOffset + PlotSize / 2} y={legendOffsetY + legendHeight - 22} style={{ fontSize: '45px', fill: 'black' }} textAnchor='middle'>Predicted Aligned Error</text>
+
+            <text x={PlotOffset + PlotSize / 2} y={50} style={{ fontSize: '45px', fontWeight: 'bold', fill: Color.toStyle(PlotColors.ScoredLabel) }} textAnchor='middle'>Scored Residue</text>
+            <text className='msp-svg-text' style={{ fontSize: '50px', fontWeight: 'bold', fill: Color.toStyle(PlotColors.AlignedLabel) }} transform={`translate(50, ${PlotOffset + PlotSize / 2}) rotate(270)`} textAnchor='middle'>Aligned Residue</text>
+
+            {chains.map(({ startOffset, endOffset, label }) => {
+                const textOffset = PlotOffset + PlotSize * (startOffset + (endOffset - startOffset) / 2) / nResidues;
+                const endLineOffset = PlotOffset + PlotSize * endOffset / nResidues;
+                const startLineOffset = PlotOffset + PlotSize * startOffset / nResidues;
+
+                const seq_id = model.atomicHierarchy.residues.label_seq_id;
+                const startIndex = seq_id.value(metric.residueRange[0] + startOffset);
+                const endIndex = seq_id.value(metric.residueRange[0] + endOffset - 1);
+
+                return <Fragment key={startOffset}>
+                    <text x={textOffset} y={PlotOffset - 15} className='msp-svg-text' style={{ fontSize: '40px' }} textAnchor='middle'>{label} {startIndex}-{endIndex}</text>
+                    <text className='msp-svg-text' style={{ fontSize: '40px' }} transform={`translate(${PlotOffset - 15}, ${textOffset}) rotate(270)`} textAnchor='middle'>{label} {startIndex}-{endIndex}</text>
+                    <line x1={startLineOffset} x2={startLineOffset} y1={PlotOffset - 20} y2={PlotOffset + PlotSize + 20} style={{ stroke: line, strokeDasharray: '15,15' }} />
+                    <line x1={endLineOffset} x2={endLineOffset} y1={PlotOffset - 20} y2={PlotOffset + PlotSize + 20} style={{ stroke: line, strokeDasharray: '15,15' }} />
+                    <line x1={PlotOffset - 20} x2={PlotOffset + PlotSize + 20} y1={startLineOffset} y2={startLineOffset} style={{ stroke: line, strokeDasharray: '15,15' }} />
+                    <line x1={PlotOffset - 20} x2={PlotOffset + PlotSize + 20} y1={endLineOffset} y2={endLineOffset} style={{ stroke: line, strokeDasharray: '15,15' }} />
+                </Fragment>;
+            })}
+        </svg>
+        <svg viewBox={viewBox} style={{ position: 'absolute', inset: 0 }}>
+            <rect x={PlotOffset} y={PlotOffset} width={PlotSize} height={PlotSize} style={{ fill: 'transparent', cursor: 'crosshair' }}
+                ref={interactivityRect as any}
+                onMouseMove={(ev) => {
+                    interactivity.next({ ...interactivity.value, inside: true });
+                    ev.currentTarget.style.stroke = 'black';
+                    ev.currentTarget.style.strokeWidth = '4px';
+                }}
+                onMouseDown={(ev) => {
+                    interactivity.next({ ...interactivity.value, mouseDown: true, boxStart: getPlotMouseOffset(ev) });
+                }}
+                onMouseLeave={(ev) => {
+                    interactivity.next({ ...interactivity.value, inside: false, crosshairOffset: undefined });
+                    ev.currentTarget.style.stroke = '#333';
+                    ev.currentTarget.style.strokeWidth = '1px';
+                }} />
+            <PlotInteractivity drawing={drawing} interactity={interactivity} />
+        </svg>
+    </div>;
+}, (prev, next) => prev.model === next.model && prev.pairwiseMetric === next.pairwiseMetric);
+
+function PlotInteractivity({ drawing, interactity }: { drawing: MAPairwiseMetricDrawing, interactity: BehaviorSubject<PlotInteractivityState> }) {
+    const state = useBehavior(interactity);
+    const { crosshairOffset, inside } = state;
+    const box = getBox(state);
+    const label = getCrosshairLabel(state);
+
+    let labelNode: ReactNode | undefined;
+    if (label) {
+        const labelStyle: CSSProperties | undefined = label ? { fontSize: '45px', fill: 'black', fontWeight: 'bold', pointerEvents: 'none', userSelect: 'none' } : undefined;
+        let x: number, y: number, anchor: string;
+        if (crosshairOffset![0] < PlotSize / 2) {
+            x = PlotOffset + crosshairOffset![0] + 20;
+            anchor = 'start';
+        } else {
+            x = PlotOffset + crosshairOffset![0] - 20;
+            anchor = 'end';
+        }
+
+        if (crosshairOffset![1] < PlotSize / 2) {
+            y = PlotOffset + crosshairOffset![1] + 65;
+        } else {
+            y = PlotOffset + crosshairOffset![1] - (label[2] ? 3 * 45 : 2 * 45) + 20;
+        }
+
+        labelNode = <text y={y} style={labelStyle} textAnchor={anchor}>
+            <tspan x={x}>S: {label[0]}</tspan>
+            <tspan x={x} dy={45}>A: {label[1]}</tspan>
+            {label[2] && <tspan x={x} dy={45}>{label[2]}</tspan>}
+        </text>;
+    }
+
+    return <>
+        {inside && crosshairOffset && <line x1={crosshairOffset[0] + PlotOffset} x2={crosshairOffset[0] + PlotOffset} y1={PlotOffset} y2={PlotOffset + PlotSize} style={{ pointerEvents: 'none', stroke: 'black', strokeDasharray: '5,5' }} />}
+        {inside && crosshairOffset && <line x1={PlotOffset} x2={PlotOffset + PlotSize} y1={crosshairOffset[1] + PlotOffset} y2={crosshairOffset[1] + PlotOffset} style={{ pointerEvents: 'none', stroke: 'black', strokeDasharray: '5,5' }} />}
+        {box && <rect x={PlotOffset + box[0]} y={PlotOffset + box[1]} width={box[2]} height={box[3]} style={{ stroke: '#eee', strokeWidth: 4, fill: 'rgba(0, 0, 0, 0.15)', pointerEvents: 'none' }} />}
+        {labelNode}
+    </>;
+}
+
+function getCrosshairLabel(state: PlotInteractivityState) {
+    if (!state.drawing || !state.crosshairOffset || !state.inside) return;
+
+    const { drawing } = state;
+    const rA = getResidueIndex(drawing, clamp(state.crosshairOffset[0], 0, PlotSize));
+    const rB = getResidueIndex(drawing, clamp(state.crosshairOffset[1], 0, PlotSize));
+
+    const value = drawing.metric.values[rA]?.[rB] ?? drawing.metric.values[rB]?.[rA];
+    const valueLabel = typeof value === 'number' ? `${round(value, 2)} Å` : '';
+
+    return [getResidueLabel(drawing, rA), getResidueLabel(drawing, rB), valueLabel];
+}
+
+function getResidueIndex(drawing: MAPairwiseMetricDrawing, offset: number) {
+    const rI = drawing.metric.residueRange[0] + Math.round(offset / PlotSize * (drawing.metric.residueRange[1] - drawing.metric.residueRange[0] + 1)) as ResidueIndex;
+    return clamp(rI, drawing.metric.residueRange[0], drawing.metric.residueRange[1]) as ResidueIndex;
+}
+
+function getResidueLabel(drawing: MAPairwiseMetricDrawing, rI: ResidueIndex) {
+    const hierarchy = drawing.model.atomicHierarchy;
+    const asym_id = hierarchy.chains.label_asym_id;
+    const seq_id = hierarchy.residues.label_seq_id;
+    const comp_id = hierarchy.atoms.label_comp_id;
+
+    return `${asym_id.value(AtomicHierarchy.residueChainIndex(hierarchy, rI))} ${seq_id.value(rI)} ${comp_id.value(AtomicHierarchy.residueFirstAtomIndex(hierarchy, rI))}`;
+}
+
+function getBox(state: PlotInteractivityState) {
+    const start = state.boxStart;
+    const end = state.mouseDown ? state.crosshairOffset : state.boxEnd;
+    if (!start || !end) return undefined;
+
+    const x = clamp(Math.min(start[0], end[0]), 0, PlotSize);
+    const width = clamp(Math.max(start[0], end[0]), 0, PlotSize) - x;
+    const y = clamp(Math.min(start[1], end[1]), 0, PlotSize);
+    const height = clamp(Math.max(start[1], end[1]), 0, PlotSize) - y;
+
+    if (width < 1 && height < 1) return undefined;
+
+    return [x, y, width, height];
+}
+
+function getPlotMouseOffset(ev: React.MouseEvent<SVGRectElement, MouseEvent>) {
+    return getPlotMouseOffsetBase(ev.currentTarget, ev.clientX, ev.clientY);
+}
+
+function getPlotMouseOffsetBase(target: HTMLElement | SVGRectElement, clientX: number, clientY: number) {
+    const rect = target.getBoundingClientRect();
+    const offsetX = PlotSize * (clientX - rect.left) / rect.width;
+    const offsetY = PlotSize * (clientY - rect.top) / rect.height;
+    return [offsetX, offsetY] as [number, number];
+}
+
+function findModelRef(plugin: PluginContext, model: Model | undefined) {
+    if (!model) return undefined;
+    for (const m of plugin.managers.structure.hierarchy.current.models) {
+        if (m.cell.obj?.data === model) return m;
+    }
+    return undefined;
+}
+
+function highlightState(plugin: PluginContext, state: PlotInteractivityState) {
+    const structure = findModelRef(plugin, state.model)?.structures[0]?.cell.obj?.data;
+    if (!state.drawing || !state.crosshairOffset || !state.inside || !structure) {
+        plugin.managers.interactivity.lociHighlights.clearHighlights();
+        return;
+    }
+
+    const { drawing } = state;
+    const rA = getResidueIndex(drawing, clamp(state.crosshairOffset[0], 0, PlotSize));
+    const rB = getResidueIndex(drawing, clamp(state.crosshairOffset[1], 0, PlotSize));
+
+    const resIdx = StructureProperties.residue.key;
+    const loci = StructureQuery.loci(atoms({
+        residueTest: ctx => {
+            const rI = resIdx(ctx.element);
+            return rI === rA || rI === rB;
+        },
+    }), structure);
+
+    plugin.managers.interactivity.lociHighlights.highlightOnly({ loci });
+}
+
+async function overpaintState(plugin: PluginContext, state: PlotInteractivityState) {
+    const tag = 'modelarchive-pae-overpaint';
+
+    const overpaints = plugin.state.data.selectQ(q => q.root.subtree().withTag(tag));
+    const update = plugin.build();
+    for (const overpaint of overpaints) update.delete(overpaint);
+
+    const model = findModelRef(plugin, state.model);
+    const structure = model?.structures[0]?.cell.obj?.data;
+    if (!state.drawing || !state.boxStart || !(state.boxEnd || state.crosshairOffset) || !structure) {
+        if (!overpaints) return;
+        return reApplyRepresentationStates(plugin, update);
+    }
+
+    const start = state.boxStart;
+    const end = state.mouseDown ? state.crosshairOffset! : state.boxEnd!;
+
+    const x0 = clamp(Math.min(start[0], end[0]), 0, PlotSize);
+    const x1 = clamp(Math.max(start[0], end[0]), 0, PlotSize);
+    const y0 = clamp(Math.min(start[1], end[1]), 0, PlotSize);
+    const y1 = clamp(Math.max(start[1], end[1]), 0, PlotSize);
+
+    if (x1 - x0 <= 1 || y1 - y0 <= 1) {
+        if (!overpaints) return;
+        return reApplyRepresentationStates(plugin, update);
+    }
+
+    const representations = plugin.state.data.selectQ(q =>
+        q.byRef(model.cell.transform.ref!)
+            .subtree()
+            .ofType(PluginStateObject.Molecule.Structure.Representation3D)
+    );
+
+    const resIdx = StructureProperties.residue.key;
+
+    const startScored = getResidueIndex(state.drawing, x0);
+    const endScored = getResidueIndex(state.drawing, x1);
+    const lociScored = StructureQuery.loci(atoms({
+        residueTest: ctx => {
+            const rI = resIdx(ctx.element);
+            return rI >= startScored && rI <= endScored;
+        },
+    }), structure);
+
+    const startAligned = getResidueIndex(state.drawing, y0);
+    const endAligned = getResidueIndex(state.drawing, y1);
+    const lociAligned = StructureQuery.loci(atoms({
+        residueTest: ctx => {
+            const rI = resIdx(ctx.element);
+            return rI >= startAligned && rI <= endAligned;
+        },
+    }), structure);
+
+    const layers = [{
+        bundle: StructureElement.Bundle.fromSubStructure(structure, structure),
+        color: Color(0x777777),
+        clear: false,
+    }, {
+        bundle: StructureElement.Bundle.fromLoci(lociScored),
+        color: PlotColors.ScoredOverpaint,
+        clear: false,
+    }, {
+        bundle: StructureElement.Bundle.fromLoci(lociAligned),
+        color: PlotColors.AlignedOverpaint,
+        clear: false,
+    }];
+
+    for (const repr of representations) {
+        update.to(repr).apply(OverpaintStructureRepresentation3DFromBundle, { layers }, { tags: [tag], state: { isGhost: true } });
+    }
+
+    return update.commit();
+}
+
+async function reApplyRepresentationStates(plugin: PluginContext, update: StateBuilder.Root) {
+    await update.commit();
+    const states = plugin.state.data.selectQ(q => q.root.subtree().ofType(PluginStateObject.Molecule.Structure.Representation3DState));
+    for (const state of states) {
+        const data = state.obj?.data;
+        if (!data) continue;
+        data.repr.setState(data.state);
+        plugin.canvas3d?.update(data.repr);
+    }
+}

src/extensions/model-archive/quality-assessment/prop.ts

@@ -1,21 +1,24 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-24 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { Unit } from '../../../mol-model/structure';
-import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CifFrame } from '../../../mol-io/reader/cif';
+import { toDatabase } from '../../../mol-io/reader/cif/schema';
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+import { Unit } from '../../../mol-model/structure';
 import { Model, ResidueIndex } from '../../../mol-model/structure/model';
-import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+import { AtomicIndex } from '../../../mol-model/structure/model/properties/atomic';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
 import { Type } from '../../../mol-script/language/type';
-import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
-import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
-import { AtomicIndex } from '../../../mol-model/structure/model/properties/atomic';
+import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 
 export { QualityAssessment };
 
@@ -26,10 +29,19 @@ interface QualityAssessment {
 }
 
 namespace QualityAssessment {
+    export interface Pairwise {
+        id: number
+        name: string
+
+        residueRange: [ResidueIndex, ResidueIndex]
+        valueRange: [number, number]
+        values: Record<ResidueIndex, Record<ResidueIndex, number | undefined> | undefined>
+    }
+
     const Empty = {
         value: {
-            localMetrics: new Map()
-        }
+            localMetrics: new Map(),
+        } satisfies QualityAssessment
     };
 
     export function isApplicable(model?: Model, localMetricName?: 'pLDDT' | 'qmean'): boolean {
@@ -106,6 +118,101 @@ namespace QualityAssessment {
         };
     }
 
+    const PairwiseSchema = {
+        ma_qa_metric: mmCIF_Schema.ma_qa_metric,
+        ma_qa_metric_local_pairwise: mmCIF_Schema.ma_qa_metric_local_pairwise
+    };
+
+    export function findModelArchiveCIFPAEMetrics(frame: CifFrame) {
+        const { ma_qa_metric, ma_qa_metric_local_pairwise } = toDatabase(PairwiseSchema, frame);
+        const result: { id: number, name: string }[] = [];
+        if (ma_qa_metric_local_pairwise._rowCount === 0) return result;
+
+        for (let i = 0, il = ma_qa_metric._rowCount; i < il; i++) {
+            if (ma_qa_metric.mode.value(i) !== 'local-pairwise') continue;
+            const id = ma_qa_metric.id.value(i);
+            const name = ma_qa_metric.name.value(i);
+            if (!name.toLowerCase().includes('pae')) continue;
+            result.push({ id, name });
+        }
+        return result;
+    }
+
+    export function pairwiseMetricFromModelArchiveCIF(model: Model, frame: CifFrame, metricId: number): Pairwise | undefined {
+        const db = toDatabase(PairwiseSchema, frame);
+        if (!db.ma_qa_metric_local_pairwise._rowCount) return undefined;
+
+        const { ma_qa_metric, ma_qa_metric_local_pairwise } = db;
+        const { model_id, label_asym_id_1, label_seq_id_1, label_asym_id_2, label_seq_id_2, metric_id, metric_value } = db.ma_qa_metric_local_pairwise;
+        const { index } = model.atomicHierarchy;
+
+        let metric: Pairwise | undefined;
+
+        for (let i = 0, il = ma_qa_metric._rowCount; i < il; i++) {
+            if (ma_qa_metric.mode.value(i) !== 'local-pairwise') continue;
+            const id = ma_qa_metric.id.value(i);
+            if (id !== metricId) continue;
+
+            const name = ma_qa_metric.name.value(i);
+            metric = {
+                id,
+                name,
+                residueRange: [Number.MAX_SAFE_INTEGER as ResidueIndex, Number.MIN_SAFE_INTEGER as ResidueIndex],
+                valueRange: [Number.MAX_VALUE, -Number.MAX_VALUE],
+                values: {}
+            };
+        }
+
+        if (!metric) return undefined;
+
+        const { values, residueRange, valueRange } = metric;
+        const residueKey: AtomicIndex.ResidueLabelKey = {
+            label_entity_id: '',
+            label_asym_id: '',
+            label_seq_id: 0,
+            pdbx_PDB_ins_code: undefined,
+        };
+
+        for (let i = 0, il = ma_qa_metric_local_pairwise._rowCount; i < il; i++) {
+            if (model_id.value(i) !== model.modelNum || metric_id.value(i) !== metricId) continue;
+
+            let labelAsymId = label_asym_id_1.value(i);
+            let entityIndex = index.findEntity(labelAsymId);
+            residueKey.label_entity_id = model.entities.data.id.value(entityIndex);
+            residueKey.label_asym_id = labelAsymId;
+            residueKey.label_seq_id = label_seq_id_1.value(i);
+
+            const rI_1 = index.findResidueLabel(residueKey);
+            if (rI_1 < 0) continue;
+
+            labelAsymId = label_asym_id_2.value(i);
+            entityIndex = index.findEntity(labelAsymId);
+            residueKey.label_entity_id = model.entities.data.id.value(entityIndex);
+            residueKey.label_asym_id = labelAsymId;
+            residueKey.label_seq_id = label_seq_id_2.value(i);
+
+            const rI_2 = index.findResidueLabel(residueKey);
+            if (rI_1 < 0) continue;
+
+            let r1 = values[rI_1];
+            if (!r1) {
+                r1 = {};
+                values[rI_1] = r1;
+            }
+            const value = metric_value.value(i);
+            r1[rI_2] = value;
+
+            if (rI_1 < residueRange[0]) residueRange[0] = rI_1;
+            if (rI_2 < residueRange[0]) residueRange[0] = rI_2;
+            if (rI_1 > residueRange[1]) residueRange[1] = rI_1;
+            if (rI_2 > residueRange[1]) residueRange[1] = rI_2;
+            if (value < valueRange[0]) valueRange[0] = value;
+            if (value > valueRange[1]) valueRange[1] = value;
+        }
+
+        return metric;
+    }
+
     export const symbols = {
         pLDDT: QuerySymbolRuntime.Dynamic(CustomPropSymbol('ma', 'quality-assessment.pLDDT', Type.Num),
             ctx => {

src/extensions/mp4-export/encoder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -72,11 +72,11 @@ export async function encodeMp4Animation<A extends PluginStateAnimation>(plugin:
         await params.pass.updateBackground();
 
         await plugin.managers.animation.play(params.animation.definition, params.animation.params);
+
         stoppedAnimation = false;
         for (let i = 0; i <= N; i++) {
-            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true });
-
-            const image = params.pass.getImageData(width, height, normalizedViewport);
+            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true, updateControls: true });
+            const image = await params.pass.getImageData(ctx, width, height, normalizedViewport);
             encoder.addFrameRgba(image.data);
 
             if (ctx.shouldUpdate) {

src/extensions/mvs/camera.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { Camera } from '../../mol-canvas3d/camera';
@@ -17,10 +18,9 @@ import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
 import { ColorNames } from '../../mol-util/color/names';
-
+import { MVSPrimitivesData } from './components/primitives';
 import { decodeColor } from './helpers/utils';
-import { ParamsOfKind } from './tree/generic/tree-schema';
-import { MolstarTree } from './tree/molstar/molstar-tree';
+import { MolstarNodeParams } from './tree/molstar/molstar-tree';
 import { MVSDefaults } from './tree/mvs/mvs-defaults';
 
 
@@ -42,7 +42,7 @@ export async function suppressCameraAutoreset(plugin: PluginContext) {
 }
 
 /** Set the camera based on a camera node params. */
-export async function setCamera(plugin: PluginContext, params: ParamsOfKind<MolstarTree, 'camera'>) {
+export async function setCamera(plugin: PluginContext, params: MolstarNodeParams<'camera'>) {
     const target = Vec3.create(...params.target);
     let position = Vec3.create(...params.position);
     if (plugin.canvas3d) position = fovAdjustedPosition(target, position, plugin.canvas3d.camera.state.mode, plugin.canvas3d.camera.state.fov);
@@ -53,34 +53,62 @@ export async function setCamera(plugin: PluginContext, params: ParamsOfKind<Mols
     await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
 }
 
+async function focusBoundingSphere(plugin: PluginContext, params: MolstarNodeParams<'focus'>, boundingSphere: Sphere3D | undefined, extraRadius: number) {
+    if (!plugin.canvas3d || !boundingSphere) return;
+
+    const direction = Vec3.create(...params.direction);
+    const up = Vec3.create(...params.up);
+    Vec3.orthogonalize(up, direction, up);
+    const snapshot = snapshotFromSphereAndDirections(plugin.canvas3d.camera, {
+        center: boundingSphere.center,
+        radius: boundingSphere.radius + extraRadius,
+        up,
+        direction,
+    });
+    resetSceneRadiusFactor(plugin);
+    await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
+}
+
+function getRenderObjectsBoundary(objects: ReadonlyArray<GraphicsRenderObject>) {
+    const spheres: Sphere3D[] = [];
+    for (const o of objects) {
+        const s = o.values.boundingSphere.ref.value;
+        if (s.radius === 0) continue;
+        spheres.push(s);
+    }
+    if (spheres.length === 0) return;
+    if (spheres.length === 1) return spheres[0];
+    return boundingSphereOfSpheres(spheres);
+}
+
 /** Focus the camera on the bounding sphere of a (sub)structure (or on the whole scene if `structureNodeSelector` is null).
- * Orient the camera based on a focus node params. */
-export async function setFocus(plugin: PluginContext, structureNodeSelector: StateObjectSelector | undefined, params: ParamsOfKind<MolstarTree, 'focus'> = MVSDefaults.focus) {
-    let structure: Structure | undefined = undefined;
+  * Orient the camera based on a focus node params.
+  **/
+export async function setFocus(plugin: PluginContext, structureNodeSelector: StateObjectSelector | undefined, params: MolstarNodeParams<'focus'> = MVSDefaults.focus) {
+    let boundingSphere: Sphere3D | undefined = undefined;
     if (structureNodeSelector) {
         const cell = plugin.state.data.cells.get(structureNodeSelector.ref);
-        structure = cell?.obj?.data;
-        if (!structure) console.warn('Focus: no structure');
-        if (!(structure instanceof Structure)) {
-            console.warn('Focus: cannot apply to a non-structure node');
-            structure = undefined;
+        const data = cell?.obj?.data;
+        if (!data) console.warn('Focus: no structure');
+        if (data instanceof Structure) {
+            boundingSphere = Loci.getBoundingSphere(Structure.Loci(data));
+        } else if (PluginStateObject.isRepresentation3D(cell?.obj)) {
+            boundingSphere = getRenderObjectsBoundary(cell.obj.data.repr.renderObjects);
+        } else if (MVSPrimitivesData.is(cell?.obj)) {
+            const representations = plugin.state.data.selectQ(q =>
+                q.byRef(cell.transform.ref).subtree().filter(c => PluginStateObject.isRepresentation3D(c?.obj))
+            );
+            const renderObjects = representations.flatMap(r => r.obj?.data?.repr?.renderObjects ?? []);
+            if (renderObjects.length) {
+                boundingSphere = getRenderObjectsBoundary(renderObjects);
+            }
+        } else {
+            console.warn('Focus: cannot apply to the specified node type');
         }
     }
-    const boundingSphere = structure ? Loci.getBoundingSphere(Structure.Loci(structure)) : getPluginBoundingSphere(plugin);
-    if (boundingSphere && plugin.canvas3d) {
-        const extraRadius = structure ? DefaultFocusOptions.extraRadiusForFocus : DefaultFocusOptions.extraRadiusForZoomAll;
-        const direction = Vec3.create(...params.direction);
-        const up = Vec3.create(...params.up);
-        Vec3.orthogonalize(up, direction, up);
-        const snapshot = snapshotFromSphereAndDirections(plugin.canvas3d.camera, {
-            center: boundingSphere.center,
-            radius: boundingSphere.radius + extraRadius,
-            up,
-            direction,
-        });
-        resetSceneRadiusFactor(plugin);
-        await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
-    }
+    const extraRadius = boundingSphere ? DefaultFocusOptions.extraRadiusForFocus : DefaultFocusOptions.extraRadiusForZoomAll;
+    boundingSphere ??= getPluginBoundingSphere(plugin);
+    return focusBoundingSphere(plugin, params, boundingSphere, extraRadius);
 }
 
 /** Adjust `sceneRadiusFactor` property so that the current scene is not cropped */
@@ -155,7 +183,7 @@ function boundingSphereOfSpheres(spheres: Sphere3D[]): Sphere3D {
 }
 
 /** Set canvas properties based on a canvas node params. */
-export function setCanvas(plugin: PluginContext, params: ParamsOfKind<MolstarTree, 'canvas'> | undefined) {
+export function setCanvas(plugin: PluginContext, params: MolstarNodeParams<'canvas'> | undefined) {
     const backgroundColor = decodeColor(params?.background_color) ?? DefaultCanvasBackgroundColor;
     if (backgroundColor !== plugin.canvas3d?.props.renderer.backgroundColor) {
         plugin.canvas3d?.setProps(old => ({

src/extensions/mvs/components/annotation-prop.ts

@@ -106,6 +106,7 @@ export class MVSAnnotations {
                 if (!file.ok) throw file.error;
                 annots[spec.id] = await MVSAnnotation.fromSpec(ctx, spec, file.value);
             } catch (err) {
+                ctx.errorContext?.add('mvs', `Failed to obtain annotation (${err}).\nAnnotation specification source params: ${JSON.stringify(spec.source.params)}`);
                 console.error(`Failed to obtain annotation (${err}).\nAnnotation specification:`, spec);
                 annots[spec.id] = MVSAnnotation.createEmpty(spec.schema);
             }

src/extensions/mvs/components/formats.ts

@@ -59,6 +59,7 @@ export const ParseMVSX = MVSTransform({
 export const LoadMvsDataParams = {
     replaceExisting: PD.Boolean(false, { description: 'If true, the loaded MVS view will replace the current state; if false, the MVS view will be added to the current state.' }),
     keepCamera: PD.Boolean(false, { description: 'If true, any camera positioning from the MVS state will be ignored and the current camera position will be kept.' }),
+    applyExtensions: PD.Boolean(true, { description: 'If true, apply builtin MVS-loading extensions (not a part of standard MVS specification).' }),
 };
 
 /** State action which loads a MVS view into Mol* */
@@ -68,7 +69,7 @@ export const LoadMvsData = StateAction.build({
     params: LoadMvsDataParams,
 })(({ a, params }, plugin: PluginContext) => Task.create('Load MVS Data', async () => {
     const { mvsData, sourceUrl } = a.data;
-    await loadMVS(plugin, mvsData, { replaceExisting: params.replaceExisting, keepCamera: params.keepCamera, sourceUrl: sourceUrl });
+    await loadMVS(plugin, mvsData, { replaceExisting: params.replaceExisting, keepCamera: params.keepCamera, sourceUrl: sourceUrl, extensions: params.applyExtensions ? undefined : [] });
 }));
 
 

src/extensions/mvs/components/primitives.ts

@@ -0,0 +1,646 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Lines } from '../../../mol-geo/geometry/lines/lines';
+import { LinesBuilder } from '../../../mol-geo/geometry/lines/lines-builder';
+import { addFixedCountDashedCylinder, addSimpleCylinder, BasicCylinderProps } from '../../../mol-geo/geometry/mesh/builder/cylinder';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { Text } from '../../../mol-geo/geometry/text/text';
+import { TextBuilder } from '../../../mol-geo/geometry/text/text-builder';
+import { Box3D, Sphere3D } from '../../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { Shape } from '../../../mol-model/shape';
+import { Structure, StructureElement, StructureSelection } from '../../../mol-model/structure';
+import { StructureQueryHelper } from '../../../mol-plugin-state/helpers/structure-query';
+import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
+import { PluginContext } from '../../../mol-plugin/context';
+import { Expression } from '../../../mol-script/language/expression';
+import { StateObject } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { round } from '../../../mol-util';
+import { Asset } from '../../../mol-util/assets';
+import { Color } from '../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { capitalize } from '../../../mol-util/string';
+import { rowsToExpression, rowToExpression } from '../helpers/selections';
+import { collectMVSReferences, decodeColor } from '../helpers/utils';
+import { MolstarNode, MolstarSubtree } from '../tree/molstar/molstar-tree';
+import { MVSPrimitive, MVSPrimitiveOptions, MVSPrimitiveParams } from '../tree/mvs/mvs-primitives';
+import { MVSNode } from '../tree/mvs/mvs-tree';
+import { isComponentExpression, isPrimitiveComponentExpressions, isVector3, PrimitivePositionT } from '../tree/mvs/param-types';
+import { MVSTransform } from './annotation-structure-component';
+
+export function getPrimitiveStructureRefs(primitives: MolstarSubtree<'primitives'>) {
+    const refs = new Set<string>();
+    for (const c of primitives.children ?? []) {
+        if (c.kind !== 'primitive') continue;
+        const p = c.params as unknown as MVSPrimitive;
+        Builders[p.kind]?.[3].refs?.(p, refs);
+    }
+    return refs;
+}
+
+export class MVSPrimitivesData extends SO.Create<PrimitiveBuilderContext>({ name: 'Primitive Data', typeClass: 'Object' }) { }
+export class MVSPrimitiveShapes extends SO.Create<{ mesh?: Shape<Mesh>, labels?: Shape<Text> }>({ name: 'Primitive Shapes', typeClass: 'Object' }) { }
+
+export type MVSDownloadPrimitiveData = typeof MVSDownloadPrimitiveData
+export const MVSDownloadPrimitiveData = MVSTransform({
+    name: 'mvs-download-primitive-data',
+    display: { name: 'MVS Primitives' },
+    from: [SO.Root, SO.Molecule.Structure],
+    to: MVSPrimitivesData,
+    params: {
+        uri: PD.Url('', { isHidden: true }),
+        format: PD.Text<'mvs-node-json'>('mvs-node-json', { isHidden: true })
+    },
+})({
+    apply({ a, params, cache }, plugin: PluginContext) {
+        return Task.create('Download Primitive Data', async ctx => {
+            const url = Asset.getUrlAsset(plugin.managers.asset, params.uri);
+            const asset = await plugin.managers.asset.resolve(url, 'string').runInContext(ctx);
+            const node = JSON.parse(asset.data) as MolstarSubtree<'primitives'>;
+            (cache as any).asset = asset;
+            return new MVSPrimitivesData({
+                node,
+                defaultStructure: SO.Molecule.Structure.is(a) ? a.data : undefined,
+                structureRefs: {},
+                primitives: getPrimitives(node),
+                options: { ...node.params },
+                positionCache: new Map(),
+                instances: getInstances(node.params),
+            }, { label: 'Primitive Data' });
+        });
+    },
+    dispose({ cache }) {
+        ((cache as any)?.asset as Asset.Wrapper | undefined)?.dispose();
+    },
+});
+
+export type MVSInlinePrimitiveData = typeof MVSInlinePrimitiveData
+export const MVSInlinePrimitiveData = MVSTransform({
+    name: 'mvs-inline-primitive-data',
+    display: { name: 'MVS Primitives' },
+    from: [SO.Root, SO.Molecule.Structure],
+    to: MVSPrimitivesData,
+    params: {
+        node: PD.Value<MolstarSubtree<'primitives'>>(undefined as any, { isHidden: true }),
+    },
+})({
+    apply({ a, params }) {
+        return new MVSPrimitivesData({
+            node: params.node,
+            defaultStructure: SO.Molecule.Structure.is(a) ? a.data : undefined,
+            structureRefs: {},
+            primitives: getPrimitives(params.node),
+            options: { ...params.node.params },
+            positionCache: new Map(),
+            instances: getInstances(params.node.params),
+        }, { label: 'Primitive Data' });
+    }
+});
+
+export type MVSBuildPrimitiveShape = typeof MVSBuildPrimitiveShape
+export const MVSBuildPrimitiveShape = MVSTransform({
+    name: 'mvs-build-primitive-shape',
+    display: { name: 'MVS Primitives' },
+    from: MVSPrimitivesData,
+    to: SO.Shape.Provider,
+    params: {
+        kind: PD.Text<'mesh' | 'labels' | 'lines'>('mesh')
+    }
+})({
+    apply({ a, params, dependencies }) {
+        const structureRefs = dependencies ? collectMVSReferences([SO.Molecule.Structure], dependencies) : {};
+        const context: PrimitiveBuilderContext = { ...a.data, structureRefs };
+
+        const label = capitalize(params.kind);
+        if (params.kind === 'mesh') {
+            if (!hasPrimitiveKind(a.data, 'mesh')) return StateObject.Null;
+
+            return new SO.Shape.Provider({
+                label,
+                data: context,
+                params: PD.withDefaults(Mesh.Params, { alpha: a.data.options?.transparency ?? 1 }),
+                getShape: (_, data, __, prev: any) => buildPrimitiveMesh(data, prev?.geometry),
+                geometryUtils: Mesh.Utils,
+            }, { label });
+        } else if (params.kind === 'labels') {
+            if (!hasPrimitiveKind(a.data, 'label')) return StateObject.Null;
+
+            return new SO.Shape.Provider({
+                label,
+                data: context,
+                params: PD.withDefaults(DefaultLabelParams, { alpha: a.data.options?.label_transparency ?? 1 }),
+                getShape: (_, data, __, prev: any) => buildPrimitiveLabels(data, prev?.geometry),
+                geometryUtils: Text.Utils,
+            }, { label });
+        } else if (params.kind === 'lines') {
+            if (!hasPrimitiveKind(a.data, 'line')) return StateObject.Null;
+
+            return new SO.Shape.Provider({
+                label,
+                data: context,
+                params: PD.withDefaults(Lines.Params, { alpha: a.data.options?.transparency ?? 1 }),
+                getShape: (_, data, __, prev: any) => buildPrimitiveLines(data, prev?.geometry),
+                geometryUtils: Lines.Utils,
+            }, { label });
+        }
+
+        return StateObject.Null;
+    }
+});
+
+/* **************************************************** */
+
+class GroupManager {
+    private current = -1;
+    groupToNodeMap = new Map<number, MVSNode<'primitive'>>();
+    sizes = new Map<number, number>();
+    colors = new Map<number, number>();
+    tooltips = new Map<number, string>();
+
+    allocateSingle(node: MVSNode<'primitive'>) {
+        const group = ++this.current;
+        this.groupToNodeMap.set(group, node);
+        return group;
+    }
+
+    allocateMany(node: MVSNode<'primitive'>, groups: number[]) {
+        const newGroups = new Map<number, number>();
+        const base = this.current;
+        for (const g of groups) {
+            if (newGroups.has(g)) continue;
+            const group = base + newGroups.size + 1;
+            this.groupToNodeMap.set(group, node);
+            newGroups.set(g, group);
+        }
+        this.current += newGroups.size + 1;
+        return newGroups;
+    }
+
+    updateColor(group: number, color?: string | null) {
+        const c = decodeColor(color);
+        if (typeof c === 'number') this.colors.set(group, c);
+    }
+
+    updateTooltip(group: number, tooltip?: string | null) {
+        if (typeof tooltip === 'string') this.tooltips.set(group, tooltip);
+    }
+
+    updateSize(group: number, size?: number | null) {
+        if (typeof size === 'number') this.sizes.set(group, size);
+    }
+}
+
+interface PrimitiveBuilderContext {
+    node: MolstarNode<'primitives'>;
+    defaultStructure?: Structure;
+    structureRefs: Record<string, Structure | undefined>;
+    primitives: MolstarNode<'primitive'>[];
+    options: MVSPrimitiveOptions;
+    positionCache: Map<string, [Sphere3D, Box3D]>;
+    instances: Mat4[] | undefined;
+}
+
+interface MeshBuilderState {
+    groups: GroupManager;
+    mesh: MeshBuilder.State;
+}
+
+interface LabelBuilderState {
+    groups: GroupManager;
+    labels: TextBuilder;
+}
+
+interface LineBuilderState {
+    groups: GroupManager;
+    lines: LinesBuilder;
+}
+
+const BaseLabelProps: PD.Values<Text.Params> = {
+    ...PD.getDefaultValues(Text.Params),
+    attachment: 'middle-center',
+    fontQuality: 3,
+    fontWeight: 'normal',
+    borderWidth: 0.15,
+    borderColor: Color(0x0),
+    background: false,
+    backgroundOpacity: 0.5,
+    tether: false,
+};
+const DefaultLabelParams = PD.withDefaults(Text.Params, BaseLabelProps);
+
+const Builders: Record<MVSPrimitive['kind'], [
+    mesh: (context: PrimitiveBuilderContext, state: MeshBuilderState, node: MVSNode<'primitive'>, params: any) => void,
+    line: (context: PrimitiveBuilderContext, state: LineBuilderState, node: MVSNode<'primitive'>, params: any) => void,
+    label: (context: PrimitiveBuilderContext, state: LabelBuilderState, node: MVSNode<'primitive'>, params: any) => void,
+    features: {
+        mesh?: boolean | ((primitive: any, context: PrimitiveBuilderContext) => boolean),
+        line?: boolean | ((primitive: any, context: PrimitiveBuilderContext) => boolean),
+        label?: boolean | ((primitive: any, context: PrimitiveBuilderContext) => boolean),
+        refs?: (params: any, refs: Set<string>) => void
+    },
+]> = {
+    mesh: [addMesh, addMeshWireframe, noOp, {
+        mesh: (m: MVSPrimitiveParams<'mesh'>) => m.show_triangles ?? true,
+        line: (m: MVSPrimitiveParams<'mesh'>) => m.show_wireframe ?? false,
+    }],
+    lines: [addMesh, addLines, noOp, { line: true }],
+    line: [addLineMesh, noOp, noOp, { mesh: true, refs: resolveLineRefs }],
+    label: [noOp, noOp, addPrimitiveLabel, { label: true, refs: resolveLabelRefs }],
+    distance_measurement: [addDistanceMesh, noOp, addDistanceLabel, { mesh: true, label: true, refs: resolveLineRefs }],
+};
+
+
+function getPrimitives(primitives: MolstarSubtree<'primitives'>) {
+    return (primitives.children ?? []).filter(c => c.kind === 'primitive') as unknown as MolstarNode<'primitive'>[];
+}
+
+function addRef(position: PrimitivePositionT, refs: Set<string>) {
+    if (isPrimitiveComponentExpressions(position) && position.structure_ref) {
+        refs.add(position.structure_ref);
+    }
+}
+
+function hasPrimitiveKind(context: PrimitiveBuilderContext, kind: 'mesh' | 'line' | 'label') {
+    for (const c of context.primitives) {
+        const p = c.params as unknown as MVSPrimitive;
+        const test = Builders[p.kind]?.[3]?.[kind];
+        if (typeof test === 'boolean') {
+            if (test) return true;
+        } else if (test?.(p, context)) {
+            return true;
+        }
+    }
+    return false;
+}
+
+function resolveBasePosition(context: PrimitiveBuilderContext, position: PrimitivePositionT, targetPosition: Vec3) {
+    return resolvePosition(context, position, targetPosition, undefined, undefined);
+}
+
+const _EmptySphere = Sphere3D.zero();
+const _EmptyBox = Box3D.zero();
+
+function resolvePosition(context: PrimitiveBuilderContext, position: PrimitivePositionT, targetPosition: Vec3 | undefined, targetSphere: Sphere3D | undefined, targetBox: Box3D | undefined) {
+    let expr: Expression | undefined;
+    let pivotRef: string | undefined;
+
+    if (isVector3(position)) {
+        if (targetPosition) Vec3.copy(targetPosition, position as any);
+        if (targetSphere) Sphere3D.set(targetSphere, position as any, 0);
+        if (targetBox) Box3D.set(targetBox, position as any, position as any);
+        return;
+    }
+
+    if (isPrimitiveComponentExpressions(position)) {
+        // TODO: take schema into account for possible optimization
+        expr = rowsToExpression(position.expressions!);
+        pivotRef = position.structure_ref;
+    } else if (isComponentExpression(position)) {
+        expr = rowToExpression(position);
+    }
+
+    if (!expr) {
+        console.error('Invalid expression', position);
+        throw new Error('Invalid primitive potition expression, see console for details.');
+    }
+
+    const pivot = !pivotRef ? context.defaultStructure : context.structureRefs[pivotRef];
+    if (!pivot) {
+        throw new Error(`Structure with ref '${pivotRef ?? '<default>'}' not found.`);
+    }
+
+    const cackeKey = JSON.stringify(position);
+    if (context.positionCache.has(cackeKey)) {
+        const cached = context.positionCache.get(cackeKey)!;
+        if (targetPosition) Vec3.copy(targetPosition, cached[0].center);
+        if (targetSphere) Sphere3D.copy(targetSphere, cached[0]);
+        if (targetBox) Box3D.copy(targetBox, cached[1]);
+        return;
+    }
+
+    const { selection } = StructureQueryHelper.createAndRun(pivot, expr);
+
+    let box: Box3D;
+    let sphere: Sphere3D;
+
+    if (StructureSelection.isEmpty(selection)) {
+        if (targetPosition) Vec3.set(targetPosition, 0, 0, 0);
+        box = _EmptyBox;
+        sphere = _EmptySphere;
+    } else {
+        const loci = StructureSelection.toLociWithSourceUnits(selection);
+        const boundary = StructureElement.Loci.getBoundary(loci);
+        if (targetPosition) Vec3.copy(targetPosition, boundary.sphere.center);
+        box = boundary.box;
+        sphere = boundary.sphere;
+    }
+
+    if (targetSphere) Sphere3D.copy(targetSphere, sphere);
+    if (targetBox) Box3D.copy(targetBox, box);
+
+    context.positionCache.set(cackeKey, [sphere, box]);
+}
+
+function getInstances(options: MVSPrimitiveOptions | undefined): Mat4[] | undefined {
+    if (!options?.instances?.length) return undefined;
+    return options.instances.map(i => Mat4.fromArray(Mat4(), i, 0));
+}
+
+function buildPrimitiveMesh(context: PrimitiveBuilderContext, prev?: Mesh): Shape<Mesh> {
+    const meshBuilder = MeshBuilder.createState(1024, 1024, prev);
+    const state: MeshBuilderState = { groups: new GroupManager(), mesh: meshBuilder };
+
+    meshBuilder.currentGroup = -1;
+
+    for (const c of context.primitives) {
+        const p = c.params as unknown as MVSPrimitive;
+        const b = Builders[p.kind];
+        if (!b) {
+            console.warn(`Primitive ${p.kind} not supported`);
+            continue;
+        }
+        b[0](context, state, c, p);
+    }
+
+    const { colors, tooltips } = state.groups;
+    const tooltip = context.options?.tooltip ?? '';
+    const color = decodeColor(context.options?.color) ?? 0x0;
+
+    return Shape.create(
+        'Mesh',
+        {
+            kind: 'mvs-primitives',
+            node: context.node,
+            groupToNode: state.groups.groupToNodeMap,
+        },
+        MeshBuilder.getMesh(meshBuilder),
+        (g) => colors.get(g) as Color ?? color as Color,
+        (g) => 1,
+        (g) => tooltips.get(g) ?? tooltip,
+        context.instances,
+    );
+}
+
+function buildPrimitiveLines(context: PrimitiveBuilderContext, prev?: Lines): Shape<Lines> {
+    const linesBuilder = LinesBuilder.create(1024, 1024, prev);
+    const state: LineBuilderState = { groups: new GroupManager(), lines: linesBuilder };
+
+    for (const c of context.primitives) {
+        const p = c.params as unknown as MVSPrimitive;
+        const b = Builders[p.kind];
+        if (!b) {
+            console.warn(`Primitive ${p.kind} not supported`);
+            continue;
+        }
+        b[1](context, state, c, p);
+    }
+
+    const color = decodeColor(context.options?.color) ?? 0x0;
+    const { colors, sizes, tooltips } = state.groups;
+
+    return Shape.create(
+        'Lines',
+        {
+            kind: 'mvs-primitives',
+            node: context.node,
+            groupToNode: state.groups.groupToNodeMap,
+        },
+        linesBuilder.getLines(),
+        (g) => colors.get(g) as Color ?? color as Color,
+        (g) => sizes.get(g) ?? 1,
+        (g) => tooltips.get(g) ?? '',
+        context.instances,
+    );
+}
+
+function buildPrimitiveLabels(context: PrimitiveBuilderContext, prev?: Text): Shape<Text> {
+    const labelsBuilder = TextBuilder.create(BaseLabelProps, 1024, 1024, prev);
+    const state: LabelBuilderState = { groups: new GroupManager(), labels: labelsBuilder };
+
+    for (const c of context.primitives) {
+        const p = c.params as unknown as MVSPrimitive;
+        const b = Builders[p.kind];
+        if (!b) {
+            console.warn(`Primitive ${p.kind} not supported`);
+            continue;
+        }
+        b[2](context, state, c, p);
+    }
+
+    const color = decodeColor(context.options?.label_color) ?? 0x0;
+    const { colors, sizes, tooltips } = state.groups;
+
+    return Shape.create(
+        'Labels',
+        {
+            kind: 'mvs-primitives',
+            node: context.node,
+            groupToNode: state.groups.groupToNodeMap,
+        },
+        labelsBuilder.getText(),
+        (g) => colors.get(g) as Color ?? color as Color,
+        (g) => sizes.get(g) ?? 1,
+        (g) => tooltips.get(g) ?? '',
+        context.instances,
+    );
+}
+
+function noOp() { }
+
+function addMesh(context: PrimitiveBuilderContext, { groups, mesh }: MeshBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'mesh'>) {
+    if (!params.show_triangles) return;
+
+    const a = Vec3.zero();
+    const b = Vec3.zero();
+    const c = Vec3.zero();
+
+    const { indices, vertices, triangle_colors, triangle_groups, group_colors, group_tooltips } = params;
+
+    const groupSet: Map<number, number> | undefined = triangle_groups?.length ? groups.allocateMany(node, triangle_groups) : undefined;
+
+    for (let i = 0, _i = indices.length / 3; i < _i; i++) {
+        if (groupSet) {
+            const grp = triangle_groups![i];
+            mesh.currentGroup = groupSet.get(grp)!;
+            groups.updateColor(mesh.currentGroup, group_colors?.[grp] ?? params.color);
+            groups.updateTooltip(mesh.currentGroup, group_tooltips?.[grp]);
+        } else {
+            mesh.currentGroup = groups.allocateSingle(node);
+            groups.updateColor(mesh.currentGroup, triangle_colors?.[i] ?? params.color);
+            groups.updateTooltip(mesh.currentGroup, params.tooltip);
+        }
+
+        Vec3.fromArray(a, vertices, 3 * indices[3 * i]);
+        Vec3.fromArray(b, vertices, 3 * indices[3 * i + 1]);
+        Vec3.fromArray(c, vertices, 3 * indices[3 * i + 2]);
+
+        MeshBuilder.addTriangle(mesh, a, b, c);
+    }
+}
+
+function addMeshWireframe(context: PrimitiveBuilderContext, { groups, lines }: LineBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'mesh'>) {
+    if (!params.show_wireframe) return;
+
+    const a = Vec3.zero();
+    const b = Vec3.zero();
+    const c = Vec3.zero();
+
+    const { indices, vertices, triangle_colors, triangle_groups, group_colors, group_tooltips } = params;
+
+    const groupSet: Map<number, number> | undefined = triangle_groups?.length ? groups.allocateMany(node, triangle_groups) : undefined;
+    const radius = params.wireframe_radius ?? 1;
+
+    for (let i = 0, _i = indices.length / 3; i < _i; i++) {
+        let group: number;
+        if (groupSet) {
+            const grp = triangle_groups![i];
+            group = groupSet.get(grp)!;
+            groups.updateColor(group, params.wireframe_color ?? group_colors?.[grp]);
+            groups.updateTooltip(group, group_tooltips?.[grp]);
+        } else {
+            group = groups.allocateSingle(node);
+            groups.updateColor(group, params.wireframe_color ?? triangle_colors?.[i]);
+            groups.updateTooltip(group, params.tooltip);
+        }
+
+        groups.updateSize(group, radius);
+
+        Vec3.fromArray(a, vertices, 3 * indices[3 * i]);
+        Vec3.fromArray(b, vertices, 3 * indices[3 * i + 1]);
+        Vec3.fromArray(c, vertices, 3 * indices[3 * i + 2]);
+
+        lines.add(a[0], a[1], a[2], b[0], b[1], b[2], group);
+        lines.add(b[0], b[1], b[2], c[0], c[1], c[2], group);
+        lines.add(c[0], c[1], c[2], a[0], a[1], a[2], group);
+    }
+}
+
+function addLines(context: PrimitiveBuilderContext, { groups, lines }: LineBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'lines'>) {
+    const a = Vec3.zero();
+    const b = Vec3.zero();
+
+    const { indices, vertices, line_colors, line_groups, group_colors, group_tooltips, group_radius } = params;
+
+    const groupSet: Map<number, number> | undefined = line_groups?.length ? groups.allocateMany(node, line_groups) : undefined;
+    const radius = params.line_radius ?? 1;
+
+    for (let i = 0, _i = indices.length / 2; i < _i; i++) {
+        let group: number;
+        if (groupSet) {
+            const grp = line_groups![i];
+            group = groupSet.get(grp)!;
+            groups.updateColor(group, group_colors?.[grp] ?? params.color);
+            groups.updateTooltip(group, group_tooltips?.[grp]);
+            groups.updateSize(group, group_radius?.[grp] ?? radius);
+        } else {
+            group = groups.allocateSingle(node);
+            groups.updateColor(group, line_colors?.[i] ?? params.color);
+            groups.updateSize(group, radius);
+            groups.updateTooltip(group, params.tooltip);
+        }
+
+        Vec3.fromArray(a, vertices, 3 * indices[2 * i]);
+        Vec3.fromArray(b, vertices, 3 * indices[2 * i + 1]);
+        lines.add(a[0], a[1], a[2], b[0], b[1], b[2], group);
+    }
+}
+
+function resolveLineRefs(params: MVSPrimitiveParams<'line' | 'distance_measurement'>, refs: Set<string>) {
+    addRef(params.start, refs);
+    addRef(params.end, refs);
+}
+
+const lStart = Vec3.zero();
+const lEnd = Vec3.zero();
+
+function addLineMesh(context: PrimitiveBuilderContext, { groups, mesh }: MeshBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'line'>, options?: { skipResolvePosition?: boolean }) {
+    if (!options?.skipResolvePosition) {
+        resolveBasePosition(context, params.start, lStart);
+        resolveBasePosition(context, params.end, lEnd);
+    }
+    const radius = params.thickness ?? 0.05;
+
+    const cylinderProps: BasicCylinderProps = {
+        radiusBottom: radius,
+        radiusTop: radius,
+        topCap: true,
+        bottomCap: true,
+    };
+
+    mesh.currentGroup = groups.allocateSingle(node);
+    groups.updateColor(mesh.currentGroup, params.color);
+    groups.updateTooltip(mesh.currentGroup, params.tooltip);
+
+    if (params.dash_length) {
+        const dist = Vec3.distance(lStart, lEnd);
+        const count = Math.ceil(dist / (2 * params.dash_length));
+        addFixedCountDashedCylinder(mesh, lStart, lEnd, 1.0, count, true, cylinderProps);
+    } else {
+        addSimpleCylinder(mesh, lStart, lEnd, cylinderProps);
+    }
+}
+
+function getDistanceLabel(context: PrimitiveBuilderContext, params: MVSPrimitiveParams<'distance_measurement'>) {
+    resolveBasePosition(context, params.start, lStart);
+    resolveBasePosition(context, params.end, lEnd);
+
+    const dist = Vec3.distance(lStart, lEnd);
+    const distance = `${round(dist, 2)} Å`;
+    const label = typeof params.label_template === 'string' ? params.label_template.replace('{{distance}}', distance) : distance;
+
+    return label;
+}
+
+function addDistanceMesh(context: PrimitiveBuilderContext, state: MeshBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'distance_measurement'>) {
+    const tooltip = getDistanceLabel(context, params);
+    addLineMesh(context, state, node, { ...params, tooltip } as any, { skipResolvePosition: true });
+}
+
+const labelPos = Vec3.zero();
+
+function addDistanceLabel(context: PrimitiveBuilderContext, state: LabelBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'distance_measurement'>) {
+    const { labels, groups } = state;
+    resolveBasePosition(context, params.start, lStart);
+    resolveBasePosition(context, params.end, lEnd);
+
+    const dist = Vec3.distance(lStart, lEnd);
+    const distance = `${round(dist, 2)} Å`;
+    const label = typeof params.label_template === 'string' ? params.label_template.replace('{{distance}}', distance) : distance;
+
+    let size: number | undefined;
+    if (params.label_size === 'auto') {
+        size = Math.max(dist * (params.label_auto_size_scale ?? 0.2), params.label_auto_size_min ?? 0.01);
+    } else if (typeof params.label_size === 'number') {
+        size = params.label_size;
+    }
+
+    Vec3.add(labelPos, lStart, lEnd);
+    Vec3.scale(labelPos, labelPos, 0.5);
+
+    const group = groups.allocateSingle(node);
+    groups.updateColor(group, params.label_color);
+    groups.updateSize(group, size);
+
+    labels.add(label, labelPos[0], labelPos[1], labelPos[2], 1.05 * (params.thickness ?? 0.05), 1, group);
+}
+
+function resolveLabelRefs(params: MVSPrimitiveParams<'label'>, refs: Set<string>) {
+    addRef(params.position, refs);
+}
+
+function addPrimitiveLabel(context: PrimitiveBuilderContext, state: LabelBuilderState, node: MVSNode<'primitive'>, params: MVSPrimitiveParams<'label'>) {
+    const { labels, groups } = state;
+    resolveBasePosition(context, params.position, labelPos);
+
+    const group = groups.allocateSingle(node);
+    groups.updateColor(group, params.label_color);
+    groups.updateSize(group, params.label_size);
+
+    labels.add(params.text, labelPos[0], labelPos[1], labelPos[2], params.label_offset ?? 0, 1, group);
+}

src/extensions/mvs/components/surroundings.ts

@@ -0,0 +1,53 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { StructureElement } from '../../../mol-model/structure';
+import { createStructureComponent } from '../../../mol-plugin-state/helpers/structure-component';
+import { PluginStateTransform, PluginStateObject as SO } from '../../../mol-plugin-state/objects';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+
+export const StructureSurroundingsParams = {
+    radius: PD.Numeric(5, { min: 0 }, { description: 'Surroundings radius in Angstroms' }),
+    includeSelf: PD.Boolean(true, { description: 'Include parent selection itself in the surroundings' }),
+    wholeResidues: PD.Boolean(true, { description: 'Include whole residues, instead of individual atoms' }),
+    nullIfEmpty: PD.Optional(PD.Boolean(true, { isHidden: true })),
+};
+export type StructureSurroundingsParams = typeof StructureSurroundingsParams;
+export type StructureSurroundingsProps = PD.ValuesFor<StructureSurroundingsParams>;
+
+
+export type StructureSurroundings = typeof StructureSurroundings;
+export const StructureSurroundings = PluginStateTransform.BuiltIn({
+    name: 'structure-surroundings',
+    display: { name: 'Surroundings', description: 'Surroundings of a structure component.' },
+    from: SO.Molecule.Structure,
+    to: SO.Molecule.Structure,
+    params: StructureSurroundingsParams,
+})({
+    apply({ a, params, cache }) {
+        const struct = a.data;
+        const rootStruct = struct.parent ?? struct;
+        const targetBundle = StructureElement.Bundle.fromSubStructure(rootStruct, struct);
+        const targetExpr = StructureElement.Bundle.toExpression(targetBundle);
+        let surroundingsExpr = MolScriptBuilder.struct.modifier.includeSurroundings({
+            0: targetExpr,
+            radius: params.radius,
+            'as-whole-residues': params.wholeResidues,
+        });
+        if (!params.includeSelf) {
+            surroundingsExpr = MolScriptBuilder.struct.modifier.exceptBy({
+                0: surroundingsExpr,
+                by: targetExpr,
+            });
+        }
+        return createStructureComponent(rootStruct, { label: `Surroundings (${params.radius} Å)`, type: { name: 'expression', params: surroundingsExpr }, nullIfEmpty: params.nullIfEmpty }, cache as any);
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});

src/extensions/mvs/helpers/selections.ts

@@ -311,6 +311,7 @@ export function rowToExpression(row: MVSAnnotationRow): Expression {
 /** Convert multiple annotation rows into a MolScript expression.
  * (with union semantics, i.e. an atom qualifies if it qualifies for at least one of the rows) */
 export function rowsToExpression(rows: readonly MVSAnnotationRow[]): Expression {
+    if (rows.length === 1) return rowToExpression(rows[0]);
     return unionExpression(rows.map(rowToExpression));
 }
 

src/extensions/mvs/helpers/utils.ts

@@ -1,10 +1,12 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { hashString } from '../../../mol-data/util';
+import { StateObject } from '../../../mol-state';
 import { Color } from '../../../mol-util/color';
 import { ColorNames } from '../../../mol-util/color/names';
 
@@ -97,8 +99,8 @@ export type ElementOfSet<S> = S extends Set<infer T> ? T : never
 
 /** Convert `colorString` (either X11 color name like 'magenta' or hex code like '#ff00ff') to Color.
  * Return `undefined` if `colorString` cannot be converted. */
-export function decodeColor(colorString: string | undefined): Color | undefined {
-    if (colorString === undefined) return undefined;
+export function decodeColor(colorString: string | undefined | null): Color | undefined {
+    if (colorString === undefined || colorString === null) return undefined;
     let result: Color | undefined;
     if (HexColor.is(colorString)) {
         if (colorString.length === 4) {
@@ -124,4 +126,28 @@ export const HexColor = {
     is(str: any): str is HexColor {
         return typeof str === 'string' && hexColorRegex.test(str);
     },
-};
+};
+
+export function collectMVSReferences<T extends StateObject.Ctor>(type: T[], dependencies: Record<string, StateObject>): Record<string, StateObject.From<T>['data']> {
+    const ret: any = {};
+
+    for (const key of Object.keys(dependencies)) {
+        const o = dependencies[key];
+        let okType = false;
+        for (const t of type) {
+            if (t.is(o)) {
+                okType = true;
+                break;
+            }
+        }
+        if (!okType || !o.tags) continue;
+        for (const tag of o.tags) {
+            if (tag.startsWith('mvs-ref:')) {
+                ret[tag.substring(8)] = o.data;
+                break;
+            }
+        }
+    }
+
+    return ret;
+}

src/extensions/mvs/load-extensions/non-covalent-interactions.ts

@@ -0,0 +1,55 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { StructureSurroundings } from '../components/surroundings';
+import { MolstarLoadingExtension } from '../load';
+import { UpdateTarget } from '../load-generic';
+import { getCustomProps } from '../tree/generic/tree-schema';
+
+
+const DefaultNonCovalentInteractionRadius = 5;
+
+export const NonCovalentInteractionsExtension: MolstarLoadingExtension<{}> = {
+    id: 'wwpdb/non-covalent-interactions',
+    description: 'Allow showing non-covalent interactions around components with molstar_show_non_covalent_interactions additional property',
+    createExtensionContext: () => ({}),
+    action: (updateTarget, node, context, extContext) => {
+        if (node.kind !== 'component' && node.kind !== 'component_from_uri' && node.kind !== 'component_from_source') return;
+
+        type CustomProps = {
+            molstar_show_non_covalent_interactions?: boolean,
+            molstar_non_covalent_interactions_radius_ang?: number,
+        };
+        const customProps = getCustomProps<CustomProps>(node);
+        if (!customProps.molstar_show_non_covalent_interactions) return undefined;
+
+        const surroundings = UpdateTarget.apply(updateTarget, StructureSurroundings, {
+            radius: customProps.molstar_non_covalent_interactions_radius_ang ?? DefaultNonCovalentInteractionRadius,
+            includeSelf: true,
+            wholeResidues: true,
+            nullIfEmpty: false,
+        });
+        // Bubble on target
+        UpdateTarget.apply(updateTarget, StateTransforms.Representation.StructureRepresentation3D, {
+            type: { name: 'ball-and-stick', params: { sizeFactor: 0.22, sizeAspectRatio: 0.73, adjustCylinderLength: true, xrayShaded: true, aromaticBonds: false, multipleBonds: 'off', excludeTypes: ['hydrogen-bond', 'metal-coordination'] } },
+            colorTheme: { name: 'element-symbol', params: {} },
+            sizeTheme: { name: 'physical', params: {} },
+        });
+        // Ball-and-stick on surrounding
+        UpdateTarget.apply(surroundings, StateTransforms.Representation.StructureRepresentation3D, {
+            type: { name: 'ball-and-stick', params: { sizeFactor: 0.16, excludeTypes: ['hydrogen-bond', 'metal-coordination'] } },
+            colorTheme: { name: 'element-symbol', params: {} },
+            sizeTheme: { name: 'physical', params: {} },
+        });
+        // Non-covalent interactions
+        UpdateTarget.apply(surroundings, StateTransforms.Representation.StructureRepresentation3D, {
+            type: { name: 'interactions', params: {} },
+            colorTheme: { name: 'interaction-type', params: {} },
+            sizeTheme: { name: 'uniform', params: {} },
+        });
+    },
+};

src/extensions/mvs/load-generic.ts

@@ -0,0 +1,190 @@
+/**
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateBuilder, StateObject, StateObjectSelector, StateTransform, StateTransformer } from '../../mol-state';
+import { stringHash } from './helpers/utils';
+import { Kind, Subtree, SubtreeOfKind, Tree } from './tree/generic/tree-schema';
+import { dfs } from './tree/generic/tree-utils';
+
+
+/** Function responsible for loading a tree node `node` into Mol*.
+ * Should apply changes within `updateParent.update` but not commit them.
+ * Should modify `context` accordingly, if it is needed for loading other nodes later.
+ * `updateParent.selector` is the result of loading the node's parent into Mol* state hierarchy (or the hierarchy root in case of root node). */
+export type LoadingAction<TNode extends Tree, TContext> = (updateParent: UpdateTarget, node: TNode, context: TContext) => UpdateTarget | undefined
+
+/** Loading actions for loading a tree into Mol*, per node kind. */
+export type LoadingActions<TTree extends Tree, TContext> = { [kind in Kind<Subtree<TTree>>]?: LoadingAction<SubtreeOfKind<TTree, kind>, TContext> }
+
+/** Type for defining custom behavior when loading trees, usually based on node custom properties. */
+export interface LoadingExtension<TTree extends Tree, TContext, TExtensionContext> {
+    id: string,
+    description: string,
+    /** Runs before the tree is loaded */
+    createExtensionContext: (tree: TTree, context: TContext) => TExtensionContext,
+    /** Runs after the tree is loaded */
+    disposeExtensionContext?: (extensionContext: TExtensionContext, tree: TTree, context: TContext) => void,
+    /** Runs on every node of the tree */
+    action: (updateTarget: UpdateTarget, node: Subtree<TTree>, context: TContext, extensionContext: TExtensionContext) => void,
+}
+
+
+/** Load a tree into Mol*, by applying loading actions in DFS order and then commiting at once.
+ * If `options.replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state. */
+export async function loadTree<TTree extends Tree, TContext>(
+    plugin: PluginContext,
+    tree: TTree,
+    loadingActions: LoadingActions<TTree, TContext>,
+    context: TContext,
+    options?: { replaceExisting?: boolean, extensions?: LoadingExtension<TTree, TContext, any>[] }
+) {
+    const mapping = new Map<Subtree<TTree>, UpdateTarget | undefined>();
+    const updateRoot: UpdateTarget = UpdateTarget.create(plugin, options?.replaceExisting ?? false);
+    if (options?.replaceExisting) {
+        UpdateTarget.deleteChildren(updateRoot);
+    }
+    const extensionContexts = (options?.extensions ?? []).map(ext => ({ ext, extCtx: ext.createExtensionContext(tree, context) }));
+    const mvsRefMap = new Map<string, string>();
+    dfs<TTree>(tree, (node, parent) => {
+        const kind: Kind<typeof node> = node.kind;
+        let msNode: UpdateTarget | undefined;
+        const updateParent = parent ? mapping.get(parent) : updateRoot;
+        const action = loadingActions[kind] as LoadingAction<typeof node, TContext> | undefined;
+        if (action) {
+            if (updateParent) {
+                msNode = action(updateParent, node, context);
+                if (msNode && node.ref) {
+                    UpdateTarget.tag(msNode, mvsRefTags(node.ref));
+                    mvsRefMap.set(node.ref, msNode.selector.ref);
+                }
+                mapping.set(node, msNode);
+            } else {
+                console.warn(`No target found for this "${node.kind}" node`);
+                return;
+            }
+        }
+        if (updateParent) {
+            for (const { ext, extCtx } of extensionContexts) {
+                ext.action(msNode ?? updateParent, node, context, extCtx);
+            }
+        }
+    });
+
+    for (const target of updateRoot.targetManager.allTargets) {
+        UpdateTarget.dependsOn(target, mvsRefMap);
+    }
+
+    extensionContexts.forEach(e => e.ext.disposeExtensionContext?.(e.extCtx, tree, context));
+    await UpdateTarget.commit(updateRoot);
+}
+
+
+/** A wrapper for updating Mol* state, while using deterministic transform refs.
+ * ```
+ * updateTarget = UpdateTarget.create(plugin); // like update = plugin.build();
+ * UpdateTarget.apply(updateTarget, transformer, params); // like update.to(selector).apply(transformer, params);
+ * await UpdateTarget.commit(updateTarget); // like await update.commit();
+ * ```
+ */
+export interface UpdateTarget {
+    readonly update: StateBuilder.Root,
+    readonly selector: StateObjectSelector,
+    readonly targetManager: TargetManager,
+    readonly mvsDependencyRefs: Set<string>,
+}
+export const UpdateTarget = {
+    /** Create a new update, with `selector` pointing to the root. */
+    create(plugin: PluginContext, replaceExisting: boolean): UpdateTarget {
+        const update = plugin.build();
+        const msTarget = update.toRoot().selector;
+        return { update, selector: msTarget, targetManager: new TargetManager(plugin, replaceExisting), mvsDependencyRefs: new Set() };
+    },
+    /** Add a child node to `target.selector`, return a new `UpdateTarget` pointing to the new child. */
+    apply<A extends StateObject, B extends StateObject, P extends {}>(target: UpdateTarget, transformer: StateTransformer<A, B, P>, params?: Partial<P>, options?: Partial<StateTransform.Options>): UpdateTarget {
+        let refSuffix: string = transformer.id;
+        if (transformer.id === StructureRepresentation3D.id) {
+            const reprType = (params as any)?.type?.name ?? '';
+            refSuffix += `:${reprType}`;
+        }
+        const ref = target.targetManager.getChildRef(target.selector, refSuffix);
+        const msResult = target.update.to(target.selector).apply(transformer, params, { ...options, ref }).selector;
+        const result: UpdateTarget = { ...target, selector: msResult, mvsDependencyRefs: new Set() };
+        target.targetManager.allTargets.push(result);
+        return result;
+    },
+    setMvsDependencies(target: UpdateTarget, refs: string[] | Set<string>): UpdateTarget {
+        refs.forEach(ref => target.mvsDependencyRefs.add(ref));
+        return target;
+    },
+    dependsOn(target: UpdateTarget, mapping: Map<string, string>): UpdateTarget {
+        if (!target.mvsDependencyRefs.size) return target;
+        const dependsOn = Array.from(target.mvsDependencyRefs).map(d => mapping.get(d)!).filter(d => d);
+        if (!dependsOn.length) return target;
+        target.update.to(target.selector).dependsOn(dependsOn);
+        return target;
+    },
+    /** Add tags to `target.selector` */
+    tag(target: UpdateTarget, tags: string[]): UpdateTarget {
+        if (tags.length > 0) {
+            target.update.to(target.selector).tag(tags);
+        }
+        return target;
+    },
+    /** Delete all children of `target.selector`. */
+    deleteChildren(target: UpdateTarget): UpdateTarget {
+        const children = target.update.currentTree.children.get(target.selector.ref);
+        children.forEach(child => target.update.delete(child));
+        return target;
+    },
+    /** Commit all changes done in the current update. */
+    commit(target: UpdateTarget): Promise<void> {
+        return target.update.commit();
+    },
+};
+
+/** Manages transform refs in a deterministic way. Uses refs like !mvs:3ce3664304d32c5d:0 */
+class TargetManager {
+    /** For each hash (e.g. 3ce3664304d32c5d), store the number of already used refs with that hash. */
+    private _counter: Record<string, number> = {};
+    constructor(plugin: PluginContext, replaceExisting: boolean) {
+        if (!replaceExisting) {
+            plugin.state.data.cells.forEach(cell => {
+                const ref = cell.transform.ref;
+                if (ref.startsWith('!mvs:')) {
+                    const [_, hash, idNumber] = ref.split(':');
+                    const nextIdNumber = parseInt(idNumber) + 1;
+                    if (nextIdNumber > (this._counter[hash] ?? 0)) {
+                        this._counter[hash] = nextIdNumber;
+                    }
+                }
+            });
+        }
+    }
+    /** Return ref for a new node with given `hash`; update the counter accordingly. */
+    private nextRef(hash: string): string {
+        this._counter[hash] ??= 0;
+        const idNumber = this._counter[hash]++;
+        return `!mvs:${hash}:${idNumber}`;
+    }
+    /** Return ref for a new node based on parent and desired suffix. */
+    getChildRef(parent: StateObjectSelector, suffix: string): string {
+        const hashBase = parent.ref.replace(/^!mvs:/, '') + ':' + suffix;
+        const hash = stringHash(hashBase);
+        const result = this.nextRef(hash);
+        return result;
+    }
+
+    readonly allTargets: UpdateTarget[] = [];
+}
+
+/** Create node tags based of MVS node.ref */
+export function mvsRefTags(mvsNodeRef: string | undefined): string[] {
+    if (mvsNodeRef === undefined) return [];
+    else return [`mvs-ref:${mvsNodeRef}`];
+}

src/extensions/mvs/load-helpers.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -8,8 +8,7 @@ import { Mat3, Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { StructureComponentParams } from '../../mol-plugin-state/helpers/structure-component';
 import { StructureFromModel, TransformStructureConformation } from '../../mol-plugin-state/transforms/model';
 import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
-import { PluginContext } from '../../mol-plugin/context';
-import { StateBuilder, StateObject, StateObjectSelector, StateTransform, StateTransformer } from '../../mol-state';
+import { StateTransformer } from '../../mol-state';
 import { arrayDistinct } from '../../mol-util/array';
 import { canonicalJsonString } from '../../mol-util/json';
 import { stringToWords } from '../../mol-util/string';
@@ -25,124 +24,12 @@ import { SelectorAll } from './components/selector';
 import { rowToExpression, rowsToExpression } from './helpers/selections';
 import { ElementOfSet, decodeColor, isDefined, stringHash } from './helpers/utils';
 import { MolstarLoadingContext } from './load';
-import { Kind, ParamsOfKind, SubTree, SubTreeOfKind, Tree, getChildren } from './tree/generic/tree-schema';
+import { Subtree, getChildren } from './tree/generic/tree-schema';
 import { dfs, formatObject } from './tree/generic/tree-utils';
-import { MolstarKind, MolstarNode, MolstarTree } from './tree/molstar/molstar-tree';
+import { MolstarKind, MolstarNode, MolstarSubtree, MolstarTree, MolstarNodeParams } from './tree/molstar/molstar-tree';
 import { DefaultColor } from './tree/mvs/mvs-defaults';
 
 
-/** Function responsible for loading a tree node `node` into Mol*.
- * Should apply changes within `updateParent.update` but not commit them.
- * Should modify `context` accordingly, if it is needed for loading other nodes later.
- * `updateParent.selector` is the result of loading the node's parent into Mol* state hierarchy (or the hierarchy root in case of root node). */
-export type LoadingAction<TNode extends Tree, TContext> = (updateParent: UpdateTarget, node: TNode, context: TContext) => UpdateTarget | undefined
-
-/** Loading actions for loading a tree into Mol*, per node kind. */
-export type LoadingActions<TTree extends Tree, TContext> = { [kind in Kind<SubTree<TTree>>]?: LoadingAction<SubTreeOfKind<TTree, kind>, TContext> }
-
-/** Load a tree into Mol*, by applying loading actions in DFS order and then commiting at once.
- * If `options.replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state. */
-export async function loadTree<TTree extends Tree, TContext>(plugin: PluginContext, tree: TTree, loadingActions: LoadingActions<TTree, TContext>, context: TContext, options?: { replaceExisting?: boolean }) {
-    const mapping = new Map<SubTree<TTree>, UpdateTarget | undefined>();
-    const updateRoot: UpdateTarget = UpdateTarget.create(plugin, options?.replaceExisting ?? false);
-    if (options?.replaceExisting) {
-        UpdateTarget.deleteChildren(updateRoot);
-    }
-    dfs<TTree>(tree, (node, parent) => {
-        const kind: Kind<typeof node> = node.kind;
-        const action = loadingActions[kind] as LoadingAction<typeof node, TContext> | undefined;
-        if (action) {
-            const updateParent = parent ? mapping.get(parent) : updateRoot;
-            if (updateParent) {
-                const msNode = action(updateParent, node, context);
-                mapping.set(node, msNode);
-            } else {
-                console.warn(`No target found for this "${node.kind}" node`);
-                return;
-            }
-        }
-    });
-    await UpdateTarget.commit(updateRoot);
-}
-
-
-/** A wrapper for updating Mol* state, while using deterministic transform refs.
- * ```
- * updateTarget = UpdateTarget.create(plugin); // like update = plugin.build();
- * UpdateTarget.apply(updateTarget, transformer, params); // like update.to(selector).apply(transformer, params);
- * await UpdateTarget.commit(updateTarget); // like await update.commit();
- * ```
- */
-export interface UpdateTarget {
-    readonly update: StateBuilder.Root,
-    readonly selector: StateObjectSelector,
-    readonly refManager: RefManager,
-}
-export const UpdateTarget = {
-    /** Create a new update, with `selector` pointing to the root. */
-    create(plugin: PluginContext, replaceExisting: boolean): UpdateTarget {
-        const update = plugin.build();
-        const msTarget = update.toRoot().selector;
-        const refManager = new RefManager(plugin, replaceExisting);
-        return { update, selector: msTarget, refManager };
-    },
-    /** Add a child node to `target.selector`, return a new `UpdateTarget` pointing to the new child. */
-    apply<A extends StateObject, B extends StateObject, P extends {}>(target: UpdateTarget, transformer: StateTransformer<A, B, P>, params?: Partial<P>, options?: Partial<StateTransform.Options>): UpdateTarget {
-        let refSuffix: string = transformer.id;
-        if (transformer.id === StructureRepresentation3D.id) {
-            const reprType = (params as any)?.type?.name ?? '';
-            refSuffix += `:${reprType}`;
-        }
-        const ref = target.refManager.getChildRef(target.selector, refSuffix);
-        const msResult = target.update.to(target.selector).apply(transformer, params, { ...options, ref }).selector;
-        return { ...target, selector: msResult };
-    },
-    /** Delete all children of `target.selector`. */
-    deleteChildren(target: UpdateTarget): UpdateTarget {
-        const children = target.update.currentTree.children.get(target.selector.ref);
-        children.forEach(child => target.update.delete(child));
-        return target;
-    },
-    /** Commit all changes done in the current update. */
-    commit(target: UpdateTarget): Promise<void> {
-        return target.update.commit();
-    },
-};
-
-/** Manages transform refs in a deterministic way. Uses refs like !mvs:3ce3664304d32c5d:0 */
-class RefManager {
-    /** For each hash (e.g. 3ce3664304d32c5d), store the number of already used refs with that hash. */
-    private _counter: Record<string, number> = {};
-    constructor(plugin: PluginContext, replaceExisting: boolean) {
-        if (!replaceExisting) {
-            plugin.state.data.cells.forEach(cell => {
-                const ref = cell.transform.ref;
-                if (ref.startsWith('!mvs:')) {
-                    const [_, hash, idNumber] = ref.split(':');
-                    const nextIdNumber = parseInt(idNumber) + 1;
-                    if (nextIdNumber > (this._counter[hash] ?? 0)) {
-                        this._counter[hash] = nextIdNumber;
-                    }
-                }
-            });
-        }
-    }
-    /** Return ref for a new node with given `hash`; update the counter accordingly. */
-    private nextRef(hash: string): string {
-        this._counter[hash] ??= 0;
-        const idNumber = this._counter[hash]++;
-        return `!mvs:${hash}:${idNumber}`;
-    }
-    /** Return ref for a new node based on parent and desired suffix. */
-    getChildRef(parent: StateObjectSelector, suffix: string): string {
-        const hashBase = parent.ref.replace(/^!mvs:/, '') + ':' + suffix;
-        const hash = stringHash(hashBase);
-        const result = this.nextRef(hash);
-        return result;
-    }
-}
-
-
 export const AnnotationFromUriKinds = new Set(['color_from_uri', 'component_from_uri', 'label_from_uri', 'tooltip_from_uri'] satisfies MolstarKind[]);
 export type AnnotationFromUriKind = ElementOfSet<typeof AnnotationFromUriKinds>
 
@@ -184,7 +71,7 @@ const _tmpVecY = Vec3();
 const _tmpVecZ = Vec3();
 
 /** Create an array of props for `TransformStructureConformation` transformers from all 'transform' nodes applied to a 'structure' node. */
-export function transformProps(node: SubTreeOfKind<MolstarTree, 'structure'>): StateTransformer.Params<TransformStructureConformation>[] {
+export function transformProps(node: MolstarSubtree<'structure'>): StateTransformer.Params<TransformStructureConformation>[] {
     const result = [] as StateTransformer.Params<TransformStructureConformation>[];
     const transforms = getChildren(node).filter(c => c.kind === 'transform') as MolstarNode<'transform'>[];
     for (const transform of transforms) {
@@ -196,7 +83,7 @@ export function transformProps(node: SubTreeOfKind<MolstarTree, 'structure'>): S
 }
 
 /** Collect distinct annotation specs from all nodes in `tree` and set `context.annotationMap[node]` to respective annotationIds */
-export function collectAnnotationReferences(tree: SubTree<MolstarTree>, context: MolstarLoadingContext): MVSAnnotationSpec[] {
+export function collectAnnotationReferences(tree: Subtree<MolstarTree>, context: MolstarLoadingContext): MVSAnnotationSpec[] {
     const distinctSpecs: { [key: string]: MVSAnnotationSpec } = {};
     dfs(tree, node => {
         let spec: Omit<MVSAnnotationSpec, 'id'> | undefined = undefined;
@@ -224,7 +111,7 @@ function blockSpec(header: string | null | undefined, index: number | null | und
 }
 
 /** Collect annotation tooltips from all nodes in `tree` and map them to annotationIds. */
-export function collectAnnotationTooltips(tree: SubTreeOfKind<MolstarTree, 'structure'>, context: MolstarLoadingContext): MVSAnnotationTooltipsProps['tooltips'] {
+export function collectAnnotationTooltips(tree: MolstarSubtree<'structure'>, context: MolstarLoadingContext): MVSAnnotationTooltipsProps['tooltips'] {
     const annotationTooltips: MVSAnnotationTooltipsProps['tooltips'] = [];
     dfs(tree, node => {
         if (node.kind === 'tooltip_from_uri' || node.kind === 'tooltip_from_source') {
@@ -237,7 +124,7 @@ export function collectAnnotationTooltips(tree: SubTreeOfKind<MolstarTree, 'stru
     return arrayDistinct(annotationTooltips);
 }
 /** Collect inline tooltips from all nodes in `tree`. */
-export function collectInlineTooltips(tree: SubTreeOfKind<MolstarTree, 'structure'>, context: MolstarLoadingContext): CustomTooltipsProps['tooltips'] {
+export function collectInlineTooltips(tree: MolstarSubtree<'structure'>, context: MolstarLoadingContext): CustomTooltipsProps['tooltips'] {
     const inlineTooltips: CustomTooltipsProps['tooltips'] = [];
     dfs(tree, (node, parent) => {
         if (node.kind === 'tooltip') {
@@ -263,7 +150,7 @@ export function collectInlineTooltips(tree: SubTreeOfKind<MolstarTree, 'structur
     return inlineTooltips;
 }
 /** Collect inline labels from all nodes in `tree`. */
-export function collectInlineLabels(tree: SubTreeOfKind<MolstarTree, 'structure'>, context: MolstarLoadingContext): CustomLabelTextProps['items'] {
+export function collectInlineLabels(tree: MolstarSubtree<'structure'>, context: MolstarLoadingContext): CustomLabelTextProps['items'] {
     const inlineLabels: CustomLabelTextProps['items'] = [];
     dfs(tree, (node, parent) => {
         if (node.kind === 'label') {
@@ -300,7 +187,9 @@ export function collectInlineLabels(tree: SubTreeOfKind<MolstarTree, 'structure'
 }
 
 /** Return `true` for components nodes which only serve for tooltip placement (not to be created in the MolStar object hierarchy) */
-export function isPhantomComponent(node: SubTreeOfKind<MolstarTree, 'component' | 'component_from_uri' | 'component_from_source'>) {
+export function isPhantomComponent(node: MolstarSubtree<'component' | 'component_from_uri' | 'component_from_source'>) {
+    if (node.ref !== undefined) return false;
+    if (node.custom !== undefined && Object.keys(node.custom).length > 0) return false;
     return node.children && node.children.every(child => child.kind === 'tooltip' || child.kind === 'label');
     // These nodes could theoretically be removed when converting MVS to Molstar tree, but would get very tricky if we allow nested components
 }
@@ -343,7 +232,7 @@ export function structureProps(node: MolstarNode<'structure'>): StateTransformer
 }
 
 /** Create value for `type` prop for `StructureComponent` transformer based on a MVS selector. */
-export function componentPropsFromSelector(selector?: ParamsOfKind<MolstarTree, 'component'>['selector']): StructureComponentParams['type'] {
+export function componentPropsFromSelector(selector?: MolstarNodeParams<'component'>['selector']): StructureComponentParams['type'] {
     if (selector === undefined) {
         return SelectorAll;
     } else if (typeof selector === 'string') {
@@ -356,7 +245,7 @@ export function componentPropsFromSelector(selector?: ParamsOfKind<MolstarTree,
 }
 
 /** Return a pretty name for a value of selector param, e.g.  "protein" -> 'Protein', {label_asym_id: "A"} -> 'Custom Selection: {label_asym_id: "A"}' */
-export function prettyNameFromSelector(selector?: ParamsOfKind<MolstarTree, 'component'>['selector']): string {
+export function prettyNameFromSelector(selector?: MolstarNodeParams<'component'>['selector']): string {
     if (selector === undefined) {
         return 'All';
     } else if (typeof selector === 'string') {
@@ -392,19 +281,20 @@ export function componentFromXProps(node: MolstarNode<'component_from_uri' | 'co
 }
 
 /** Create props for `StructureRepresentation3D` transformer from a representation node. */
-export function representationProps(params: ParamsOfKind<MolstarTree, 'representation'>): Partial<StateTransformer.Params<StructureRepresentation3D>> {
-    switch (params.type) {
+export function representationProps(node: MolstarSubtree<'representation'>): Partial<StateTransformer.Params<StructureRepresentation3D>> {
+    const alpha = alphaForNode(node);
+    switch (node.params.type) {
         case 'cartoon':
             return {
-                type: { name: 'cartoon', params: {} },
+                type: { name: 'cartoon', params: { alpha } },
             };
         case 'ball_and_stick':
             return {
-                type: { name: 'ball-and-stick', params: { sizeFactor: 0.5, sizeAspectRatio: 0.5 } },
+                type: { name: 'ball-and-stick', params: { sizeFactor: 0.5, sizeAspectRatio: 0.5, alpha } },
             };
         case 'surface':
             return {
-                type: { name: 'molecular-surface', params: {} },
+                type: { name: 'molecular-surface', params: { alpha } },
                 sizeTheme: { name: 'physical', params: { scale: 1 } },
             };
         default:
@@ -412,8 +302,18 @@ export function representationProps(params: ParamsOfKind<MolstarTree, 'represent
     }
 }
 
+/** Create value for `type.params.alpha` prop for `StructureRepresentation3D` transformer from a representation node based on 'transparency' nodes in its subtree. */
+export function alphaForNode(node: MolstarSubtree<'representation'>): number {
+    const children = getChildren(node).filter(c => c.kind === 'transparency');
+    if (children.length > 0) {
+        const transparency = children[children.length - 1].params.transparency;
+        return 1 - transparency;
+    } else {
+        return 1;
+    }
+}
 /** Create value for `colorTheme` prop for `StructureRepresentation3D` transformer from a representation node based on color* nodes in its subtree. */
-export function colorThemeForNode(node: SubTreeOfKind<MolstarTree, 'color' | 'color_from_uri' | 'color_from_source' | 'representation'> | undefined, context: MolstarLoadingContext): StateTransformer.Params<StructureRepresentation3D>['colorTheme'] {
+export function colorThemeForNode(node: MolstarSubtree<'color' | 'color_from_uri' | 'color_from_source' | 'representation'> | undefined, context: MolstarLoadingContext): StateTransformer.Params<StructureRepresentation3D>['colorTheme'] {
     if (node?.kind === 'representation') {
         const children = getChildren(node).filter(c => c.kind === 'color' || c.kind === 'color_from_uri' || c.kind === 'color_from_source') as MolstarNode<'color' | 'color_from_uri' | 'color_from_source'>[];
         if (children.length === 0) {

src/extensions/mvs/load.ts

@@ -2,11 +2,14 @@
  * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Aliaksei Chareshneu <chareshneu.tech@gmail.com>
  */
 
 import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
 import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif, TrajectoryFromPDB, TransformStructureConformation } from '../../mol-plugin-state/transforms/model';
-import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { ShapeRepresentation3D, StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
 import { MolViewSpec } from './behavior';
@@ -17,11 +20,14 @@ import { MVSAnnotationTooltipsProvider } from './components/annotation-tooltips-
 import { CustomLabelProps, CustomLabelRepresentationProvider } from './components/custom-label/representation';
 import { CustomTooltipsProvider } from './components/custom-tooltips-prop';
 import { IsMVSModelProps, IsMVSModelProvider } from './components/is-mvs-model-prop';
-import { AnnotationFromSourceKind, AnnotationFromUriKind, LoadingActions, UpdateTarget, collectAnnotationReferences, collectAnnotationTooltips, collectInlineLabels, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, loadTree, makeNearestReprMap, prettyNameFromSelector, representationProps, structureProps, transformProps } from './load-helpers';
+import { getPrimitiveStructureRefs, MVSBuildPrimitiveShape, MVSDownloadPrimitiveData, MVSInlinePrimitiveData } from './components/primitives';
+import { NonCovalentInteractionsExtension } from './load-extensions/non-covalent-interactions';
+import { LoadingActions, LoadingExtension, loadTree, UpdateTarget } from './load-generic';
+import { AnnotationFromSourceKind, AnnotationFromUriKind, collectAnnotationReferences, collectAnnotationTooltips, collectInlineLabels, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, makeNearestReprMap, prettyNameFromSelector, representationProps, structureProps, transformProps } from './load-helpers';
 import { MVSData } from './mvs-data';
-import { ParamsOfKind, SubTreeOfKind, validateTree } from './tree/generic/tree-schema';
+import { validateTree } from './tree/generic/tree-schema';
 import { convertMvsToMolstar, mvsSanityCheck } from './tree/molstar/conversion';
-import { MolstarNode, MolstarTree, MolstarTreeSchema } from './tree/molstar/molstar-tree';
+import { MolstarNode, MolstarNodeParams, MolstarSubtree, MolstarTree, MolstarTreeSchema } from './tree/molstar/molstar-tree';
 import { MVSTreeSchema } from './tree/mvs/mvs-tree';
 
 
@@ -29,32 +35,46 @@ import { MVSTreeSchema } from './tree/mvs/mvs-tree';
  * If `options.replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state.
  * If `options.keepCamera`, ignore any camera positioning from the MVS state and keep the current camera position instead.
  * If `options.sanityChecks`, run some sanity checks and print potential issues to the console.
+ * If `options.extensions` is provided, apply specified set of MVS-loading extensions (not a part of standard MVS specification); default: apply all builtin extensions; use `extensions: []` to avoid applying builtin extensions.
  * `options.sourceUrl` serves as the base for resolving relative URLs/URIs and may itself be relative to the window URL. */
-export async function loadMVS(plugin: PluginContext, data: MVSData, options: { replaceExisting?: boolean, keepCamera?: boolean, sanityChecks?: boolean, sourceUrl?: string } = {}) {
+export async function loadMVS(plugin: PluginContext, data: MVSData, options: { replaceExisting?: boolean, keepCamera?: boolean, extensions?: MolstarLoadingExtension<any>[], sanityChecks?: boolean, sourceUrl?: string, doNotReportErrors?: boolean } = {}) {
+    plugin.errorContext.clear('mvs');
     try {
         // console.log(`MVS tree:\n${MVSData.toPrettyString(data)}`)
         validateTree(MVSTreeSchema, data.root, 'MVS');
         if (options.sanityChecks) mvsSanityCheck(data.root);
         const molstarTree = convertMvsToMolstar(data.root, options.sourceUrl);
-        // console.log(`Converted MolStar tree:\n${MVSData.toPrettyString({ root: molstarTree, metadata: { version: 'x', timestamp: 'x' } })}`)
+        // console.log(`Converted MolStar tree:\n${MVSData.toPrettyString({ root: molstarTree as any, metadata: { version: 'x', timestamp: 'x' } })}`)
         validateTree(MolstarTreeSchema, molstarTree, 'Converted Molstar');
         await loadMolstarTree(plugin, molstarTree, options);
     } catch (err) {
         plugin.log.error(`${err}`);
         throw err;
+    } finally {
+        if (!options.doNotReportErrors) {
+            for (const error of plugin.errorContext.get('mvs')) {
+                plugin.log.warn(error);
+                PluginCommands.Toast.Show(plugin, {
+                    title: 'Error',
+                    message: error,
+                    timeoutMs: 10000
+                });
+            }
+        }
+        plugin.errorContext.clear('mvs');
     }
 }
 
 
 /** Load a `MolstarTree` into the Mol* plugin.
  * If `replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state. */
-async function loadMolstarTree(plugin: PluginContext, tree: MolstarTree, options?: { replaceExisting?: boolean, keepCamera?: boolean }) {
+async function loadMolstarTree(plugin: PluginContext, tree: MolstarTree, options?: { replaceExisting?: boolean, keepCamera?: boolean, extensions?: MolstarLoadingExtension<any>[] }) {
     const mvsExtensionLoaded = plugin.state.hasBehavior(MolViewSpec);
     if (!mvsExtensionLoaded) throw new Error('MolViewSpec extension is not loaded.');
 
     const context: MolstarLoadingContext = {};
 
-    await loadTree(plugin, tree, MolstarLoadingActions, context, options);
+    await loadTree(plugin, tree, MolstarLoadingActions, context, { ...options, extensions: options?.extensions ?? BuiltinLoadingExtensions });
 
     setCanvas(plugin, context.canvas);
 
@@ -77,8 +97,8 @@ export interface MolstarLoadingContext {
     annotationMap?: Map<MolstarNode<AnnotationFromUriKind | AnnotationFromSourceKind>, string>,
     /** Maps each node (on 'structure' or lower level) to its nearest 'representation' node */
     nearestReprMap?: Map<MolstarNode, MolstarNode<'representation'>>,
-    focus?: { kind: 'camera', params: ParamsOfKind<MolstarTree, 'camera'> } | { kind: 'focus', focusTarget: StateObjectSelector, params: ParamsOfKind<MolstarTree, 'focus'> },
-    canvas?: ParamsOfKind<MolstarTree, 'canvas'>,
+    focus?: { kind: 'camera', params: MolstarNodeParams<'camera'> } | { kind: 'focus', focusTarget: StateObjectSelector, params: MolstarNodeParams<'focus'> },
+    canvas?: MolstarNodeParams<'canvas'>,
 }
 
 
@@ -119,7 +139,7 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
             return undefined;
         }
     },
-    model(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'model'>, context: MolstarLoadingContext): UpdateTarget {
+    model(updateParent: UpdateTarget, node: MolstarSubtree<'model'>, context: MolstarLoadingContext): UpdateTarget {
         const annotations = collectAnnotationReferences(node, context);
         const model = UpdateTarget.apply(updateParent, ModelFromTrajectory, {
             modelIndex: node.params.model_index,
@@ -136,7 +156,7 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
         });
         return model;
     },
-    structure(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'structure'>, context: MolstarLoadingContext): UpdateTarget {
+    structure(updateParent: UpdateTarget, node: MolstarSubtree<'structure'>, context: MolstarLoadingContext): UpdateTarget {
         const props = structureProps(node);
         const struct = UpdateTarget.apply(updateParent, StructureFromModel, props);
         let transformed = struct;
@@ -173,7 +193,7 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
     tooltip: undefined, // No action needed, already loaded in `structure`
     tooltip_from_uri: undefined, // No action needed, already loaded in `structure`
     tooltip_from_source: undefined, // No action needed, already loaded in `structure`
-    component(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'component'>): UpdateTarget | undefined {
+    component(updateParent: UpdateTarget, node: MolstarSubtree<'component'>): UpdateTarget | undefined {
         if (isPhantomComponent(node)) {
             return updateParent;
         }
@@ -184,19 +204,19 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
             nullIfEmpty: false,
         });
     },
-    component_from_uri(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'component_from_uri'>, context: MolstarLoadingContext): UpdateTarget | undefined {
+    component_from_uri(updateParent: UpdateTarget, node: MolstarSubtree<'component_from_uri'>, context: MolstarLoadingContext): UpdateTarget | undefined {
         if (isPhantomComponent(node)) return undefined;
         const props = componentFromXProps(node, context);
         return UpdateTarget.apply(updateParent, MVSAnnotationStructureComponent, props);
     },
-    component_from_source(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'component_from_source'>, context: MolstarLoadingContext): UpdateTarget | undefined {
+    component_from_source(updateParent: UpdateTarget, node: MolstarSubtree<'component_from_source'>, context: MolstarLoadingContext): UpdateTarget | undefined {
         if (isPhantomComponent(node)) return undefined;
         const props = componentFromXProps(node, context);
         return UpdateTarget.apply(updateParent, MVSAnnotationStructureComponent, props);
     },
     representation(updateParent: UpdateTarget, node: MolstarNode<'representation'>, context: MolstarLoadingContext): UpdateTarget {
         return UpdateTarget.apply(updateParent, StructureRepresentation3D, {
-            ...representationProps(node.params),
+            ...representationProps(node),
             colorTheme: colorThemeForNode(node, context),
         });
     },
@@ -224,4 +244,29 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
         context.canvas = node.params;
         return updateParent;
     },
+    primitives(updateParent: UpdateTarget, tree: MolstarSubtree<'primitives'>, context: MolstarLoadingContext): UpdateTarget {
+        const refs = getPrimitiveStructureRefs(tree);
+        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree });
+        return applyPrimitiveVisuals(data, refs);
+    },
+    primitives_from_uri(updateParent: UpdateTarget, tree: MolstarNode<'primitives_from_uri'>, context: MolstarLoadingContext): UpdateTarget {
+        const data = UpdateTarget.apply(updateParent, MVSDownloadPrimitiveData, { uri: tree.params.uri, format: tree.params.format });
+        return applyPrimitiveVisuals(data, new Set(tree.params.references ?? []));
+    },
 };
+
+function applyPrimitiveVisuals(data: UpdateTarget, refs: Set<string>) {
+    const mesh = UpdateTarget.setMvsDependencies(UpdateTarget.apply(data, MVSBuildPrimitiveShape, { kind: 'mesh' }, { state: { isGhost: true } }), refs);
+    UpdateTarget.apply(mesh, ShapeRepresentation3D);
+    const labels = UpdateTarget.setMvsDependencies(UpdateTarget.apply(data, MVSBuildPrimitiveShape, { kind: 'labels' }, { state: { isGhost: true } }), refs);
+    UpdateTarget.apply(labels, ShapeRepresentation3D);
+    const lines = UpdateTarget.setMvsDependencies(UpdateTarget.apply(data, MVSBuildPrimitiveShape, { kind: 'lines' }, { state: { isGhost: true } }), refs);
+    UpdateTarget.apply(lines, ShapeRepresentation3D);
+    return data;
+}
+
+export type MolstarLoadingExtension<TExtensionContext> = LoadingExtension<MolstarTree, MolstarLoadingContext, TExtensionContext>;
+
+export const BuiltinLoadingExtensions: MolstarLoadingExtension<any>[] = [
+    NonCovalentInteractionsExtension,
+];

src/extensions/mvs/tree/generic/params-schema.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import * as iots from 'io-ts';
@@ -28,6 +29,11 @@ export const tuple = iots.tuple;
 export const list = iots.array;
 /** Type definition for union types, e.g. `union([str, int])` means string or integer  */
 export const union = iots.union;
+/** Type definition used to create objects */
+export const obj = iots.type;
+/** Type definition used to create partial objects */
+export const partial = iots.partial;
+
 /** Type definition for nullable types, e.g. `nullable(str)` means string or `null`  */
 export function nullable<T extends iots.Type<any>>(type: T) {
     return union([type, iots.null]);
@@ -45,6 +51,10 @@ export function literal<V extends string | number | boolean>(...values: V[]) {
         value => value
     );
 }
+/** Mapping between two types */
+export function mapping<A extends iots.Type<any>, B extends iots.Type<any>>(from: A, to: B) {
+    return iots.record(from, to);
+}
 
 
 /** Schema for one field in params (i.e. a value in a top-level key-value pair) */
@@ -122,6 +132,13 @@ export function paramsValidationIssues<P extends ParamsSchema, V extends { [k: s
     if (!isPlainObject(values)) return [`Parameters must be an object, not ${values}`];
     for (const key in schema) {
         const paramDef = schema[key];
+
+        // Special handling of "union" param type
+        // TODO: figure out how to do this properly, ignoring the validation for now
+        if (key === '_union_') {
+            return undefined;
+        }
+
         if (Object.hasOwn(values, key)) {
             const value = values[key];
             const issues = fieldValidationIssues(paramDef, value);

src/extensions/mvs/tree/generic/tree-schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -10,15 +10,22 @@ import { AllRequired, DefaultsFor, ParamsSchema, ValuesFor, paramsValidationIssu
 import { treeToString } from './tree-utils';
 
 
+/** Type of "custom" of a tree node (key-value storage with arbitrary JSONable values) */
+export type CustomProps = Partial<Record<string, any>>
+
 /** Tree node without children */
 export type Node<TKind extends string = string, TParams extends {} = {}> =
     {} extends TParams ? {
         kind: TKind,
-        params?: TParams,
+        params?: TParams, // params can be dropped if {} is valid value for params
+        custom?: CustomProps,
+        ref?: string,
     } : {
         kind: TKind,
-        params: TParams,
-    } // params can be dropped if {} is valid value for params
+        params: TParams, // params must be here if {} is not valid value for params
+        custom?: CustomProps,
+        ref?: string,
+    }
 
 /** Kind type for a tree node */
 export type Kind<TNode extends Node> = TNode['kind']
@@ -34,23 +41,27 @@ export type Tree<TNode extends Node<string, {}> = Node<string, {}>, TRoot extend
     }
 
 /** Type of any subtree that can occur within given `TTree` tree type */
-export type SubTree<TTree extends Tree> = NonNullable<TTree['children']>[number]
+export type Subtree<TTree extends Tree> = NonNullable<TTree['children']>[number]
 
 /** Type of any subtree that can occur within given `TTree` tree type and has kind type `TKind` */
-export type SubTreeOfKind<TTree extends Tree, TKind extends Kind<SubTree<TTree>> = Kind<SubTree<TTree>>> = RootOfKind<SubTree<TTree>, TKind>
+export type SubtreeOfKind<TTree extends Tree, TKind extends Kind<Subtree<TTree>> = Kind<Subtree<TTree>>> = RootOfKind<Subtree<TTree>, TKind>
 
 type RootOfKind<TTree extends Tree, TKind extends Kind<TTree>> = Extract<TTree, Tree<any, Node<TKind>>>
 
 /** Params type for a given kind type within a tree */
-export type ParamsOfKind<TTree extends Tree, TKind extends Kind<SubTree<TTree>> = Kind<SubTree<TTree>>> = NonNullable<SubTreeOfKind<TTree, TKind>['params']>
+export type ParamsOfKind<TTree extends Tree, TKind extends Kind<Subtree<TTree>> = Kind<Subtree<TTree>>> = NonNullable<SubtreeOfKind<TTree, TKind>['params']>
 
 
 /** Get params from a tree node */
 export function getParams<TNode extends Node>(node: TNode): Params<TNode> {
     return node.params ?? {};
 }
+/** Get custom properties from a tree node */
+export function getCustomProps<TCustomProps extends CustomProps = CustomProps>(node: Node): TCustomProps {
+    return (node.custom ?? {}) as TCustomProps;
+}
 /** Get children from a tree node */
-export function getChildren<TTree extends Tree>(tree: TTree): SubTree<TTree>[] {
+export function getChildren<TTree extends Tree>(tree: TTree): Subtree<TTree>[] {
     return tree.children ?? [];
 }
 
@@ -123,6 +134,9 @@ export function treeValidationIssues(schema: TreeSchema, tree: Tree, options: {
     }
     const issues = paramsValidationIssues(nodeSchema.params, getParams(tree), options);
     if (issues) return [`Invalid parameters for node of kind "${tree.kind}":`, ...issues.map(s => '  ' + s)];
+    if (tree.custom !== undefined && (typeof tree.custom !== 'object' || tree.custom === null)) {
+        return [`Invalid "custom" for node of kind "${tree.kind}": must be an object, not ${tree.custom}.`];
+    }
     for (const child of getChildren(tree)) {
         const issues = treeValidationIssues(schema, child, { ...options, anyRoot: true, parent: tree.kind });
         if (issues) return issues;

src/extensions/mvs/tree/generic/tree-utils.ts

@@ -1,23 +1,23 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { canonicalJsonString } from '../../../../mol-util/json';
-import { DefaultsForTree, Kind, SubTree, SubTreeOfKind, Tree, TreeFor, TreeSchema, TreeSchemaWithAllRequired, getParams } from './tree-schema';
+import { CustomProps, DefaultsForTree, Kind, Node, Subtree, SubtreeOfKind, Tree, TreeFor, TreeSchema, TreeSchemaWithAllRequired, getParams } from './tree-schema';
 
 
 /** Run DFS (depth-first search) algorithm on a rooted tree.
  * Runs `visit` function when a node is discovered (before visiting any descendants).
  * Runs `postVisit` function when leaving a node (after all descendants have been visited). */
-export function dfs<TTree extends Tree>(root: TTree, visit?: (node: SubTree<TTree>, parent?: SubTree<TTree>) => any, postVisit?: (node: SubTree<TTree>, parent?: SubTree<TTree>) => any) {
-    return _dfs<SubTree<TTree>>(root, undefined, visit, postVisit);
+export function dfs<TTree extends Tree>(root: TTree, visit?: (node: Subtree<TTree>, parent?: Subtree<TTree>) => any, postVisit?: (node: Subtree<TTree>, parent?: Subtree<TTree>) => any) {
+    return _dfs<Subtree<TTree>>(root, undefined, visit, postVisit);
 }
-function _dfs<TTree extends Tree>(root: TTree, parent: SubTree<TTree> | undefined, visit?: (node: SubTree<TTree>, parent?: SubTree<TTree>) => any, postVisit?: (node: SubTree<TTree>, parent?: SubTree<TTree>) => any) {
+function _dfs<TTree extends Tree>(root: TTree, parent: Subtree<TTree> | undefined, visit?: (node: Subtree<TTree>, parent?: Subtree<TTree>) => any, postVisit?: (node: Subtree<TTree>, parent?: Subtree<TTree>) => any) {
     if (visit) visit(root, parent);
     for (const child of root.children ?? []) {
-        _dfs<SubTree<TTree>>(child, root, visit, postVisit);
+        _dfs<Subtree<TTree>>(child, root, visit, postVisit);
     }
     if (postVisit) postVisit(root, parent);
 }
@@ -26,9 +26,12 @@ function _dfs<TTree extends Tree>(root: TTree, parent: SubTree<TTree> | undefine
 export function treeToString(tree: Tree) {
     let level = 0;
     const lines: string[] = [];
-    dfs(tree, node => lines.push('  '.repeat(level++) + `- ${node.kind} ${formatObject(node.params ?? {})}`), node => level--);
+    dfs(tree, node => lines.push('  '.repeat(level++) + nodeToString(node)), node => level--);
     return lines.join('\n');
 }
+function nodeToString(node: Node) {
+    return `- ${node.kind} ${formatObject(node.params ?? {})}${formatCustomProps(node.custom)}${formatRef(node.ref)}`;
+}
 
 /** Convert object to a human-friendly string (similar to JSON.stringify but without quoting keys) */
 export function formatObject(obj: {} | undefined): string {
@@ -36,12 +39,26 @@ export function formatObject(obj: {} | undefined): string {
     return JSON.stringify(obj).replace(/,("\w+":)/g, ', $1').replace(/"(\w+)":/g, '$1: ');
 }
 
+/** Return human-friendly string with node custom properties, if any */
+function formatCustomProps(customProps: CustomProps | undefined): string {
+    if (!customProps || Object.keys(customProps).length === 0) return '';
+    return `, custom: ${formatObject(customProps)}`;
+}
+
+/** Return human-friendly string with node ref, if any */
+function formatRef(ref: string | undefined): string {
+    if (ref === undefined) return '';
+    return `, ref: "${ref}"`;
+}
+
 
 /** Create a copy of a tree node, ignoring children. */
 export function copyNodeWithoutChildren<TTree extends Tree>(node: TTree): TTree {
     return {
         kind: node.kind,
         params: node.params ? { ...node.params } : undefined,
+        custom: node.custom ? { ...node.custom } : undefined,
+        ref: node.ref,
     } as TTree;
 }
 /** Create a copy of a tree node, including a shallow copy of children. */
@@ -49,6 +66,8 @@ export function copyNode<TTree extends Tree>(node: TTree): TTree {
     return {
         kind: node.kind,
         params: node.params ? { ...node.params } : undefined,
+        custom: node.custom ? { ...node.custom } : undefined,
+        ref: node.ref,
         children: node.children ? [...node.children] : undefined,
     } as TTree;
 }
@@ -66,15 +85,15 @@ export function copyTree<T extends Tree>(root: T): T {
  * nodes of kind `C` will be converted to `Y` with a child `Z` (original children moved to `Z`),
  * nodes of other kinds will just be copied. */
 export type ConversionRules<A extends Tree, B extends Tree> = {
-    [kind in Kind<SubTree<A>>]?: (node: SubTreeOfKind<A, kind>, parent?: SubTree<A>) => SubTree<B>[]
+    [kind in Kind<Subtree<A>>]?: (node: SubtreeOfKind<A, kind>, parent?: Subtree<A>) => Subtree<B>[]
 };
 
 /** Apply a set of conversion rules to a tree to change to a different schema. */
-export function convertTree<A extends Tree, B extends Tree>(root: A, conversions: ConversionRules<A, B>): SubTree<B> {
-    const mapping = new Map<SubTree<A>, SubTree<B>>();
-    let convertedRoot: SubTree<B>;
+export function convertTree<A extends Tree, B extends Tree>(root: A, conversions: ConversionRules<A, B>): Subtree<B> {
+    const mapping = new Map<Subtree<A>, Subtree<B>>();
+    let convertedRoot: Subtree<B>;
     dfs<A>(root, (node, parent) => {
-        const conversion = conversions[node.kind as (typeof node)['kind']] as ((n: typeof node, p?: SubTree<A>) => SubTree<B>[]) | undefined;
+        const conversion = conversions[node.kind as (typeof node)['kind']] as ((n: typeof node, p?: Subtree<A>) => Subtree<B>[]) | undefined;
         if (conversion) {
             const convertidos = conversion(node, parent);
             if (!parent && convertidos.length === 0) throw new Error('Cannot convert root to empty path');
@@ -104,13 +123,13 @@ export function convertTree<A extends Tree, B extends Tree>(root: A, conversions
 /** Create a copy of the tree where twins (siblings of the same kind with the same params) are merged into one node.
  * Applies only to the node kinds listed in `condenseNodes` (or all if undefined) except node kinds in `skipNodes`. */
 export function condenseTree<T extends Tree>(root: T, condenseNodes?: Set<Kind<Tree>>, skipNodes?: Set<Kind<Tree>>): T {
-    const map = new Map<string, SubTree<T>>();
+    const map = new Map<string, Subtree<T>>();
     const result = copyTree(root);
     dfs<T>(result, node => {
         map.clear();
-        const newChildren: SubTree<T>[] = [];
+        const newChildren: Subtree<T>[] = [];
         for (const child of node.children ?? []) {
-            let twin: SubTree<T> | undefined = undefined;
+            let twin: Subtree<T> | undefined = undefined;
             const doApply = (!condenseNodes || condenseNodes.has(child.kind)) && !skipNodes?.has(child.kind);
             if (doApply) {
                 const key = child.kind + canonicalJsonString(getParams(child));
@@ -120,7 +139,7 @@ export function condenseTree<T extends Tree>(root: T, condenseNodes?: Set<Kind<T
             if (twin) {
                 (twin.children ??= []).push(...child.children ?? []);
             } else {
-                newChildren.push(child as SubTree<T>);
+                newChildren.push(child as Subtree<T>);
             }
         }
         node.children = newChildren;
@@ -132,7 +151,12 @@ export function condenseTree<T extends Tree>(root: T, condenseNodes?: Set<Kind<T
 export function addDefaults<S extends TreeSchema>(tree: TreeFor<S>, defaults: DefaultsForTree<S>): TreeFor<TreeSchemaWithAllRequired<S>> {
     const rules: ConversionRules<TreeFor<S>, TreeFor<S>> = {};
     for (const kind in defaults) {
-        rules[kind] = node => [{ kind: node.kind, params: { ...defaults[kind], ...node.params } } as any];
+        rules[kind] = node => [{
+            kind: node.kind,
+            params: { ...defaults[kind], ...node.params },
+            custom: node.custom,
+            ref: node.ref,
+        } as Node as any];
     }
     return convertTree(tree, rules) as any;
 }

src/extensions/mvs/tree/molstar/conversion.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -26,10 +26,10 @@ const mvsToMolstarConversionRules: ConversionRules<FullMVSTree, MolstarTree> = {
     'download': node => [],
     'parse': (node, parent) => {
         const { format, is_binary } = ParseFormatMvsToMolstar[node.params.format];
-        const convertedNode: MolstarNode<'parse'> = { kind: 'parse', params: { ...node.params, format } };
+        const convertedNode: MolstarNode<'parse'> = { kind: 'parse', params: { ...node.params, format }, custom: node.custom, ref: node.ref };
         if (parent?.kind === 'download') {
             return [
-                { kind: 'download', params: { ...parent.params, is_binary } },
+                { kind: 'download', params: { ...parent.params, is_binary }, custom: parent.custom, ref: parent.ref },
                 convertedNode,
             ] satisfies MolstarNode[];
         } else {
@@ -38,12 +38,12 @@ const mvsToMolstarConversionRules: ConversionRules<FullMVSTree, MolstarTree> = {
         }
     },
     'structure': (node, parent) => {
-        if (parent?.kind !== 'parse') throw new Error('Parent of "structure" must be "parse".');
+        if (parent?.kind !== 'parse') throw new Error(`Parent of "structure" must be "parse", not "${parent?.kind}".`);
         const { format } = ParseFormatMvsToMolstar[parent.params.format];
         return [
             { kind: 'trajectory', params: { format, ...pickObjectKeys(node.params, ['block_header', 'block_index']) } },
             { kind: 'model', params: pickObjectKeys(node.params, ['model_index']) },
-            { kind: 'structure', params: omitObjectKeys(node.params, ['block_header', 'block_index', 'model_index']) },
+            { kind: 'structure', params: omitObjectKeys(node.params, ['block_header', 'block_index', 'model_index']), custom: node.custom, ref: node.ref },
         ] satisfies MolstarNode[];
     },
 };

src/extensions/mvs/tree/molstar/molstar-tree.ts

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { omitObjectKeys, pickObjectKeys } from '../../../../mol-util/object';
 import { RequiredField, bool } from '../generic/params-schema';
-import { NodeFor, TreeFor, TreeSchema } from '../generic/tree-schema';
+import { NodeFor, ParamsOfKind, SubtreeOfKind, TreeFor, TreeSchema } from '../generic/tree-schema';
 import { FullMVSTreeSchema } from '../mvs/mvs-tree';
 import { MolstarParseFormatT } from '../mvs/param-types';
 
@@ -60,5 +60,11 @@ export type MolstarKind = keyof typeof MolstarTreeSchema.nodes;
 /** Node in a `MolstarTree` */
 export type MolstarNode<TKind extends MolstarKind = MolstarKind> = NodeFor<typeof MolstarTreeSchema, TKind>
 
+/** Params for a specific node kind in a `MolstarTree` */
+export type MolstarNodeParams<TKind extends MolstarKind> = ParamsOfKind<MolstarTree, TKind>
+
 /** Intermediate tree representation between `MVSTree` and a real Molstar state */
 export type MolstarTree = TreeFor<typeof MolstarTreeSchema>
+
+/** Any subtree in a `MolstarTree` (e.g. its root doesn't need to be 'root') */
+export type MolstarSubtree<TKind extends MolstarKind = MolstarKind> = SubtreeOfKind<MolstarTree, TKind>

src/extensions/mvs/tree/mvs/mvs-builder.ts

@@ -1,14 +1,14 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { deepClone, pickObjectKeys } from '../../../../mol-util/object';
 import { MVSData } from '../../mvs-data';
-import { ParamsOfKind, SubTreeOfKind } from '../generic/tree-schema';
+import { CustomProps } from '../generic/tree-schema';
 import { MVSDefaults } from './mvs-defaults';
-import { MVSKind, MVSNode, MVSTree, MVSTreeSchema } from './mvs-tree';
+import { MVSKind, MVSNode, MVSSubtree, MVSNodeParams, MVSTreeSchema } from './mvs-tree';
 
 
 /** Create a new MolViewSpec builder containing only a root node. Example of MVS builder usage:
@@ -21,8 +21,8 @@ import { MVSKind, MVSNode, MVSTree, MVSTreeSchema } from './mvs-tree';
  * console.log(JSON.stringify(builder.getState()));
  * ```
  */
-export function createMVSBuilder() {
-    return new Root();
+export function createMVSBuilder(params: CustomAndRef = {}) {
+    return new Root(params);
 }
 
 
@@ -30,15 +30,18 @@ export function createMVSBuilder() {
 class _Base<TKind extends MVSKind> {
     protected constructor(
         protected readonly _root: Root,
-        protected readonly _node: SubTreeOfKind<MVSTree, TKind>,
+        protected readonly _node: MVSSubtree<TKind>,
     ) { }
     /** Create a new node, append as child to current _node, and return the new node */
-    protected addChild<TChildKind extends MVSKind>(kind: TChildKind, params: ParamsOfKind<MVSTree, TChildKind>) {
-        const allowedParamNames = Object.keys(MVSTreeSchema.nodes[kind].params) as (keyof ParamsOfKind<MVSTree, TChildKind>)[];
+    protected addChild<TChildKind extends MVSKind>(kind: TChildKind, params_: MVSNodeParams<TChildKind> & CustomAndRef) {
+        const { params, custom, ref } = splitParams<MVSNodeParams<TChildKind>>(params_);
+        const allowedParamNames = Object.keys(MVSTreeSchema.nodes[kind].params) as (keyof MVSNodeParams<TChildKind>)[];
         const node = {
             kind,
             params: pickObjectKeys(params, allowedParamNames) as unknown,
-        } as SubTreeOfKind<MVSTree, TChildKind>;
+            custom,
+            ref,
+        } as MVSSubtree<TChildKind>;
         this._node.children ??= [];
         this._node.children.push(node);
         return node;
@@ -48,8 +51,9 @@ class _Base<TKind extends MVSKind> {
 
 /** MVS builder pointing to the 'root' node */
 export class Root extends _Base<'root'> {
-    constructor() {
-        const node: MVSNode<'root'> = { kind: 'root' };
+    constructor(params_: CustomAndRef) {
+        const { custom, ref } = params_;
+        const node: MVSNode<'root'> = { kind: 'root', custom, ref };
         super(undefined as any, node);
         (this._root as Root) = this;
     }
@@ -67,17 +71,17 @@ export class Root extends _Base<'root'> {
     // omitting `saveState`, filesystem operations are responsibility of the caller code (platform-dependent)
 
     /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
-    camera(params: ParamsOfKind<MVSTree, 'camera'>): Root {
+    camera(params: MVSNodeParams<'camera'> & CustomAndRef): Root {
         this.addChild('camera', params);
         return this;
     }
     /** Add a 'canvas' node and return builder pointing to the root. 'canvas' node sets canvas properties. */
-    canvas(params: ParamsOfKind<MVSTree, 'canvas'>): Root {
+    canvas(params: MVSNodeParams<'canvas'> & CustomAndRef): Root {
         this.addChild('canvas', params);
         return this;
     }
     /** Add a 'download' node and return builder pointing to it. 'download' node instructs to retrieve a data resource. */
-    download(params: ParamsOfKind<MVSTree, 'download'>): Download {
+    download(params: MVSNodeParams<'download'> & CustomAndRef): Download {
         return new Download(this._root, this.addChild('download', params));
     }
 }
@@ -86,7 +90,7 @@ export class Root extends _Base<'root'> {
 /** MVS builder pointing to a 'download' node */
 export class Download extends _Base<'download'> {
     /** Add a 'parse' node and return builder pointing to it. 'parse' node instructs to parse a data resource. */
-    parse(params: ParamsOfKind<MVSTree, 'parse'>) {
+    parse(params: MVSNodeParams<'parse'> & CustomAndRef) {
         return new Parse(this._root, this.addChild('parse', params));
     }
 }
@@ -98,41 +102,49 @@ const StructureParamsSubsets = {
     assembly: ['block_header', 'block_index', 'model_index', 'assembly_id'],
     symmetry: ['block_header', 'block_index', 'model_index', 'ijk_min', 'ijk_max'],
     symmetry_mates: ['block_header', 'block_index', 'model_index', 'radius'],
-} satisfies { [kind in ParamsOfKind<MVSTree, 'structure'>['type']]: (keyof ParamsOfKind<MVSTree, 'structure'>)[] };
+} satisfies { [kind in MVSNodeParams<'structure'>['type']]: (keyof MVSNodeParams<'structure'>)[] };
 
 
 /** MVS builder pointing to a 'parse' node */
 export class Parse extends _Base<'parse'> {
     /** Add a 'structure' node representing a "model structure", i.e. includes all coordinates from the original model without applying any transformations.
      * Return builder pointing to the new node. */
-    modelStructure(params: Pick<ParamsOfKind<MVSTree, 'structure'>, typeof StructureParamsSubsets['model'][number]> = {}): Structure {
+    modelStructure(params: Pick<MVSNodeParams<'structure'>, typeof StructureParamsSubsets['model'][number]> & CustomAndRef = {}): Structure {
         return new Structure(this._root, this.addChild('structure', {
             type: 'model',
-            ...pickObjectKeys(params, StructureParamsSubsets.model),
+            ...pickObjectKeys(params, [...StructureParamsSubsets.model]),
+            custom: params.custom,
+            ref: params.ref,
         }));
     }
     /** Add a 'structure' node representing an "assembly structure", i.e. may apply filters and symmetry operators to the original model coordinates.
      * Return builder pointing to the new node. */
-    assemblyStructure(params: Pick<ParamsOfKind<MVSTree, 'structure'>, typeof StructureParamsSubsets['assembly'][number]> = {}): Structure {
+    assemblyStructure(params: Pick<MVSNodeParams<'structure'>, typeof StructureParamsSubsets['assembly'][number]> & CustomAndRef = {}): Structure {
         return new Structure(this._root, this.addChild('structure', {
             type: 'assembly',
             ...pickObjectKeys(params, StructureParamsSubsets.assembly),
+            custom: params.custom,
+            ref: params.ref,
         }));
     }
     /** Add a 'structure' node representing a "symmetry structure", i.e. applies symmetry operators to build crystal unit cells within given Miller indices.
      * Return builder pointing to the new node. */
-    symmetryStructure(params: Pick<ParamsOfKind<MVSTree, 'structure'>, typeof StructureParamsSubsets['symmetry'][number]> = {}): Structure {
+    symmetryStructure(params: Pick<MVSNodeParams<'structure'>, typeof StructureParamsSubsets['symmetry'][number]> & CustomAndRef = {}): Structure {
         return new Structure(this._root, this.addChild('structure', {
             type: 'symmetry',
             ...pickObjectKeys(params, StructureParamsSubsets.symmetry),
+            custom: params.custom,
+            ref: params.ref,
         }));
     }
     /** Add a 'structure' node representing a "symmetry mates structure", i.e. applies symmetry operators to build asymmetric units within a radius from the original model.
      * Return builder pointing to the new node. */
-    symmetryMatesStructure(params: Pick<ParamsOfKind<MVSTree, 'structure'>, typeof StructureParamsSubsets['symmetry_mates'][number]> = {}): Structure {
+    symmetryMatesStructure(params: Pick<MVSNodeParams<'structure'>, typeof StructureParamsSubsets['symmetry_mates'][number]> & CustomAndRef = {}): Structure {
         return new Structure(this._root, this.addChild('structure', {
             type: 'symmetry_mates',
             ...pickObjectKeys(params, StructureParamsSubsets.symmetry_mates),
+            custom: params.custom,
+            ref: params.ref,
         }));
     }
 }
@@ -141,40 +153,40 @@ export class Parse extends _Base<'parse'> {
 /** MVS builder pointing to a 'structure' node */
 export class Structure extends _Base<'structure'> {
     /** Add a 'component' node and return builder pointing to it. 'component' node instructs to create a component (i.e. a subset of the parent structure). */
-    component(params: Partial<ParamsOfKind<MVSTree, 'component'>> = {}): Component {
+    component(params: Partial<MVSNodeParams<'component'>> & CustomAndRef = {}): Component {
         const fullParams = { ...params, selector: params.selector ?? MVSDefaults.component.selector };
         return new Component(this._root, this.addChild('component', fullParams));
     }
     /** Add a 'component_from_uri' node and return builder pointing to it. 'component_from_uri' node instructs to create a component defined by an external annotation resource. */
-    componentFromUri(params: ParamsOfKind<MVSTree, 'component_from_uri'>): Component {
+    componentFromUri(params: MVSNodeParams<'component_from_uri'> & CustomAndRef): Component {
         return new Component(this._root, this.addChild('component_from_uri', params));
     }
     /** Add a 'component_from_source' node and return builder pointing to it. 'component_from_source' node instructs to create a component defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file. */
-    componentFromSource(params: ParamsOfKind<MVSTree, 'component_from_source'>): Component {
+    componentFromSource(params: MVSNodeParams<'component_from_source'> & CustomAndRef): Component {
         return new Component(this._root, this.addChild('component_from_source', params));
     }
     /** Add a 'label_from_uri' node and return builder pointing back to the structure node. 'label_from_uri' node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an external annotation resource. */
-    labelFromUri(params: ParamsOfKind<MVSTree, 'label_from_uri'>): Structure {
+    labelFromUri(params: MVSNodeParams<'label_from_uri'> & CustomAndRef): Structure {
         this.addChild('label_from_uri', params);
         return this;
     }
     /** Add a 'label_from_source' node and return builder pointing back to the structure node. 'label_from_source' node instructs to add labels (textual visual representations) to parts of a structure. The labels are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file. */
-    labelFromSource(params: ParamsOfKind<MVSTree, 'label_from_source'>): Structure {
+    labelFromSource(params: MVSNodeParams<'label_from_source'> & CustomAndRef): Structure {
         this.addChild('label_from_source', params);
         return this;
     }
     /** Add a 'tooltip_from_uri' node and return builder pointing back to the structure node. 'tooltip_from_uri' node instructs to add tooltips to parts of a structure. The tooltips are defined by an external annotation resource. */
-    tooltipFromUri(params: ParamsOfKind<MVSTree, 'tooltip_from_uri'>): Structure {
+    tooltipFromUri(params: MVSNodeParams<'tooltip_from_uri'> & CustomAndRef): Structure {
         this.addChild('tooltip_from_uri', params);
         return this;
     }
     /** Add a 'tooltip_from_source' node and return builder pointing back to the structure node. 'tooltip_from_source' node instructs to add tooltips to parts of a structure. The tooltips are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file. */
-    tooltipFromSource(params: ParamsOfKind<MVSTree, 'tooltip_from_source'>): Structure {
+    tooltipFromSource(params: MVSNodeParams<'tooltip_from_source' & CustomAndRef>): Structure {
         this.addChild('tooltip_from_source', params);
         return this;
     }
     /** Add a 'transform' node and return builder pointing back to the structure node. 'transform' node instructs to rotate and/or translate structure coordinates. */
-    transform(params: ParamsOfKind<MVSTree, 'transform'> = {}): Structure {
+    transform(params: MVSNodeParams<'transform'> & CustomAndRef = {}): Structure {
         if (params.rotation && params.rotation.length !== 9) {
             throw new Error('ValueError: `rotation` parameter must be an array of 9 numbers');
         }
@@ -187,22 +199,22 @@ export class Structure extends _Base<'structure'> {
 /** MVS builder pointing to a 'component' or 'component_from_uri' or 'component_from_source' node */
 export class Component extends _Base<'component' | 'component_from_uri' | 'component_from_source'> {
     /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
-    representation(params: Partial<ParamsOfKind<MVSTree, 'representation'>> = {}): Representation {
-        const fullParams: ParamsOfKind<MVSTree, 'representation'> = { ...params, type: params.type ?? 'cartoon' };
+    representation(params: Partial<MVSNodeParams<'representation'>> & CustomAndRef = {}): Representation {
+        const fullParams: MVSNodeParams<'representation'> = { ...params, type: params.type ?? 'cartoon' };
         return new Representation(this._root, this.addChild('representation', fullParams));
     }
     /** Add a 'label' node and return builder pointing back to the component node. 'label' node instructs to add a label (textual visual representation) to a component. */
-    label(params: ParamsOfKind<MVSTree, 'label'>): Component {
+    label(params: MVSNodeParams<'label'> & CustomAndRef): Component {
         this.addChild('label', params);
         return this;
     }
     /** Add a 'tooltip' node and return builder pointing back to the component node. 'tooltip' node instructs to add a text which is not a part of the visualization but should be presented to the users when they interact with the component (typically, the tooltip will be shown somewhere on the screen when the user hovers over a visual representation of the component). */
-    tooltip(params: ParamsOfKind<MVSTree, 'tooltip'>): Component {
+    tooltip(params: MVSNodeParams<'tooltip'> & CustomAndRef): Component {
         this.addChild('tooltip', params);
         return this;
     }
     /** Add a 'focus' node and return builder pointing back to the component node. 'focus' node instructs to set the camera focus to a component (zoom in). */
-    focus(params: ParamsOfKind<MVSTree, 'focus'> = {}): Component {
+    focus(params: MVSNodeParams<'focus'> & CustomAndRef = {}): Component {
         this.addChild('focus', params);
         return this;
     }
@@ -212,17 +224,17 @@ export class Component extends _Base<'component' | 'component_from_uri' | 'compo
 /** MVS builder pointing to a 'representation' node */
 export class Representation extends _Base<'representation'> {
     /** Add a 'color' node and return builder pointing back to the representation node. 'color' node instructs to apply color to a visual representation. */
-    color(params: ParamsOfKind<MVSTree, 'color'>): Representation {
+    color(params: MVSNodeParams<'color'> & CustomAndRef): Representation {
         this.addChild('color', params);
         return this;
     }
     /** Add a 'color_from_uri' node and return builder pointing back to the representation node. 'color_from_uri' node instructs to apply colors to a visual representation. The colors are defined by an external annotation resource. */
-    colorFromUri(params: ParamsOfKind<MVSTree, 'color_from_uri'>): Representation {
+    colorFromUri(params: MVSNodeParams<'color_from_uri'> & CustomAndRef): Representation {
         this.addChild('color_from_uri', params);
         return this;
     }
     /** Add a 'color_from_source' node and return builder pointing back to the representation node. 'color_from_source' node instructs to apply colors to a visual representation. The colors are defined by an annotation resource included in the same file this structure was loaded from. Only applicable if the structure was loaded from an mmCIF or BinaryCIF file. */
-    colorFromSource(params: ParamsOfKind<MVSTree, 'color_from_source'>): Representation {
+    colorFromSource(params: MVSNodeParams<'color_from_source'> & CustomAndRef): Representation {
         this.addChild('color_from_source', params);
         return this;
     }
@@ -235,7 +247,7 @@ export function builderDemo() {
     builder.canvas({ background_color: 'white' });
     const struct = builder.download({ url: 'https://www.ebi.ac.uk/pdbe/entry-files/download/1og2_updated.cif' }).parse({ format: 'mmcif' }).modelStructure();
     struct.component().representation().color({ color: 'white' });
-    struct.component({ selector: 'ligand' }).representation({ type: 'ball_and_stick' })
+    struct.component({ selector: 'ligand' }).representation({ type: 'ball_and_stick', custom: { repr_quality: 'high' }, ref: 'Ligand' })
         .color({ color: '#555555' })
         .color({ selector: { type_symbol: 'N' }, color: '#3050F8' })
         .color({ selector: { type_symbol: 'O' }, color: '#FF0D0D' })
@@ -259,3 +271,13 @@ export function builderDemo() {
 function utcNowISO(): string {
     return new Date().toISOString();
 }
+
+export interface CustomAndRef {
+    custom?: CustomProps,
+    ref?: string,
+};
+
+function splitParams<TParams extends {}>(params_custom_ref: TParams & CustomAndRef): { params: TParams, custom?: CustomProps, ref?: string } {
+    const { custom, ref, ...params } = params_custom_ref;
+    return { params: params as TParams, custom, ref };
+}

src/extensions/mvs/tree/mvs/mvs-defaults.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { DefaultsForTree } from '../generic/tree-schema';
@@ -58,6 +59,8 @@ export const MVSDefaults = {
         category_name: null,
         field_name: 'color',
     },
+    transparency: {
+    },
     label: {
     },
     label_from_uri: {
@@ -99,6 +102,18 @@ export const MVSDefaults = {
     camera: {
         up: [0, 1, 0],
     },
+    primitives: {
+        color: null,
+        label_color: null,
+        tooltip: null,
+        transparency: null,
+        label_transparency: null,
+        instances: null,
+    },
+    primitives_from_uri: {
+        references: null,
+    },
+    primitive: { },
 } satisfies DefaultsForTree<typeof MVSTreeSchema>;
 
 /** Color to be used e.g. for representations without 'color' node */

src/extensions/mvs/tree/mvs/mvs-primitives.ts

@@ -0,0 +1,81 @@
+/**
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { bool, float, int, literal, mapping, nullable, obj, str, union, ValueFor } from '../generic/params-schema';
+import type { MVSNode } from './mvs-tree';
+import { ColorT, FloatList, IntList, PrimitivePositionT, StrList } from './param-types';
+
+// TODO: Figure out validation and default values for these
+
+const _LineBase = {
+    start: PrimitivePositionT,
+    end: PrimitivePositionT,
+    thickness: nullable(float),
+    color: nullable(ColorT),
+    dash_length: nullable(float),
+};
+
+const MeshParams = obj({
+    kind: literal('mesh'),
+    vertices: FloatList,
+    indices: IntList,
+    triangle_colors: nullable(StrList),
+    triangle_groups: nullable(IntList),
+    group_colors: nullable(mapping(int, ColorT)),
+    group_tooltips: nullable(mapping(int, str)),
+    tooltip: nullable(str),
+    show_triangles: nullable(bool),
+    show_wireframe: nullable(bool),
+    color: nullable(ColorT),
+    wireframe_radius: nullable(float),
+    wireframe_color: nullable(ColorT),
+});
+
+const LinesParams = obj({
+    kind: literal('lines'),
+    vertices: FloatList,
+    indices: IntList,
+    line_colors: nullable(StrList),
+    line_groups: nullable(IntList),
+    group_colors: nullable(mapping(int, ColorT)),
+    group_tooltips: nullable(mapping(int, str)),
+    group_radius: nullable(mapping(int, float)),
+    tooltip: nullable(str),
+    color: nullable(ColorT),
+    line_radius: nullable(float),
+});
+
+const LineParams = obj({
+    kind: literal('line'),
+    ..._LineBase,
+    tooltip: nullable(str),
+});
+
+const DistanceMeasurementParams = obj({
+    kind: literal('distance_measurement'),
+    ..._LineBase,
+    label_template: nullable(str),
+    label_size: nullable(union([float, literal('auto')])),
+    label_auto_size_scale: nullable(float),
+    label_auto_size_min: nullable(float),
+    label_color: nullable(ColorT),
+});
+
+const PrimitiveLabelParams = obj({
+    kind: literal('label'),
+    position: PrimitivePositionT,
+    text: str,
+    label_size: nullable(float),
+    label_color: nullable(ColorT),
+    label_offset: nullable(float),
+});
+
+export const MVSPrimitiveParams = union([MeshParams, LinesParams, LineParams, DistanceMeasurementParams, PrimitiveLabelParams]);
+
+export type MVSPrimitive = ValueFor<typeof MVSPrimitiveParams>
+export type MVSPrimitiveKind = MVSPrimitive['kind']
+export type MVSPrimitiveOptions = MVSNode<'primitives'>['params']
+export type MVSPrimitiveParams<T extends MVSPrimitiveKind = MVSPrimitiveKind> = Extract<MVSPrimitive, { kind: T }>

src/extensions/mvs/tree/mvs/mvs-tree.ts

@@ -1,12 +1,14 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { OptionalField, RequiredField, float, int, list, nullable, str, tuple, union } from '../generic/params-schema';
-import { NodeFor, TreeFor, TreeSchema, TreeSchemaWithAllRequired } from '../generic/tree-schema';
-import { ColorT, ComponentExpressionT, ComponentSelectorT, Matrix, ParseFormatT, RepresentationTypeT, SchemaFormatT, SchemaT, StructureTypeT, Vector3 } from './param-types';
+import { float, int, list, literal, nullable, OptionalField, RequiredField, str, tuple, union } from '../generic/params-schema';
+import { NodeFor, ParamsOfKind, SubtreeOfKind, TreeFor, TreeSchema, TreeSchemaWithAllRequired } from '../generic/tree-schema';
+import { MVSPrimitiveParams } from './mvs-primitives';
+import { ColorT, ComponentExpressionT, ComponentSelectorT, Matrix, ParseFormatT, RepresentationTypeT, SchemaFormatT, SchemaT, StrList, StructureTypeT, Vector3 } from './param-types';
 
 
 const _DataFromUriParams = {
@@ -39,7 +41,6 @@ const _DataFromSourceParams = {
     field_name: OptionalField(str, 'Name of the column in CIF or field name (key) in JSON that contains the dependent variable (color/label/tooltip/component_id...).'),
 };
 
-
 /** Schema for `MVSTree` (MolViewSpec tree) */
 export const MVSTreeSchema = TreeSchema({
     rootKind: 'root',
@@ -168,6 +169,15 @@ export const MVSTreeSchema = TreeSchema({
                 ..._DataFromSourceParams,
             },
         },
+        /** This node instructs to apply transparency to a visual representation. */
+        transparency: {
+            description: 'This node instructs to apply transparency to a visual representation.',
+            parent: ['representation'],
+            params: {
+                /** Transparency of the representation. 0.0: fully opaque, 1.0: fully transparent. */
+                transparency: RequiredField(float, 'Color to apply to the representation. Can be either an X11 color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`).'),
+            },
+        },
         /** This node instructs to add a label (textual visual representation) to a component. */
         label: {
             description: 'This node instructs to add a label (textual visual representation) to a component.',
@@ -221,7 +231,7 @@ export const MVSTreeSchema = TreeSchema({
         /** This node instructs to set the camera focus to a component (zoom in). */
         focus: {
             description: 'This node instructs to set the camera focus to a component (zoom in).',
-            parent: ['component', 'component_from_uri', 'component_from_source'],
+            parent: ['component', 'component_from_uri', 'component_from_source', 'primitives', 'primitives_from_uri'],
             params: {
                 /** Vector describing the direction of the view (camera position -> focused target). */
                 direction: OptionalField(Vector3, 'Vector describing the direction of the view (camera position -> focused target).'),
@@ -251,22 +261,55 @@ export const MVSTreeSchema = TreeSchema({
                 background_color: RequiredField(ColorT, 'Color of the canvas background. Can be either an X11 color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`).'),
             },
         },
+        primitives: {
+            description: 'This node groups a list of geometrical primitives',
+            parent: ['structure', 'root'],
+            params: {
+                color: OptionalField(nullable(ColorT)),
+                label_color: OptionalField(nullable(ColorT)),
+                tooltip: OptionalField(nullable(str)),
+                transparency: OptionalField(nullable(float)),
+                label_transparency: OptionalField(nullable(float)),
+                instances: OptionalField(nullable(list(Matrix))),
+            },
+        },
+        primitives_from_uri: {
+            description: 'This node loads a list of primitives from URI',
+            parent: ['structure', 'root'],
+            params: {
+                uri: RequiredField(str),
+                format: RequiredField(literal('mvs-node-json')),
+                references: OptionalField(nullable(StrList)),
+            },
+        },
+        primitive: {
+            description: 'This node represents a geometrical primitive',
+            parent: ['primitives'],
+            params: {
+                // TODO: validation
+                _union_: RequiredField(MVSPrimitiveParams),
+            },
+        },
     }
 });
 
-
 /** Node kind in a `MVSTree` */
 export type MVSKind = keyof typeof MVSTreeSchema.nodes
 
 /** Node in a `MVSTree` */
 export type MVSNode<TKind extends MVSKind = MVSKind> = NodeFor<typeof MVSTreeSchema, TKind>
 
+/** Params for a specific node kind in a `MVSTree` */
+export type MVSNodeParams<TKind extends MVSKind> = ParamsOfKind<MVSTree, TKind>
+
 /** MolViewSpec tree */
 export type MVSTree = TreeFor<typeof MVSTreeSchema>
 
+/** Any subtree in a `MVSTree` (e.g. its root doesn't need to be 'root') */
+export type MVSSubtree<TKind extends MVSKind = MVSKind> = SubtreeOfKind<MVSTree, TKind>
 
 /** Schema for `MVSTree` (MolViewSpec tree with all params provided) */
 export const FullMVSTreeSchema = TreeSchemaWithAllRequired(MVSTreeSchema);
 
 /** MolViewSpec tree with all params provided */
-export type FullMVSTree = TreeFor<typeof FullMVSTreeSchema>
+export type FullMVSTree = TreeFor<typeof FullMVSTreeSchema>

src/extensions/mvs/tree/mvs/param-types.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import * as iots from 'io-ts';
@@ -42,6 +43,7 @@ export const ComponentExpressionT = iots.partial({
     atom_id: int,
     atom_index: int,
 });
+export type ComponentExpressionT = ValueFor<typeof ComponentExpressionT>
 
 /** `type` parameter values for `representation` node in MVS tree */
 export const RepresentationTypeT = literal('ball_and_stick', 'cartoon', 'surface');
@@ -54,10 +56,22 @@ export const SchemaFormatT = literal('cif', 'bcif', 'json');
 
 /** Parameter values for vector params, e.g. `position` */
 export const Vector3 = tuple([float, float, float]);
+export type Vector3 = ValueFor<typeof Vector3>
 
 /** Parameter values for matrix params, e.g. `rotation` */
 export const Matrix = list(float);
 
+/** Primitives-related types */
+export const PrimitiveComponentExpressionT = iots.partial({ structure_ref: str, expression_schema: SchemaT, expressions: list(ComponentExpressionT) });
+export type PrimitiveComponentExpressionT = ValueFor<typeof PrimitiveComponentExpressionT>
+export const PrimitivePositionT = iots.union([Vector3, ComponentExpressionT, list(PrimitiveComponentExpressionT)]);
+export type PrimitivePositionT = ValueFor<typeof PrimitivePositionT>
+
+export const FloatList = list(float);
+export const IntList = list(int);
+export const StrList = list(str);
+
+
 /** `color` parameter values for `color` node in MVS tree */
 export const HexColorT = new iots.Type<HexColor>(
     'HexColor',
@@ -71,3 +85,16 @@ export const ColorNamesT = literal(...Object.keys(ColorNames) as (keyof ColorNam
 
 /** `color` parameter values for `color` node in MVS tree */
 export const ColorT = union([HexColorT, ColorNamesT]);
+
+/** Type helpers */
+export function isVector3(x: any): x is Vector3 {
+    return !!x && Array.isArray(x) && x.length === 3 && typeof x[0] === 'number';
+}
+
+export function isPrimitiveComponentExpressions(x: any): x is PrimitiveComponentExpressionT {
+    return !!x && Array.isArray(x.expressions);
+}
+
+export function isComponentExpression(x: any): x is ComponentExpressionT {
+    return !!x && typeof x === 'object' && !x.expressions;
+}

src/extensions/rcsb/validation-report/behavior.ts

@@ -313,7 +313,7 @@ export const ValidationReportGeometryQualityPreset = StructureRepresentationPres
         if (!structureCell || !structure) return {};
 
         await plugin.runTask(Task.create('Validation Report', async runtime => {
-            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure.models[0]);
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, structure.models[0]);
         }));
 
         const colorTheme = GeometryQualityColorThemeProvider.name as any;
@@ -350,7 +350,7 @@ export const ValidationReportDensityFitPreset = StructureRepresentationPresetPro
         if (!structureCell || !structure) return {};
 
         await plugin.runTask(Task.create('Validation Report', async runtime => {
-            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure.models[0]);
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, structure.models[0]);
         }));
 
         const colorTheme = DensityFitColorThemeProvider.name as any;
@@ -374,7 +374,7 @@ export const ValidationReportRandomCoilIndexPreset = StructureRepresentationPres
         if (!structureCell || !structure) return {};
 
         await plugin.runTask(Task.create('Validation Report', async runtime => {
-            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure.models[0]);
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, structure.models[0]);
         }));
 
         const colorTheme = RandomCoilIndexColorThemeProvider.name as any;

src/extensions/sb-ncbr/index.ts

@@ -1,3 +1,12 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
 export { SbNcbrPartialCharges } from './partial-charges/behavior';
 export { SbNcbrPartialChargesPreset } from './partial-charges/preset';
-export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrTunnels } from './tunnels/behavior';
+export { TunnelsFromRawData, SelectTunnel, TunnelFromRawData, TunnelShapeProvider } from './tunnels/representation';

src/extensions/sb-ncbr/tunnels/actions.ts

@@ -0,0 +1,99 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { PluginContext } from '../../../mol-plugin/context';
+import { StateAction } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { Asset } from '../../../mol-util/assets';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { ChannelsDBdata, Tunnel, TunnelDB } from './data-model';
+import { TunnelsServerConfig } from './props';
+import { TunnelsFromRawData, SelectTunnel, TunnelShapeProvider } from './representation';
+
+export const TunnelDownloadServer = {
+    'channelsdb': PD.EmptyGroup({ label: 'ChannelsDB' })
+};
+
+type DownloadTunnels = typeof DownloadTunnels
+export const DownloadTunnels = StateAction.build({
+    display: { name: 'Download Tunnels', description: 'Load a tunnels from the provided source and create theirs representations' },
+    from: PluginStateObject.Root,
+    params: (_, plugin: PluginContext) => {
+        return {
+            source: PD.MappedStatic('pdb', {
+                'pdb': PD.Group({
+                    provider: PD.Group({
+                        id: PD.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
+                        server: PD.MappedStatic('channelsdb', TunnelDownloadServer),
+                    }, { pivot: 'id' }),
+                }, { isFlat: true, label: 'PDB' }),
+                'alphafolddb': PD.Group({
+                    provider: PD.Group({
+                        id: PD.Text('Q8W3K0', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
+                        server: PD.MappedStatic('channelsdb', TunnelDownloadServer),
+                    }, { pivot: 'id' })
+                }, { isFlat: true, label: 'AlphaFold DB', description: 'Loads the predicted model if available' }),
+                'url': PD.Group({
+                    url: PD.Url(''),
+                }, { isFlat: true, label: 'URL' })
+            })
+        };
+    }
+})(({ params, state }, plugin: PluginContext) => Task.create('Download Tunnels', async ctx => {
+    plugin.behaviors.layout.leftPanelTabName.next('data');
+
+    const src = params.source;
+    let downloadParams: PD.Normalize<{ url: string | Asset.Url }>[];
+
+    switch (src.name) {
+        case 'url':
+            downloadParams = [{ url: src.params.url }];
+            break;
+        case 'pdb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin?.config.get(TunnelsServerConfig.DefaultServerUrl)}/channels/pdb/${src.params.provider.id}` }]
+                : assertUnreachable(src as never);
+            break;
+        case 'alphafolddb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin?.config.get(TunnelsServerConfig.DefaultServerUrl)}/channels/alphafill/${src.params.provider.id.toLowerCase()}` }]
+                : assertUnreachable(src as never);
+            break;
+        default: assertUnreachable(src);
+    }
+
+    await state.transaction(async () => {
+        const update = plugin.build();
+        const webgl = plugin.canvas3dContext?.webgl;
+
+        for (const download of downloadParams) {
+            const response = await (await fetch(download.url.toString())).json();
+            const tunnels: Tunnel[] = [];
+
+            Object.entries(response.Channels as ChannelsDBdata).forEach(([key, values]) => {
+                if (values.length > 0) {
+                    values.forEach((item: TunnelDB) => {
+                        tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
+                    });
+                }
+            });
+
+            update
+                .toRoot()
+                .apply(TunnelsFromRawData, { data: tunnels })
+                .apply(SelectTunnel)
+                .apply(TunnelShapeProvider, {
+                    webgl,
+                })
+                .apply(StateTransforms.Representation.ShapeRepresentation3D);
+
+            await update.commit();
+        }
+    }).runInContext(ctx);
+}));

src/extensions/sb-ncbr/tunnels/algorithm.ts

@@ -0,0 +1,607 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
+import { OrderedSet } from '../../../mol-data/int';
+import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { Texture } from '../../../mol-gl/webgl/texture';
+import { PositionData, Sphere3D, Box3D, GridLookup3D, fillGridDim } from '../../../mol-math/geometry';
+import { Boundary, getBoundary } from '../../../mol-math/geometry/boundary';
+import { DefaultMolecularSurfaceCalculationProps, MolecularSurfaceCalculationProps } from '../../../mol-math/geometry/molecular-surface';
+import { lerp, spline } from '../../../mol-math/interpolate';
+import { Vec3, Tensor, Mat4 } from '../../../mol-math/linear-algebra';
+import { Shape } from '../../../mol-model/shape';
+import { ensureReasonableResolution } from '../../../mol-repr/structure/visual/util/common';
+import { Task, RuntimeContext } from '../../../mol-task';
+import { ValueCell } from '../../../mol-util';
+import { Color } from '../../../mol-util/color';
+import { Tunnel, Profile } from './data-model';
+
+type MolecularSurfaceMeta = {
+    resolution?: number
+    colorTexture?: Texture
+}
+
+export async function createSpheresShape(options: { tunnel: Tunnel, color: Color, resolution: number, sampleRate: number, showRadii: boolean, prev?: Shape<Mesh> }) {
+    const builder = MeshBuilder.createState(512, 512, options.prev?.geometry);
+    const tunnel = options.tunnel;
+
+    const processedData = interpolateTunnel(tunnel.data, options.sampleRate);
+
+    if (options.showRadii) {
+        for (let i = 0; i < processedData.length; i += 1) {
+            const p = processedData[i];
+            builder.currentGroup = i;
+            const center = [p.X, p.Y, p.Z];
+            addSphere(builder, center as Vec3, p.Radius, options.resolution);
+        }
+    } else {
+        for (let i = 0; i < processedData.length; i += 1) {
+            const p = processedData[i];
+            builder.currentGroup = 0;
+            const center = [p.X, p.Y, p.Z];
+            addSphere(builder, center as Vec3, p.Radius, options.resolution);
+        }
+    }
+
+    const mesh = MeshBuilder.getMesh(builder);
+    const name = tunnel.props.highlight_label ?
+        tunnel.props.highlight_label :
+        tunnel.props.type && tunnel.props.id ?
+            `${tunnel.props.type} ${tunnel.props.id}` :
+            'Tunnel';
+
+    if (options.showRadii)
+        return Shape.create(
+            name,
+            tunnel.props,
+            mesh,
+            () => Color(options.color),
+            () => 1,
+            (i) => `[${processedData[i].X.toFixed(3)}, ${processedData[i].Y.toFixed(3)}, ${processedData[i].Z.toFixed(3)}] - radius: ${processedData[i].Radius.toFixed(3)}`,
+        );
+    return Shape.create(
+        name,
+        tunnel.props,
+        mesh,
+        () => Color(options.color),
+        () => 1,
+        () => name,
+    );
+}
+
+export async function createTunnelShape(options: { tunnel: Tunnel, color: Color, resolution: number, sampleRate: number, webgl: WebGLContext | undefined, prev?: Shape<Mesh> }) {
+    const tunnel = options.tunnel;
+    const mesh = await createTunnelMesh(tunnel.data, {
+        detail: options.resolution,
+        sampleRate: options.sampleRate,
+        webgl: options.webgl,
+        prev: options.prev?.geometry
+    });
+
+    const name = tunnel.props.highlight_label ?
+        tunnel.props.highlight_label :
+        tunnel.props.type && tunnel.props.id ?
+            `${tunnel.props.type} ${tunnel.props.id}` :
+            'Tunnel';
+
+    return Shape.create(
+        name,
+        tunnel.props,
+        mesh,
+        () => Color(options.color),
+        () => 1,
+        () => name,
+    );
+}
+
+function profileToVec3(profile: Profile): Vec3 {
+    return Vec3.create(profile.X, profile.Y, profile.Z);
+}
+
+// Centripetal Catmull–Rom spline interpolation
+function interpolateTunnel(profile: Profile[], sampleRate: number) {
+    const interpolatedProfiles: Profile[] = [];
+    if (profile.length < 4) return profile; // Ensuring there are enough points to interpolate
+
+    interpolatedProfiles.push(profile[0]);
+
+    let lastPoint = profileToVec3(profile[0]);
+    let currentDistance = 0;
+    const pointInterval = 1 / sampleRate;
+
+    for (let i = 1; i < profile.length - 2; i++) {
+        const P0 = profile[i - 1];
+        const P1 = profile[i];
+        const P2 = profile[i + 1];
+        const P3 = profile[i + 2];
+
+        for (let t = 0; t <= 1; t += 0.05) {
+            const interpolatedX = spline(P0.X, P1.X, P2.X, P3.X, t, 0.5);
+            const interpolatedY = spline(P0.Y, P1.Y, P2.Y, P3.Y, t, 0.5);
+            const interpolatedZ = spline(P0.Z, P1.Z, P2.Z, P3.Z, t, 0.5);
+            const interpolatedPoint = Vec3.create(interpolatedX, interpolatedY, interpolatedZ);
+
+            const distanceToAdd = Vec3.distance(lastPoint, interpolatedPoint);
+            currentDistance += distanceToAdd;
+
+            if (currentDistance >= pointInterval) {
+                interpolatedProfiles.push({
+                    X: interpolatedX,
+                    Y: interpolatedY,
+                    Z: interpolatedZ,
+                    Radius: spline(P0.Radius, P1.Radius, P2.Radius, P3.Radius, t, 0.5),
+                    Charge: lerp(P1.Charge, P2.Charge, t),
+                    FreeRadius: spline(P0.FreeRadius, P1.FreeRadius, P2.FreeRadius, P3.FreeRadius, t, 0.5),
+                    T: lerp(P1.T, P2.T, t),
+                    Distance: lerp(P1.Distance, P2.Distance, t)
+                });
+                lastPoint = interpolatedPoint;
+                currentDistance -= pointInterval;
+            }
+        }
+    }
+
+    // Ensuring the last profile point is included
+    interpolatedProfiles.push(profile[profile.length - 1]);
+
+    return interpolatedProfiles;
+}
+
+
+function convertToPositionData(profile: Profile[], probeRadius: number): Required<PositionData> {
+    let position = {} as PositionData;
+
+    const x: number[] = [];
+    const y: number[] = [];
+    const z: number[] = [];
+    const indices: Array<number> = [];
+    const radius: number[] = [];
+
+    let maxRadius: number = Number.MIN_SAFE_INTEGER;
+
+    let sphereCounter = 0;
+    for (const sphere of profile) {
+        x.push(sphere.X);
+        y.push(sphere.Y);
+        z.push(sphere.Z);
+        indices.push(sphereCounter);
+        radius.push(sphere.Radius + probeRadius);
+        if (sphere.Radius > maxRadius) maxRadius = sphere.Radius;
+        sphereCounter++;
+    }
+
+    position = { x, y, z, indices: OrderedSet.ofSortedArray(indices), radius, id: indices };
+
+    return position as Required<PositionData>;
+}
+
+async function createTunnelMesh(
+    data: Profile[],
+    options: {
+        detail: number,
+        sampleRate: number,
+        webgl?: WebGLContext,
+        prev?: Mesh
+    }
+) {
+    const props = {
+        ...DefaultMolecularSurfaceCalculationProps,
+    };
+    const preprocessedData = interpolateTunnel(data, options.sampleRate);
+    const positions = convertToPositionData(preprocessedData, props.probeRadius);
+    const bounds: Boundary = getBoundary(positions);
+
+    let maxR = 0;
+    for (let i = 0; i < positions.radius.length; ++i) {
+        const r = positions.radius[i];
+        if (maxR < r) maxR = r;
+    }
+
+    const p = ensureReasonableResolution(bounds.box, props);
+
+    const { field, transform, /* resolution,*/ maxRadius, /* idField */ } = await computeTunnelSurface(
+        {
+            positions,
+            boundary: bounds,
+            maxRadius: maxR,
+            box: bounds.box,
+            props: p
+        }
+    ).run();
+
+    const params = {
+        isoLevel: p.probeRadius,
+        scalarField: field,
+    };
+    const surface = await computeMarchingCubesMesh(params, options.prev).run();
+    const iterations = Math.ceil(2 / 1);
+    Mesh.smoothEdges(surface, { iterations, maxNewEdgeLength: Math.sqrt(2) });
+
+    Mesh.transform(surface, transform);
+    if (options.webgl && !options.webgl.isWebGL2) {
+        Mesh.uniformTriangleGroup(surface);
+        ValueCell.updateIfChanged(surface.varyingGroup, false);
+    } else {
+        ValueCell.updateIfChanged(surface.varyingGroup, true);
+    }
+
+    const sphere = Sphere3D.expand(Sphere3D(), bounds.sphere, maxRadius);
+    surface.setBoundingSphere(sphere);
+    (surface.meta as MolecularSurfaceMeta).resolution = options.detail;
+
+    return surface;
+}
+
+function normalToLine(out: Vec3, p: Vec3) {
+    out[0] = out[1] = out[2] = 1.0;
+    if (p[0] !== 0) {
+        out[0] = (p[1] + p[2]) / -p[0];
+    } else if (p[1] !== 0) {
+        out[1] = (p[0] + p[2]) / -p[1];
+    } else if (p[2] !== 0) {
+        out[2] = (p[0] + p[1]) / -p[2];
+    }
+    return out;
+}
+
+function computeTunnelSurface(
+    surfaceData: {
+        positions: Required<PositionData>,
+        boundary: Boundary,
+        maxRadius: number,
+        box: Box3D | null,
+        props: MolecularSurfaceCalculationProps
+    }
+) {
+    return Task.create('Tunnel Surface', async (ctx) => {
+        return await calcTunnelSurface(ctx, surfaceData);
+    });
+}
+
+type AnglesTables = { cosTable: Float32Array, sinTable: Float32Array }
+function getAngleTables(probePositions: number): AnglesTables {
+    let theta = 0.0;
+    const step = 2 * Math.PI / probePositions;
+
+    const cosTable = new Float32Array(probePositions);
+    const sinTable = new Float32Array(probePositions);
+    for (let i = 0; i < probePositions; i++) {
+        cosTable[i] = Math.cos(theta);
+        sinTable[i] = Math.sin(theta);
+        theta += step;
+    }
+    return { cosTable, sinTable };
+}
+
+// From '../../../\mol-math\geometry\molecular-surface.ts'
+async function calcTunnelSurface(ctx: RuntimeContext,
+    surfaceData: {
+        positions: Required<PositionData>,
+        boundary: Boundary,
+        maxRadius: number,
+        box: Box3D | null,
+        props: MolecularSurfaceCalculationProps
+    }) {
+    // Field generation method adapted from AstexViewer (Mike Hartshorn) by Fred Ludlow.
+    // Other parts based heavily on NGL (Alexander Rose) EDT Surface class
+
+    let lastClip = -1;
+
+    /**
+     * Is the point at x,y,z obscured by any of the atoms specifeid by indices in neighbours.
+     * Ignore indices a and b (these are the relevant atoms in projectPoints/Torii)
+     *
+     * Cache the last clipped atom (as very often the same one in subsequent calls)
+     *
+     * `a` and `b` must be resolved indices
+     */
+    function obscured(x: number, y: number, z: number, a: number, b: number) {
+        if (lastClip !== -1) {
+            const ai = lastClip;
+            if (ai !== a && ai !== b && singleAtomObscures(ai, x, y, z)) {
+                return ai;
+            } else {
+                lastClip = -1;
+            }
+        }
+
+        for (let j = 0, jl = neighbours.count; j < jl; ++j) {
+            const ai = OrderedSet.getAt(indices, neighbours.indices[j]);
+            if (ai !== a && ai !== b && singleAtomObscures(ai, x, y, z)) {
+                lastClip = ai;
+                return ai;
+            }
+        }
+
+        return -1;
+    }
+
+    /**
+     * `ai` must be a resolved index
+     */
+    function singleAtomObscures(ai: number, x: number, y: number, z: number) {
+        const r = radius[ai];
+        const dx = px[ai] - x;
+        const dy = py[ai] - y;
+        const dz = pz[ai] - z;
+        const dSq = dx * dx + dy * dy + dz * dz;
+        return dSq < (r * r);
+    }
+
+    /**
+     * For each atom:
+     *     Iterate over a subsection of the grid, for each point:
+     *         If current value < 0.0, unvisited, set positive
+     *
+     *         In any case: Project this point onto surface of the atomic sphere
+     *         If this projected point is not obscured by any other atom
+     *             Calculate delta distance and set grid value to minimum of
+     *             itself and delta
+     */
+    function projectPointsRange(begI: number, endI: number) {
+        for (let i = begI; i < endI; ++i) {
+            const j = OrderedSet.getAt(indices, i);
+            const vx = px[j], vy = py[j], vz = pz[j];
+            const rad = radius[j];
+            const rSq = rad * rad;
+
+            lookup3d.find(vx, vy, vz, rad);
+
+            // Number of grid points, round this up...
+            const ng = Math.ceil(rad * scaleFactor);
+
+            // Center of the atom, mapped to grid points (take floor)
+            const iax = Math.floor(scaleFactor * (vx - minX));
+            const iay = Math.floor(scaleFactor * (vy - minY));
+            const iaz = Math.floor(scaleFactor * (vz - minZ));
+
+            // Extents of grid to consider for this atom
+            const begX = Math.max(0, iax - ng);
+            const begY = Math.max(0, iay - ng);
+            const begZ = Math.max(0, iaz - ng);
+
+            // Add two to these points:
+            // - iax are floor'd values so this ensures coverage
+            // - these are loop limits (exclusive)
+            const endX = Math.min(dimX, iax + ng + 2);
+            const endY = Math.min(dimY, iay + ng + 2);
+            const endZ = Math.min(dimZ, iaz + ng + 2);
+
+            for (let xi = begX; xi < endX; ++xi) {
+                const dx = gridx[xi] - vx;
+                const xIdx = xi * iuv;
+                for (let yi = begY; yi < endY; ++yi) {
+                    const dy = gridy[yi] - vy;
+                    const dxySq = dx * dx + dy * dy;
+                    const xyIdx = yi * iu + xIdx;
+                    for (let zi = begZ; zi < endZ; ++zi) {
+                        const dz = gridz[zi] - vz;
+                        const dSq = dxySq + dz * dz;
+
+                        if (dSq < rSq) {
+                            const idx = zi + xyIdx;
+
+                            // if unvisited, make positive
+                            if (data[idx] < 0.0) data[idx] *= -1;
+
+                            // Project on to the surface of the sphere
+                            // sp is the projected point ( dx, dy, dz ) * ( ra / d )
+                            const d = Math.sqrt(dSq);
+                            const ap = rad / d;
+                            const spx = dx * ap + vx;
+                            const spy = dy * ap + vy;
+                            const spz = dz * ap + vz;
+
+                            if (obscured(spx, spy, spz, j, -1) === -1) {
+                                const dd = rad - d;
+                                if (dd < data[idx]) {
+                                    data[idx] = dd;
+                                    idData[idx] = id[i];
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    async function projectPoints() {
+        for (let i = 0; i < n; i += updateChunk) {
+            projectPointsRange(i, Math.min(i + updateChunk, n));
+
+            if (ctx.shouldUpdate) {
+                await ctx.update({ message: 'projecting points', current: i, max: n });
+            }
+        }
+    }
+
+    // Vectors for Torus Projection
+    const atob = Vec3();
+    const mid = Vec3();
+    const n1 = Vec3();
+    const n2 = Vec3();
+    /**
+     * `a` and `b` must be resolved indices
+     */
+    function projectTorus(a: number, b: number) {
+        const rA = radius[a];
+        const rB = radius[b];
+        const dx = atob[0] = px[b] - px[a];
+        const dy = atob[1] = py[b] - py[a];
+        const dz = atob[2] = pz[b] - pz[a];
+        const dSq = dx * dx + dy * dy + dz * dz;
+
+        // This check now redundant as already done in AVHash.withinRadii
+        // if (dSq > ((rA + rB) * (rA + rB))) { return }
+
+        const d = Math.sqrt(dSq);
+
+        // Find angle between a->b vector and the circle
+        // of their intersection by cosine rule
+        const cosA = (rA * rA + d * d - rB * rB) / (2.0 * rA * d);
+
+        // distance along a->b at intersection
+        const dmp = rA * cosA;
+
+        Vec3.normalize(atob, atob);
+
+        // Create normal to line
+        normalToLine(n1, atob);
+        Vec3.normalize(n1, n1);
+
+        // Cross together for second normal vector
+        Vec3.cross(n2, atob, n1);
+        Vec3.normalize(n2, n2);
+
+        // r is radius of circle of intersection
+        const rInt = Math.sqrt(rA * rA - dmp * dmp);
+
+        Vec3.scale(n1, n1, rInt);
+        Vec3.scale(n2, n2, rInt);
+        Vec3.scale(atob, atob, dmp);
+
+        mid[0] = atob[0] + px[a];
+        mid[1] = atob[1] + py[a];
+        mid[2] = atob[2] + pz[a];
+
+        lastClip = -1;
+
+        for (let i = 0; i < probePositions; ++i) {
+            const cost = cosTable[i];
+            const sint = sinTable[i];
+
+            const px = mid[0] + cost * n1[0] + sint * n2[0];
+            const py = mid[1] + cost * n1[1] + sint * n2[1];
+            const pz = mid[2] + cost * n1[2] + sint * n2[2];
+
+            if (obscured(px, py, pz, a, b) === -1) {
+                const iax = Math.floor(scaleFactor * (px - minX));
+                const iay = Math.floor(scaleFactor * (py - minY));
+                const iaz = Math.floor(scaleFactor * (pz - minZ));
+
+                const begX = Math.max(0, iax - ngTorus);
+                const begY = Math.max(0, iay - ngTorus);
+                const begZ = Math.max(0, iaz - ngTorus);
+
+                const endX = Math.min(dimX, iax + ngTorus + 2);
+                const endY = Math.min(dimY, iay + ngTorus + 2);
+                const endZ = Math.min(dimZ, iaz + ngTorus + 2);
+
+                for (let xi = begX; xi < endX; ++xi) {
+                    const dx = px - gridx[xi];
+                    const xIdx = xi * iuv;
+
+                    for (let yi = begY; yi < endY; ++yi) {
+                        const dy = py - gridy[yi];
+                        const dxySq = dx * dx + dy * dy;
+                        const xyIdx = yi * iu + xIdx;
+
+                        for (let zi = begZ; zi < endZ; ++zi) {
+                            const dz = pz - gridz[zi];
+                            const dSq = dxySq + dz * dz;
+
+                            const idx = zi + xyIdx;
+                            const current = data[idx];
+
+                            if (current > 0.0 && dSq < (current * current)) {
+                                data[idx] = Math.sqrt(dSq);
+                                // Is this grid point closer to a or b?
+                                // Take dot product of atob and gridpoint->p (dx, dy, dz)
+                                const dp = dx * atob[0] + dy * atob[1] + dz * atob[2];
+                                idData[idx] = id[OrderedSet.indexOf(indices, dp < 0.0 ? b : a)];
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    function projectToriiRange(begI: number, endI: number) {
+        for (let i = begI; i < endI; ++i) {
+            const k = OrderedSet.getAt(indices, i);
+            lookup3d.find(px[k], py[k], pz[k], radius[k]);
+            for (let j = 0, jl = neighbours.count; j < jl; ++j) {
+                const l = OrderedSet.getAt(indices, neighbours.indices[j]);
+                if (k < l) projectTorus(k, l);
+            }
+        }
+    }
+
+    async function projectTorii() {
+        for (let i = 0; i < n; i += updateChunk) {
+            projectToriiRange(i, Math.min(i + updateChunk, n));
+
+            if (ctx.shouldUpdate) {
+                await ctx.update({ message: 'projecting torii', current: i, max: n });
+            }
+        }
+    }
+
+    // console.time('MolecularSurface')
+    // console.time('MolecularSurface createState')
+    const { resolution, probeRadius, probePositions } = surfaceData.props;
+    const scaleFactor = 1 / resolution;
+    const ngTorus = Math.max(5, 2 + Math.floor(probeRadius * scaleFactor));
+
+    const cellSize = Vec3.create(surfaceData.maxRadius, surfaceData.maxRadius, surfaceData.maxRadius);
+    Vec3.scale(cellSize, cellSize, 2);
+    const lookup3d = GridLookup3D(surfaceData.positions, surfaceData.boundary, cellSize);
+    const neighbours = lookup3d.result;
+    if (surfaceData.box === null) surfaceData.box = lookup3d.boundary.box;
+
+    const { indices, x: px, y: py, z: pz, id, radius } = surfaceData.positions;
+    const n = OrderedSet.size(indices);
+
+    const pad = surfaceData.maxRadius + resolution;
+    const expandedBox = Box3D.expand(Box3D(), surfaceData.box, Vec3.create(pad, pad, pad));
+    const [minX, minY, minZ] = expandedBox.min;
+    const scaledBox = Box3D.scale(Box3D(), expandedBox, scaleFactor);
+    const dim = Box3D.size(Vec3(), scaledBox);
+    Vec3.ceil(dim, dim);
+
+    const [dimX, dimY, dimZ] = dim;
+    const iu = dimZ, iv = dimY, iuv = iu * iv;
+
+    const { cosTable, sinTable } = getAngleTables(probePositions);
+
+    const space = Tensor.Space(dim, [0, 1, 2], Float32Array);
+    const data = space.create();
+    const idData = space.create();
+
+    data.fill(-1001.0);
+    idData.fill(-1);
+
+    const gridx = fillGridDim(dimX, minX, resolution);
+    const gridy = fillGridDim(dimY, minY, resolution);
+    const gridz = fillGridDim(dimZ, minZ, resolution);
+
+    const updateChunk = Math.ceil(100000 / ((Math.pow(Math.pow(surfaceData.maxRadius, 3), 3) * scaleFactor)));
+    // console.timeEnd('MolecularSurface createState')
+
+    // console.time('MolecularSurface projectPoints')
+    await projectPoints();
+    // console.timeEnd('MolecularSurface projectPoints')
+
+    // console.time('MolecularSurface projectTorii')
+    await projectTorii();
+    // console.timeEnd('MolecularSurface projectTorii')
+    // console.timeEnd('MolecularSurface')
+
+    const field = Tensor.create(space, data);
+    const idField = Tensor.create(space, idData);
+
+    const transform = Mat4.identity();
+    Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
+    Mat4.setTranslation(transform, expandedBox.min);
+    // console.log({ field, idField, transform, updateChunk })
+    return { field, idField, transform, resolution, maxRadius: surfaceData.maxRadius };
+}

src/extensions/sb-ncbr/tunnels/behavior.ts

@@ -0,0 +1,105 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
+import { PluginBehavior } from '../../../mol-plugin/behavior';
+import { DownloadTunnels } from './actions';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
+import { Model, Structure } from '../../../mol-model/structure';
+import { PluginContext } from '../../../mol-plugin/context';
+import { StateObjectRef } from '../../../mol-state';
+import { getTunnelsConfig, TunnelsDataParams } from './props';
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { Tunnel, ChannelsDBdata, TunnelDB } from './data-model';
+import { TunnelShapeProvider, TunnelFromRawData } from './representation';
+import { ColorGenerator } from '../../meshes/mesh-utils';
+
+export const SbNcbrTunnels = PluginBehavior.create<{ autoAttach: boolean }>({
+    name: 'sb-ncbr-tunnels',
+    category: 'misc',
+    display: {
+        name: 'SB NCBR Tunnels',
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
+        register(): void {
+            this.ctx.state.data.actions.add(DownloadTunnels);
+            this.ctx.builders.structure.representation.registerPreset(TunnelsPreset);
+        }
+        unregister() {
+            this.ctx.state.data.actions.remove(DownloadTunnels);
+            this.ctx.builders.structure.representation.unregisterPreset(TunnelsPreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(true),
+    })
+});
+
+
+export function isApplicable(structure?: Structure): boolean {
+    return (
+        !!structure && structure.models.length === 1 &&
+        Model.hasPdbId(structure.models[0])
+    );
+}
+
+export const TunnelsPreset = StructureRepresentationPresetProvider({
+    id: 'sb-ncbr-preset-structure-tunnels',
+    display: {
+        name: 'Tunnels', group: 'Annotation',
+        description: 'Shows Tunnels from ChannelsDB contained in the structure.'
+    },
+    isApplicable(a) {
+        return isApplicable(a.data);
+    },
+    params: (a, plugin) => {
+        return {
+            ...StructureRepresentationPresetProvider.CommonParams,
+            ...getConfiguredDefaultParams(plugin)
+        };
+    },
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        const update = plugin.build();
+        const webgl = plugin.canvas3dContext?.webgl;
+        const response = await (await fetch(`${params.serverUrl}/channels/${params.serverType}/${structure.model.entryId.toLowerCase()}`)).json();
+        const tunnels: Tunnel[] = [];
+
+        Object.entries(response.Channels as ChannelsDBdata).forEach(([key, values]) => {
+            if (values.length > 0) {
+                values.forEach((item: TunnelDB) => {
+                    tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
+                });
+            }
+        });
+
+        await tunnels.forEach(async (tunnel) => {
+            await update
+                .toRoot()
+                .apply(TunnelFromRawData, { data: tunnel })
+                .apply(TunnelShapeProvider, {
+                    webgl,
+                    colorTheme: ColorGenerator.next().value,
+                })
+                .apply(StateTransforms.Representation.ShapeRepresentation3D);
+            await update.commit();
+        });
+
+        const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);
+
+        return { components: preset.components, representations: { ...preset.representations, } };
+    }
+});
+
+function getConfiguredDefaultParams(plugin: PluginContext) {
+    const config = getTunnelsConfig(plugin);
+    const params = PD.clone(TunnelsDataParams);
+    PD.setDefaultValues(params, { serverType: config.DefaultServerType, serverUrl: config.DefaultServerUrl });
+    return params;
+}

src/extensions/sb-ncbr/tunnels/data-model.ts

@@ -0,0 +1,119 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { Color } from '../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+export interface Profile {
+    Charge: number,
+    Radius: number,
+    FreeRadius: number,
+    T: number,
+    Distance: number,
+    X: number,
+    Y: number,
+    Z: number
+}
+
+export interface Layerweightedproperties {
+    Hydrophobicity: number,
+    Hydropathy: number,
+    Polarity: number,
+    Mutability: number
+}
+
+export interface LayerGeometry {
+    MinRadius: number,
+    MinFreeRadius: number,
+    StartDistance: number,
+    EndDistance: number,
+    LocalMinimum: boolean,
+    Bottleneck: boolean,
+    bottleneck: boolean
+}
+
+export interface Properties {
+    Charge: number,
+    NumPositives: number,
+    NumNegatives: number,
+    Hydrophobicity: number,
+    Hydropathy: number,
+    Polarity: number,
+    Mutability: number
+}
+
+export interface LayersInfo {
+    LayerGeometry: LayerGeometry,
+    Residues: string[],
+    FlowIndices: string[],
+    Properties: Properties
+}
+
+export interface Layers {
+    ResidueFlow: string[],
+    HetResidues: any[],
+    LayerWeightedProperties: Layerweightedproperties
+    LayersInfo: LayersInfo[]
+}
+
+export interface TunnelDB {
+    Type: string,
+    Id: string,
+    Cavity: string,
+    Auto: boolean,
+    Properties: Properties,
+    Profile: Profile[],
+    Layers: Layers
+};
+
+export interface ChannelsDBdata {
+    'CSATunnels_MOLE': TunnelDB[],
+    'CSATunnels_Caver': TunnelDB[],
+    'ReviewedChannels_MOLE': TunnelDB[],
+    'ReviewedChannels_Caver': TunnelDB[],
+    'CofactorTunnels_MOLE': TunnelDB[],
+    'CofactorTunnels_Caver': TunnelDB[],
+    'TransmembranePores_MOLE': TunnelDB[],
+    'TransmembranePores_Caver': TunnelDB[],
+    'ProcognateTunnels_MOLE': TunnelDB[],
+    'ProcognateTunnels_Caver': TunnelDB[],
+    'AlphaFillTunnels_MOLE': TunnelDB[],
+    'AlphaFillTunnels_Caver': TunnelDB[]
+}
+
+export interface ChannelsCache {
+    Channels: ChannelsDBdata
+}
+
+export interface Tunnel {
+    data: Profile[],
+    props: {
+        highlight_label?: string,
+        type?: string,
+        id?: string,
+        label?: string,
+        description?: string
+    }
+}
+
+export const TunnelShapeParams = {
+    webgl: PD.Value<WebGLContext | null>(null),
+    colorTheme: PD.Color(Color(0xff0000)),
+    visual: PD.MappedStatic(
+        'mesh',
+        {
+            mesh: PD.Group({ resolution: PD.Numeric(2) }),
+            spheres: PD.Group({ resolution: PD.Numeric(2) })
+        }
+    ),
+    samplingRate: PD.Numeric(1, { min: 0.05, max: 1, step: 0.05 }),
+    showRadii: PD.Boolean(false),
+};
+
+export class TunnelStateObject extends PluginStateObject.Create<{ tunnel: Tunnel }>({ name: 'Tunnel Entry', typeClass: 'Data' }) { }
+export class TunnelsStateObject extends PluginStateObject.Create<{ tunnels: Tunnel[] }>({ name: 'Tunnels', typeClass: 'Data' }) { }

src/extensions/sb-ncbr/tunnels/examples.ts

@@ -0,0 +1,63 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
+import { StateTransforms } from '../../../mol-plugin-state/transforms';
+import { PluginContext } from '../../../mol-plugin/context';
+import { ChannelsDBdata, Tunnel, TunnelDB } from './data-model';
+import { TunnelsFromRawData, SelectTunnel, TunnelShapeProvider, TunnelFromRawData } from './representation';
+
+
+export const DB_URL = 'https://channelsdb2.biodata.ceitec.cz/api/channels/';
+export const SUB_DB = 'pdb';
+export const CHANNEL = '1ymg';
+
+export const URL = `${DB_URL}${SUB_DB}/${CHANNEL}`;
+
+export async function runVisualizeTunnels(plugin: PluginContext, url: string = URL) {
+    const update = plugin.build();
+    const webgl = plugin.canvas3dContext?.webgl;
+
+    const response = await (await fetch(url)).json();
+
+    const tunnels: Tunnel[] = [];
+    Object.entries(response.Channels as ChannelsDBdata).forEach(([key, values]) => {
+        if (values.length > 0) {
+            values.forEach((item: TunnelDB) => {
+                tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
+            });
+        }
+    });
+
+    update
+        .toRoot()
+        .apply(TunnelsFromRawData, { data: tunnels })
+        .apply(SelectTunnel)
+        .apply(TunnelShapeProvider, {
+            webgl,
+        })
+        .apply(StateTransforms.Representation.ShapeRepresentation3D);
+
+    await update.commit();
+}
+
+export async function runVisualizeTunnel(plugin: PluginContext) {
+    const update = plugin.build();
+    const webgl = plugin.canvas3dContext?.webgl;
+
+    const response = await (await fetch(URL)).json();
+
+    const tunnel = response.Channels.TransmembranePores_MOLE[0];
+
+    update
+        .toRoot()
+        .apply(TunnelFromRawData, { data: { data: tunnel.Profile, props: { id: tunnel.Id, type: tunnel.Type } } })
+        .apply(TunnelShapeProvider, {
+            webgl,
+        })
+        .apply(StateTransforms.Representation.ShapeRepresentation3D);
+
+    await update.commit();
+}

src/extensions/sb-ncbr/tunnels/props.ts

@@ -0,0 +1,27 @@
+import { PluginConfigItem } from '../../../mol-plugin/config';
+import { PluginContext } from '../../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+export namespace TunnelsData {
+    export const DefaultServerUrl = 'https://channelsdb2.biodata.ceitec.cz/api';
+    export const DefaultServerType = 'pdb';
+}
+
+export const TunnelsDataParams = {
+    serverType: PD.Select('pdb', [['pdb', 'pdb']] as const),
+    serverUrl: PD.Text(TunnelsData.DefaultServerUrl)
+};
+export type TunnelsDataParams = typeof TunnelsDataParams
+
+export const TunnelsServerConfig = {
+    DefaultServerUrl: new PluginConfigItem('channelsdb-server', 'https://channelsdb2.biodata.ceitec.cz/api'),
+    DefaultServerType: new PluginConfigItem<'pdb'>('serverType', 'pdb')
+};
+
+export function getTunnelsConfig(plugin: PluginContext): { [key in keyof typeof TunnelsServerConfig]: NonNullable<typeof TunnelsServerConfig[key]['defaultValue']> } {
+    return {
+        DefaultServerUrl: plugin.config.get(TunnelsServerConfig.DefaultServerUrl) ?? TunnelsServerConfig.DefaultServerUrl.defaultValue ?? TunnelsData.DefaultServerUrl,
+        DefaultServerType: plugin.config.get(TunnelsServerConfig.DefaultServerType) ?? TunnelsServerConfig.DefaultServerType.defaultValue ?? TunnelsData.DefaultServerType,
+    };
+}
+

src/extensions/sb-ncbr/tunnels/representation.ts

@@ -0,0 +1,102 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateTransformer } from '../../../mol-state';
+import { TunnelStateObject, Tunnel, TunnelShapeParams, TunnelsStateObject } from './data-model';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { Task } from '../../../mol-task';
+import { createTunnelShape, createSpheresShape } from './algorithm';
+
+const Transform = StateTransformer.builderFactory('sb-ncbr-tunnels');
+
+export const TunnelsFromRawData = Transform({
+    name: 'sb-ncbr-tunnels-from-data',
+    display: { name: 'Tunnels' },
+    from: PluginStateObject.Root,
+    to: TunnelsStateObject,
+    params: {
+        data: PD.Value<Tunnel[]>([]),
+    },
+})({
+    apply({ params }) {
+        return new TunnelsStateObject({ tunnels: params.data });
+    },
+});
+
+export const SelectTunnel = Transform({
+    name: 'sb-ncbr-tunnel-from-tunnels',
+    display: { name: 'Tunnel Selection' },
+    from: TunnelsStateObject,
+    to: TunnelStateObject,
+    params: a => {
+        return {
+            index: PD.Numeric(0, { min: 0, max: a!.data.tunnels.length - 1, step: 1 })
+        };
+    }
+})({
+    apply({ a, params }) {
+        return new TunnelStateObject({ tunnel: a.data.tunnels[params.index] });
+    }
+});
+
+export const TunnelFromRawData = Transform({
+    name: 'sb-ncbr-tunnel-from-data',
+    display: { name: 'Tunnel Entry' },
+    from: PluginStateObject.Root,
+    to: TunnelStateObject,
+    params: {
+        data: PD.Value<Tunnel>(undefined as any, { isHidden: true })
+    },
+})({
+    apply({ params }) {
+        return new TunnelStateObject({ tunnel: params.data });
+    },
+});
+
+export const TunnelShapeProvider = Transform({
+    name: 'sb-ncbr-tunnel-shape-provider',
+    display: { name: 'Tunnel' },
+    from: TunnelStateObject,
+    to: PluginStateObject.Shape.Provider,
+    params: a => { return TunnelShapeParams; },
+})({
+    apply({ a, params }) {
+        return Task.create('Tunnel Shape Representation', async ctx => {
+            return new PluginStateObject.Shape.Provider({
+                label: 'Surface',
+                data: { params, data: a.data },
+                params: Mesh.Params,
+                geometryUtils: Mesh.Utils,
+                getShape: (_, data, __, mesh) => {
+                    if (data.params.visual.name === 'mesh' && !data.params.showRadii) {
+                        return createTunnelShape({
+                            tunnel: data.data.tunnel,
+                            color: data.params.colorTheme,
+                            resolution: data.params.visual.params.resolution,
+                            sampleRate: data.params.samplingRate,
+                            webgl: data.params.webgl, prev: mesh
+                        });
+                    }
+                    return createSpheresShape({
+                        tunnel: data.data.tunnel,
+                        color: data.params.colorTheme,
+                        resolution: data.params.visual.params.resolution,
+                        sampleRate: data.params.samplingRate,
+                        showRadii: data.params.showRadii, prev: mesh
+                    });
+                }
+            }, {
+                label: a.data.tunnel.props.label ?? 'Tunnel',
+                description: a.data.tunnel.props.description
+                ?? (a.data.tunnel.props.type && a.data.tunnel.props.id)
+                    ? `${a.data.tunnel.props.type} ${a.data.tunnel.props.id}`
+                    : '',
+            });
+        });
+    },
+});

src/mol-canvas3d/camera.ts

@@ -28,8 +28,6 @@ interface ICamera {
     readonly fogNear: number,
 }
 
-const tmpPos1 = Vec3();
-const tmpPos2 = Vec3();
 const tmpClip = Vec4();
 
 class Camera implements ICamera {
@@ -186,14 +184,11 @@ class Camera implements ICamera {
 
     /** World space pixel size at given `point` */
     getPixelSize(point: Vec3) {
-        // project -> unproject of `point` does not exactly return the same
-        // to get a sufficiently accurate measure we unproject the original
-        // clip position in addition to the one shifted by one pixel
         this.project(tmpClip, point);
-        this.unproject(tmpPos1, tmpClip);
-        tmpClip[0] += 1;
-        this.unproject(tmpPos2, tmpClip);
-        return Vec3.distance(tmpPos1, tmpPos2);
+        const w = tmpClip[3];
+        const rx = this.viewport.width;
+        const P00 = this.projection[0];
+        return (2 / w) / (rx * Math.abs(P00));
     }
 
     constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(0, 0, 128, 128)) {

src/mol-canvas3d/camera/transition.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -87,22 +87,48 @@ class CameraTransitionManager {
 namespace CameraTransitionManager {
     export type TransitionFunc = (out: Camera.Snapshot, t: number, source: Camera.Snapshot, target: Camera.Snapshot) => void
 
-    const _rot = Quat.identity();
+    const _rotUp = Quat.identity();
+    const _rotDist = Quat.identity();
+
+    const _sourcePosition = Vec3();
+    const _targetPosition = Vec3();
+
     export function defaultTransition(out: Camera.Snapshot, t: number, source: Camera.Snapshot, target: Camera.Snapshot): void {
         Camera.copySnapshot(out, target);
 
         // Rotate up
-        Quat.slerp(_rot, Quat.Identity, Quat.rotationTo(_rot, source.up, target.up), t);
-        Vec3.transformQuat(out.up, source.up, _rot);
+        Quat.slerp(_rotUp, Quat.Identity, Quat.rotationTo(_rotUp, source.up, target.up), t);
+        Vec3.transformQuat(out.up, source.up, _rotUp);
 
         // Lerp target, position & radius
         Vec3.lerp(out.target, source.target, target.target, t);
-        Vec3.lerp(out.position, source.position, target.position, t);
+
+        // Interpolate distance
+        const distSource = Vec3.distance(source.target, source.position);
+        const distTarget = Vec3.distance(target.target, target.position);
+        const dist = lerp(distSource, distTarget, t);
+
+        // Rotate between source and targer direction
+        Vec3.sub(_sourcePosition, source.position, source.target);
+        Vec3.normalize(_sourcePosition, _sourcePosition);
+
+        Vec3.sub(_targetPosition, target.position, target.target);
+        Vec3.normalize(_targetPosition, _targetPosition);
+
+        Quat.rotationTo(_rotDist, _sourcePosition, _targetPosition);
+        Quat.slerp(_rotDist, Quat.Identity, _rotDist, t);
+
+        Vec3.transformQuat(_sourcePosition, _sourcePosition, _rotDist);
+        Vec3.scale(_sourcePosition, _sourcePosition, dist);
+
+        Vec3.add(out.position, out.target, _sourcePosition);
+
+        // Interpolate radius
         out.radius = lerp(source.radius, target.radius, t);
         // TODO take change of `clipFar` into account
         out.radiusMax = lerp(source.radiusMax, target.radiusMax, t);
 
-        // Lerp fov & fog
+        // Interpolate fov & fog
         out.fov = lerp(source.fov, target.fov, t);
         out.fog = lerp(source.fog, target.fog, t);
     }

src/mol-canvas3d/canvas3d.ts

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
-import { BehaviorSubject, Subscription } from 'rxjs';
+import { BehaviorSubject, Subject, Subscription, debounceTime, merge } from 'rxjs';
 import { now } from '../mol-util/now';
 import { Vec3, Vec2 } from '../mol-math/linear-algebra';
 import { InputObserver, ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
@@ -44,6 +44,8 @@ import { degToRad, radToDeg } from '../mol-math/misc';
 import { AssetManager } from '../mol-util/assets';
 import { deepClone } from '../mol-util/object';
 import { HiZParams, HiZPass } from './passes/hi-z';
+import { IlluminationParams } from './passes/illumination';
+import { isMobileBrowser } from '../mol-util/browser';
 
 export const Canvas3DParams = {
     camera: PD.Group({
@@ -87,11 +89,13 @@ export const Canvas3DParams = {
     sceneRadiusFactor: PD.Numeric(1, { min: 1, max: 10, step: 0.1 }),
     transparentBackground: PD.Boolean(false),
     dpoitIterations: PD.Numeric(2, { min: 1, max: 10, step: 1 }),
-    pickPadding: PD.Numeric(3, { min: 0, max: 10, step: 1 }, { description: 'extra pixels to around target to check in case target is empty' }),
+    pickPadding: PD.Numeric(3, { min: 0, max: 10, step: 1 }, { description: 'Extra pixels to around target to check in case target is empty.' }),
+    userInteractionReleaseMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time before the user is not considered interacting anymore.' }),
 
     multiSample: PD.Group(MultiSampleParams),
     postprocessing: PD.Group(PostprocessingParams),
     marking: PD.Group(MarkingParams),
+    illumination: PD.Group(IlluminationParams),
     hiZ: PD.Group(HiZParams),
     renderer: PD.Group(RendererParams),
     trackball: PD.Group(TrackballControlsParams),
@@ -119,7 +123,9 @@ interface Canvas3DContext {
     readonly contextRestored?: BehaviorSubject<now.Timestamp>
     readonly assetManager: AssetManager
     readonly changed?: BehaviorSubject<undefined>
+    readonly pixelScale: number
 
+    syncPixelScale(): void
     setProps: (props?: Partial<Canvas3DContext.Props>) => void
     dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => void
 }
@@ -139,6 +145,7 @@ namespace Canvas3DContext {
     export type Attribs = typeof DefaultAttribs
 
     export const Params = {
+        resolutionMode: PD.Select('auto', PD.arrayToOptions(['auto', 'scaled', 'native'] as const)),
         pixelScale: PD.Numeric(1, { min: 0.1, max: 2, step: 0.05 }),
         pickScale: PD.Numeric(0.25, { min: 0.1, max: 1, step: 0.05 }),
         transparency: PD.Select('wboit', [['blended', 'Blended'], ['wboit', 'Weighted, Blended'], ['dpoit', 'Depth Peeling']] as const),
@@ -163,7 +170,21 @@ namespace Canvas3DContext {
         });
         if (gl === null) throw new Error('Could not create a WebGL rendering context');
 
-        const { pixelScale, pickScale, transparency } = p;
+        const getPixelScale = () => {
+            const scaled = (p.pixelScale / (typeof window !== 'undefined' ? (window?.devicePixelRatio || 1) : 1));
+            if (p.resolutionMode === 'auto') {
+                return isMobileBrowser() ? scaled : p.pixelScale;
+            }
+            return p.resolutionMode === 'native' ? p.pixelScale : scaled;
+        };
+        const syncPixelScale = () => {
+            const pixelScale = getPixelScale();
+            input.setPixelScale(pixelScale);
+            webgl.setPixelScale(pixelScale);
+        };
+
+        const { pickScale, transparency } = p;
+        const pixelScale = getPixelScale();
         const input = InputObserver.fromElement(canvas, { pixelScale, preventGestures: true });
         const webgl = createContext(gl, { pixelScale });
         const passes = new Passes(webgl, assetManager, { pickScale, transparency });
@@ -224,16 +245,27 @@ namespace Canvas3DContext {
             contextRestored: webgl.contextRestored,
             assetManager,
             changed,
+            get pixelScale() { return getPixelScale(); },
 
+            syncPixelScale,
             setProps: (props?: Partial<Props>) => {
                 if (!props) return;
 
                 let hasChanged = false;
+                let pixelScaleNeedsUpdate = false;
+
+                if (props.resolutionMode !== undefined && props.resolutionMode !== p.resolutionMode) {
+                    p.resolutionMode = props.resolutionMode;
+                    pixelScaleNeedsUpdate = true;
+                }
 
                 if (props.pixelScale !== undefined && props.pixelScale !== p.pixelScale) {
                     p.pixelScale = props.pixelScale;
-                    input.setPixelScale(props.pixelScale);
-                    webgl.setPixelScale(props.pixelScale);
+                    pixelScaleNeedsUpdate = true;
+                }
+
+                if (pixelScaleNeedsUpdate) {
+                    syncPixelScale();
                     a.handleResize();
                     hasChanged = true;
                 }
@@ -278,7 +310,7 @@ interface Canvas3D {
      * Function for external "animation" control
      * Calls commit.
      */
-    tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean }): void
+    tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean, updateControls?: boolean }): void
     update(repr?: Representation.Any, keepBoundingSphere?: boolean): void
     clear(): void
     syncVisibility(): void
@@ -346,6 +378,7 @@ namespace Canvas3D {
         const reprRenderObjects = new Map<Representation.Any, Set<GraphicsRenderObject>>();
         const reprUpdatedSubscriptions = new Map<Representation.Any, Subscription>();
         const reprCount = new BehaviorSubject(0);
+        const interactionEvent = new Subject<void>();
 
         let startTime = now();
         const didDraw = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
@@ -443,6 +476,8 @@ namespace Canvas3D {
                 scene.update(void 0, true);
                 helper.handle.scene.update(void 0, true);
                 helper.camera.scene.update(void 0, true);
+
+                interactionEvent.next();
             }
             return changed;
         }
@@ -460,6 +495,8 @@ namespace Canvas3D {
             return changed;
         }
 
+        let fenceSync: WebGLSync | null = null;
+
         function render(force: boolean) {
             if (webgl.isContextLost) return false;
 
@@ -474,6 +511,14 @@ namespace Canvas3D {
                 y > gl.drawingBufferHeight || y + height < 0
             ) return false;
 
+            if (fenceSync !== null) {
+                if (webgl.checkSyncStatus(fenceSync)) {
+                    fenceSync = null;
+                } else {
+                    return false;
+                }
+            }
+
             const markingUpdated = resolveMarking() && (renderer.props.colorMarker || p.marking.enabled);
 
             let didRender = false;
@@ -483,29 +528,55 @@ namespace Canvas3D {
             const shouldRender = force || cameraChanged || resized || forceNextRender;
             forceNextRender = false;
 
-            const multiSampleChanged = multiSampleHelper.update(markingUpdated || shouldRender, p.multiSample);
-
-            if (shouldRender || multiSampleChanged || markingUpdated) {
-                let cam: Camera | StereoCamera = camera;
-                if (p.camera.stereo.name === 'on') {
-                    stereoCamera.update();
-                    cam = stereoCamera;
+            if (passes.illumination.supported && p.illumination.enabled) {
+                if (shouldRender || markingUpdated) {
+                    renderer.setOcclusionTest(null);
+                    passes.illumination.reset();
                 }
 
-                if (isTimingMode) webgl.timer.mark('Canvas3D.render', true);
-                const ctx = { renderer, camera: cam, scene, helper };
-                if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    const forceOn = p.multiSample.reduceFlicker && !cameraChanged && markingUpdated && !controls.isAnimating;
-                    multiSampleHelper.render(ctx, p, true, forceOn);
-                } else {
-                    passes.draw.render(ctx, p, true);
-                }
-                hiZ.render(camera);
-                if (isTimingMode) webgl.timer.markEnd('Canvas3D.render');
+                if (passes.illumination.shouldRender(p)
+                    && ((!isActivelyInteracting && scene.count > 0) || passes.illumination.iteration === 0 || p.userInteractionReleaseMs === 0)
+                ) {
+                    if (isTimingMode) webgl.timer.mark('Canvas3D.render', { captureStats: true });
+                    const ctx = { renderer, camera, scene, helper };
+                    passes.illumination.render(ctx, p, true);
+                    if (isTimingMode) webgl.timer.markEnd('Canvas3D.render');
 
-                // if only marking has updated, do not set the flag to dirty
-                pickHelper.dirty = pickHelper.dirty || shouldRender;
-                didRender = true;
+                    // if only marking has updated, do not set the flag to dirty
+                    pickHelper.dirty = pickHelper.dirty || shouldRender;
+                    didRender = true;
+                }
+            } else {
+                const multiSampleChanged = multiSampleHelper.update(markingUpdated || shouldRender, p.multiSample);
+
+                if (shouldRender || multiSampleChanged || markingUpdated) {
+                    renderer.setOcclusionTest(hiZ.isOccluded);
+
+                    let cam: Camera | StereoCamera = camera;
+                    if (p.camera.stereo.name === 'on') {
+                        stereoCamera.update();
+                        cam = stereoCamera;
+                    }
+
+                    if (isTimingMode) webgl.timer.mark('Canvas3D.render', { captureStats: true });
+                    const ctx = { renderer, camera: cam, scene, helper };
+                    if (MultiSamplePass.isEnabled(p.multiSample)) {
+                        const forceOn = p.multiSample.reduceFlicker && !cameraChanged && markingUpdated && !controls.isAnimating;
+                        multiSampleHelper.render(ctx, p, true, forceOn);
+                    } else {
+                        passes.draw.render(ctx, p, true);
+                    }
+                    hiZ.render(camera);
+                    if (isTimingMode) webgl.timer.markEnd('Canvas3D.render');
+
+                    // if only marking has updated, do not set the flag to dirty
+                    pickHelper.dirty = pickHelper.dirty || shouldRender;
+                    didRender = true;
+                }
+            }
+
+            if (didRender) {
+                fenceSync = webgl.getFenceSync();
             }
 
             return didRender;
@@ -527,9 +598,15 @@ namespace Canvas3D {
 
         let animationFrameHandle = 0;
 
-        function tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean }) {
+        function tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean, updateControls?: boolean }) {
             currentTime = t;
             commit(options?.isSynchronous);
+
+            // update the controler before the camera transition
+            if (options?.updateControls) {
+                controls.update(currentTime);
+            }
+
             camera.transition.tick(currentTime);
             hiZ.tick();
 
@@ -768,11 +845,13 @@ namespace Canvas3D {
                 transparentBackground: p.transparentBackground,
                 dpoitIterations: p.dpoitIterations,
                 pickPadding: p.pickPadding,
+                userInteractionReleaseMs: p.userInteractionReleaseMs,
                 viewport: p.viewport,
 
                 postprocessing: { ...p.postprocessing },
                 marking: { ...p.marking },
                 multiSample: { ...p.multiSample },
+                illumination: { ...p.illumination },
                 hiZ: { ...hiZ.props },
                 renderer: { ...renderer.props },
                 trackball: { ...controls.props },
@@ -808,6 +887,37 @@ namespace Canvas3D {
             requestDraw();
         });
 
+        // Monitor user interactions
+        let isDragging = false;
+        let isActivelyInteracting = false;
+        let interactionSubs = [
+            input.drag.subscribe(() => {
+                isDragging = true;
+            }),
+            input.interactionEnd.subscribe(() => {
+                isDragging = false;
+            }),
+            merge(
+                input.drag,
+                input.pinch,
+                input.wheel,
+                input.interactionEnd,
+            ).subscribe(() => {
+                interactionEvent.next();
+            }),
+            interactionEvent.subscribe(() => {
+                isActivelyInteracting = true;
+            }),
+            interactionEvent.pipe(
+                debounceTime(p.userInteractionReleaseMs)
+            ).subscribe(() => {
+                isActivelyInteracting = isDragging;
+                if (!isDragging && passes.illumination.supported && p.illumination.enabled) {
+                    requestDraw();
+                }
+            }),
+        ];
+
         //
 
         if (isDebugMode && canvas) {
@@ -863,6 +973,7 @@ namespace Canvas3D {
                 reprRenderObjects.clear();
                 scene.clear();
                 helper.debug.clear();
+                if (fenceSync !== null) webgl.deleteSync(fenceSync);
                 requestDraw();
                 reprCount.next(reprRenderObjects.size);
             },
@@ -956,6 +1067,7 @@ namespace Canvas3D {
                 if (props.transparentBackground !== undefined) p.transparentBackground = props.transparentBackground;
                 if (props.dpoitIterations !== undefined) p.dpoitIterations = props.dpoitIterations;
                 if (props.pickPadding !== undefined) p.pickPadding = props.pickPadding;
+                if (props.userInteractionReleaseMs !== undefined) p.userInteractionReleaseMs = props.userInteractionReleaseMs;
                 if (props.viewport !== undefined) {
                     const doNotUpdate = p.viewport === props.viewport ||
                         (p.viewport.name === props.viewport.name && shallowEqual(p.viewport.params, props.viewport.params));
@@ -975,6 +1087,7 @@ namespace Canvas3D {
                 }
                 if (props.postprocessing) Object.assign(p.postprocessing, props.postprocessing);
                 if (props.marking) Object.assign(p.marking, props.marking);
+                if (props.illumination) Object.assign(p.illumination, props.illumination);
                 if (props.multiSample) Object.assign(p.multiSample, props.multiSample);
                 if (props.hiZ) hiZ.setProps(props.hiZ);
                 if (props.renderer) renderer.setProps(props.renderer);
@@ -1015,6 +1128,10 @@ namespace Canvas3D {
             dispose: () => {
                 contextRestoredSub.unsubscribe();
                 ctxChangedSub?.unsubscribe();
+
+                for (const s of interactionSubs) s.unsubscribe();
+                interactionSubs = [];
+
                 cancelAnimationFrame(animationFrameHandle);
 
                 markBuffer = [];
@@ -1025,6 +1142,7 @@ namespace Canvas3D {
                 renderer.dispose();
                 interactionHelper.dispose();
                 hiZ.dispose();
+                if (fenceSync !== null) webgl.deleteSync(fenceSync);
 
                 removeConsoleStatsProvider(consoleStats);
             }

src/mol-canvas3d/controls/trackball.ts

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Herman Bergwerf <post@hbergwerf.nl>
  *
  * This code has been modified from https://github.com/mrdoob/three.js/,
  * copyright (c) 2010-2018 three.js authors. MIT License
@@ -10,7 +11,7 @@
 
 import { Quat, Vec2, Vec3, EPSILON } from '../../mol-math/linear-algebra';
 import { Viewport } from '../camera/util';
-import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys, GestureInput, KeyInput, MoveInput } from '../../mol-util/input/input-observer';
+import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys, KeyInput, MoveInput } from '../../mol-util/input/input-observer';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera } from '../camera';
 import { absMax, degToRad } from '../../mol-math/misc';
@@ -67,7 +68,7 @@ export const TrackballControlsParams = {
     animate: PD.MappedStatic('off', {
         off: PD.EmptyGroup(),
         spin: PD.Group({
-            speed: PD.Numeric(1, { min: -20, max: 20, step: 1 }),
+            speed: PD.Numeric(1, { min: -20, max: 20, step: 1 }, { description: 'Rotation speed in radians per second' }),
         }, { description: 'Spin the 3D scene around the x-axis in view space' }),
         rock: PD.Group({
             speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }),
@@ -134,7 +135,6 @@ namespace TrackballControls {
         const interactionEndSub = input.interactionEnd.subscribe(onInteractionEnd);
         const wheelSub = input.wheel.subscribe(onWheel);
         const pinchSub = input.pinch.subscribe(onPinch);
-        const gestureSub = input.gesture.subscribe(onGesture);
         const keyDownSub = input.keyDown.subscribe(onKeyDown);
         const keyUpSub = input.keyUp.subscribe(onKeyUp);
         const moveSub = input.move.subscribe(onMove);
@@ -614,18 +614,27 @@ namespace TrackballControls {
             }
         }
 
-        function onPinch({ fractionDelta, buttons, modifiers }: PinchInput) {
-            if (Binding.match(b.scrollZoom, buttons, modifiers)) {
-                _isInteracting = true;
+        function onPinch({ isStart, startX, startY, centerPageX, centerPageY, fractionDelta, buttons, modifiers }: PinchInput) {
+            if (outsideViewport(startX, startY)) return;
+
+            const pan = Binding.match(b.dragPan, buttons, modifiers);
+            const zoom = Binding.match(b.scrollZoom, buttons, modifiers);
+            _isInteracting = pan || zoom;
+
+            if (pan) {
+                getMouseOnScreen(centerPageX, centerPageY);
+                if (isStart) {
+                    Vec2.copy(_panStart, mouseOnScreenVec2);
+                    Vec2.copy(_panEnd, _panStart);
+                } else {
+                    Vec2.copy(_panEnd, mouseOnScreenVec2);
+                }
+            }
+            if (zoom) {
                 _zoomEnd[1] += p.gestureScaleFactor * fractionDelta;
             }
         }
 
-        function onGesture({ deltaScale }: GestureInput) {
-            _isInteracting = true;
-            _zoomEnd[1] += p.gestureScaleFactor * deltaScale;
-        }
-
         function onMove({ movementX, movementY }: MoveInput) {
             if (!input.pointerLock || movementX === undefined || movementY === undefined) return;
 
@@ -804,7 +813,6 @@ namespace TrackballControls {
             dragSub.unsubscribe();
             wheelSub.unsubscribe();
             pinchSub.unsubscribe();
-            gestureSub.unsubscribe();
             interactionEndSub.unsubscribe();
             keyDownSub.unsubscribe();
             keyUpSub.unsubscribe();
@@ -817,8 +825,8 @@ namespace TrackballControls {
         function spin(deltaT: number) {
             if (p.animate.name !== 'spin' || p.animate.params.speed === 0 || _isInteracting) return;
 
-            const frameSpeed = p.animate.params.speed / 1000;
-            _spinSpeed[0] = 60 * Math.min(Math.abs(deltaT), 1000 / 8) / 1000 * frameSpeed;
+            const radPerMs = p.animate.params.speed / 1000;
+            _spinSpeed[0] = deltaT * radPerMs / getRotateFactor();
             Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
         }
 

src/mol-canvas3d/passes/background.ts

@@ -310,8 +310,29 @@ export class BackgroundPass {
         );
     }
 
-    render() {
-        if (!this.isReady()) return;
+    private readonly bgColor = Vec3();
+
+    clear(props: BackgroundProps, transparentBackground: boolean, backgroundColor: Color) {
+        const { gl, state } = this.webgl;
+
+        if (this.isEnabled(props)) {
+            if (transparentBackground) {
+                state.clearColor(0, 0, 0, 0);
+            } else {
+                Color.toVec3Normalized(this.bgColor, backgroundColor);
+                state.clearColor(this.bgColor[0], this.bgColor[1], this.bgColor[2], 1);
+            }
+            gl.clear(gl.COLOR_BUFFER_BIT);
+            state.enable(gl.BLEND);
+            state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
+        } else {
+            state.clearColor(0, 0, 0, 1);
+            gl.clear(gl.COLOR_BUFFER_BIT);
+        }
+    }
+
+    render(props: BackgroundProps) {
+        if (!this.isEnabled(props) || !this.isReady()) return;
 
         if (this.renderable.values.dVariant.ref.value === 'image') {
             this.updateImageScaling();

src/mol-canvas3d/passes/dof.ts

@@ -0,0 +1,212 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Ludovic Autin <autin@scripps.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { TextureSpec, UniformSpec, DefineSpec, Values } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Texture, createNullTexture } from '../../mol-gl/webgl/texture';
+import { Mat4, Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
+import { ValueCell } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { dof_frag } from '../../mol-gl/shader/dof.frag';
+import { Viewport } from '../camera/util';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { isTimingMode } from '../../mol-util/debug';
+import { ICamera } from '../../mol-canvas3d/camera';
+import { Sphere3D } from '../../mol-math/geometry';
+import { PostprocessingProps } from './postprocessing';
+
+export const DofParams = {
+    blurSize: PD.Numeric(9, { min: 1, max: 32, step: 1 }),
+    blurSpread: PD.Numeric(1.0, { min: 0.0, max: 10.0, step: 0.1 }),
+    inFocus: PD.Numeric(0.0, { min: -5000.0, max: 5000.0, step: 1.0 }, { description: 'Distance from the scene center that will be in focus' }),
+    PPM: PD.Numeric(20.0, { min: 0.0, max: 5000.0, step: 0.1 }, { description: 'Size of the area that will be in focus' }),
+    center: PD.Select('camera-target', PD.arrayToOptions(['scene-center', 'camera-target'])),
+    mode: PD.Select('plane', PD.arrayToOptions(['plane', 'sphere'])),
+};
+
+export type DofProps = PD.Values<typeof DofParams>
+
+export class DofPass {
+    static isEnabled(props: PostprocessingProps) {
+        return props.dof.name !== 'off';
+    }
+
+    readonly target: RenderTarget;
+    private readonly renderable: DofRenderable;
+
+    constructor(private webgl: WebGLContext, width: number, height: number) {
+        this.target = webgl.createRenderTarget(width, height, false);
+
+        const nullTexture = createNullTexture();
+        this.renderable = getDofRenderable(webgl, nullTexture, nullTexture, nullTexture);
+    }
+
+    private updateState(viewport: Viewport) {
+        const { gl, state } = this.webgl;
+
+        state.enable(gl.SCISSOR_TEST);
+        state.disable(gl.BLEND);
+        state.disable(gl.DEPTH_TEST);
+        state.depthMask(false);
+
+        const { x, y, width, height } = viewport;
+        state.viewport(x, y, width, height);
+        state.scissor(x, y, width, height);
+
+        state.clearColor(0, 0, 0, 1);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+    }
+
+    setSize(width: number, height: number) {
+        const w = this.target.texture.getWidth();
+        const h = this.target.texture.getHeight();
+
+        if (width !== w || height !== h) {
+            this.target.setSize(width, height);
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    update(camera: ICamera, input: Texture, depthOpaque: Texture, depthTransparent: Texture, props: DofProps, sphere: Sphere3D) {
+        let needsUpdate = false;
+        if (this.renderable.values.tColor.ref.value !== input) {
+            ValueCell.update(this.renderable.values.tColor, input);
+            needsUpdate = true;
+        }
+        if (this.renderable.values.tDepthOpaque.ref.value !== depthOpaque) {
+            ValueCell.update(this.renderable.values.tDepthOpaque, depthOpaque);
+            needsUpdate = true;
+        }
+        if (this.renderable.values.tDepthTransparent.ref.value !== depthTransparent) {
+            ValueCell.update(this.renderable.values.tDepthTransparent, depthTransparent);
+            needsUpdate = true;
+        }
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+        const invProjection = this.renderable.values.uInvProjection.ref.value;
+        Mat4.invert(invProjection, camera.projection);
+
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        const v = camera.viewport;
+
+        ValueCell.update(this.renderable.values.uProjection, camera.projection);
+        ValueCell.update(this.renderable.values.uInvProjection, invProjection);
+        ValueCell.update(this.renderable.values.uMode, props.mode === 'sphere' ? 1 : 0);
+
+        Vec4.set(this.renderable.values.uBounds.ref.value,
+            v.x / w,
+            v.y / h,
+            (v.x + v.width) / w,
+            (v.y + v.height) / h
+        );
+        ValueCell.update(this.renderable.values.uBounds, this.renderable.values.uBounds.ref.value);
+
+        ValueCell.updateIfChanged(this.renderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.renderable.values.uFar, camera.far);
+        ValueCell.updateIfChanged(this.renderable.values.dOrthographic, orthographic);
+
+        const blurSize = Math.round(props.blurSize * this.webgl.pixelRatio);
+        if (this.renderable.values.dBlurSize.ref.value !== blurSize) {
+            ValueCell.update(this.renderable.values.dBlurSize, blurSize);
+            needsUpdate = true;
+        }
+
+        const wolrdCenter = (props.center === 'scene-center' ? sphere.center : camera.state.target);
+        const distance = Vec3.distance(camera.state.position, wolrdCenter);
+        const inFocus = distance + props.inFocus;
+        ValueCell.updateIfChanged(this.renderable.values.uInFocus, inFocus);
+
+        // transform center in view space
+        const center = this.renderable.values.uCenter.ref.value;
+        Vec3.transformMat4(center, wolrdCenter, camera.view);
+        ValueCell.update(this.renderable.values.uCenter, center);
+
+        ValueCell.updateIfChanged(this.renderable.values.uBlurSpread, props.blurSpread);
+        ValueCell.updateIfChanged(this.renderable.values.uPPM, props.PPM);
+
+        if (needsUpdate) {
+            this.renderable.update();
+        }
+    }
+
+    render(viewport: Viewport, target: undefined | RenderTarget) {
+        if (isTimingMode) this.webgl.timer.mark('DofPass.render');
+        if (target) {
+            target.bind();
+        } else {
+            this.webgl.unbindFramebuffer();
+        }
+        this.updateState(viewport);
+        this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('DofPass.render');
+    }
+}
+
+//
+
+const DofSchema = {
+    ...QuadSchema,
+    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    uProjection: UniformSpec('m4'),
+    uInvProjection: UniformSpec('m4'),
+    uBounds: UniformSpec('v4'),
+    uCenter: UniformSpec('v3'),
+    uMode: UniformSpec('i'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+
+    dBlurSize: DefineSpec('number'),
+    uBlurSpread: UniformSpec('f'),
+    uInFocus: UniformSpec('f'),
+    uPPM: UniformSpec('f'),
+};
+
+const DofShaderCode = ShaderCode('dof', quad_vert, dof_frag);
+type DofRenderable = ComputeRenderable<Values<typeof DofSchema>>
+
+function getDofRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture): DofRenderable {
+    const width = colorTexture.getWidth();
+    const height = colorTexture.getHeight();
+
+    const values: Values<typeof DofSchema> = {
+        ...QuadValues,
+        tDepthOpaque: ValueCell.create(depthTextureOpaque),
+        tDepthTransparent: ValueCell.create(depthTextureTransparent),
+        tColor: ValueCell.create(colorTexture),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
+
+        uProjection: ValueCell.create(Mat4.identity()),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+        uBounds: ValueCell.create(Vec4()),
+        uCenter: ValueCell.create(Vec3()),
+        uMode: ValueCell.create(0),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+
+        dBlurSize: ValueCell.create(5),
+        uBlurSpread: ValueCell.create(300.0),
+        uInFocus: ValueCell.create(20.0),
+        uPPM: ValueCell.create(20.0),
+    };
+
+    const schema = { ...DofSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', DofShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-canvas3d/passes/draw.ts

@@ -24,6 +24,7 @@ import { MarkingPass, MarkingProps } from './marking';
 import { CopyRenderable, createCopyRenderable } from '../../mol-gl/compute/util';
 import { isDebugMode, isTimingMode } from '../../mol-util/debug';
 import { AssetManager } from '../../mol-util/assets';
+import { DofPass } from './dof';
 import { BloomPass } from './bloom';
 
 type Props = {
@@ -46,12 +47,13 @@ export class DrawPass {
     private readonly drawTarget: RenderTarget;
 
     readonly colorTarget: RenderTarget;
+    readonly transparentColorTarget: RenderTarget;
     readonly depthTextureTransparent: Texture;
     readonly depthTextureOpaque: Texture;
 
     readonly packedDepth: boolean;
 
-    private depthTargetTransparent: RenderTarget;
+    readonly depthTargetTransparent: RenderTarget;
     private depthTargetOpaque: RenderTarget | null;
 
     private copyFboTarget: CopyRenderable;
@@ -63,6 +65,7 @@ export class DrawPass {
     readonly postprocessing: PostprocessingPass;
     readonly antialiasing: AntialiasingPass;
     readonly bloom: BloomPass;
+    readonly dof: DofPass;
 
     private transparencyMode: TransparencyMode = 'blended';
     setTransparency(transparency: 'wboit' | 'dpoit' | 'blended') {
@@ -89,6 +92,8 @@ export class DrawPass {
         const { extensions, resources, isWebGL2 } = webgl;
         this.drawTarget = createNullRenderTarget(webgl.gl);
         this.colorTarget = webgl.createRenderTarget(width, height, true, 'uint8', 'linear');
+        this.transparentColorTarget = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
+
         this.packedDepth = !extensions.depthTexture;
 
         this.depthTargetTransparent = webgl.createRenderTarget(width, height);
@@ -107,6 +112,7 @@ export class DrawPass {
         this.postprocessing = new PostprocessingPass(webgl, assetManager, this);
         this.antialiasing = new AntialiasingPass(webgl, width, height);
         this.bloom = new BloomPass(webgl, width, height);
+        this.dof = new DofPass(webgl, width, height);
 
         this.copyFboTarget = createCopyRenderable(webgl, this.colorTarget.texture);
         this.copyFboPostprocessing = createCopyRenderable(webgl, this.postprocessing.target.texture);
@@ -126,6 +132,7 @@ export class DrawPass {
         if (width !== w || height !== h) {
             this.colorTarget.setSize(width, height);
             this.depthTargetTransparent.setSize(width, height);
+            this.transparentColorTarget.setSize(width, height);
 
             if (this.depthTargetOpaque) {
                 this.depthTargetOpaque.setSize(width, height);
@@ -148,6 +155,7 @@ export class DrawPass {
         this.marking.setSize(width, height);
         this.postprocessing.setSize(width, height);
         this.antialiasing.setSize(width, height);
+        this.dof.setSize(width, height);
         this.bloom.setSize(width, height);
     }
 
@@ -159,27 +167,27 @@ export class DrawPass {
 
         // render opaque primitives
         if (scene.hasOpaque) {
-            renderer.renderDpoitOpaque(scene.primitives, camera, null);
-        }
-
-        if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
-                this.depthTargetTransparent.bind();
-                renderer.clearDepth(true);
-                if (scene.opacityAverage < 1) {
-                    renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
-                }
-            }
-
-            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
+            renderer.renderOpaque(scene.primitives, camera);
         }
 
         this.depthTextureOpaque.detachFramebuffer(this.colorTarget.framebuffer, 'depth');
 
+        if (PostprocessingPass.isTransparentDepthRequired(scene, postprocessingProps)) {
+            this.depthTargetTransparent.bind();
+            renderer.clearDepth(true);
+            if (scene.opacityAverage < 1) {
+                renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
+            }
+        }
+
         // render transparent primitives
+        const isPostprocessingEnabled = PostprocessingPass.isEnabled(postprocessingProps);
         if (scene.opacityAverage < 1) {
-            const target = PostprocessingPass.isEnabled(postprocessingProps)
-                ? this.postprocessing.target : this.colorTarget;
+            const target = isPostprocessingEnabled ? this.transparentColorTarget : this.colorTarget;
+            if (isPostprocessingEnabled) {
+                target.bind();
+                renderer.clear(false, false, true);
+            }
 
             const dpoitTextures = this.dpoit.bind();
             renderer.renderDpoitTransparent(scene.primitives, camera, this.depthTextureOpaque, dpoitTextures);
@@ -199,9 +207,13 @@ export class DrawPass {
             this.dpoit.render();
         }
 
+        if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            this.postprocessing.render(camera, scene, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light, renderer.ambientColor);
+        }
+
         // render transparent volumes
         if (scene.volumes.renderables.length > 0) {
-            renderer.renderDpoitVolume(scene.volumes, camera, this.depthTextureOpaque);
+            renderer.renderVolume(scene.volumes, camera, this.depthTextureOpaque);
         }
     }
 
@@ -213,39 +225,49 @@ export class DrawPass {
 
         // render opaque primitives
         if (scene.hasOpaque) {
-            renderer.renderWboitOpaque(scene.primitives, camera, null);
+            renderer.renderOpaque(scene.primitives, camera);
+        }
+
+        if (PostprocessingPass.isTransparentDepthRequired(scene, postprocessingProps)) {
+            this.depthTargetTransparent.bind();
+            renderer.clearDepth(true);
+            if (scene.opacityAverage < 1) {
+                renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
+            }
+        }
+
+        // render transparent primitives
+        const isPostprocessingEnabled = PostprocessingPass.isEnabled(postprocessingProps);
+        if (scene.opacityAverage < 1) {
+            const target = isPostprocessingEnabled ? this.transparentColorTarget : this.colorTarget;
+            if (isPostprocessingEnabled) {
+                target.bind();
+                renderer.clear(false, false, true);
+            }
+
+            this.wboit.bind();
+            renderer.renderWboitTransparent(scene.primitives, camera, this.depthTextureOpaque);
+
+            // evaluate wboit
+            target.bind();
+            this.wboit.render();
         }
 
         if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
-                this.depthTargetTransparent.bind();
-                renderer.clearDepth(true);
-                if (scene.opacityAverage < 1) {
-                    renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
-                }
-            }
-
-            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
+            this.postprocessing.render(camera, scene, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light, renderer.ambientColor);
         }
 
-        // render transparent primitives and volumes
-        if (scene.opacityAverage < 1 || scene.volumes.renderables.length > 0) {
+        // render volumes
+        if (scene.volumes.renderables.length > 0) {
             this.wboit.bind();
-            if (scene.opacityAverage < 1) {
-                renderer.renderWboitTransparent(scene.primitives, camera, this.depthTextureOpaque);
-            }
-            if (scene.volumes.renderables.length > 0) {
-                renderer.renderWboitTransparent(scene.volumes, camera, this.depthTextureOpaque);
-            }
+            renderer.renderWboitTransparent(scene.volumes, camera, this.depthTextureOpaque);
 
             // evaluate wboit
-            if (PostprocessingPass.isEnabled(postprocessingProps)) {
-                this.postprocessing.target.bind();
-            } else {
-                this.colorTarget.bind();
-            }
+            const target = isPostprocessingEnabled ? this.postprocessing.target : this.colorTarget;
+            target.bind();
             this.wboit.render();
         }
+
     }
 
     private _renderBlended(renderer: Renderer, camera: ICamera, scene: Scene, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
@@ -261,7 +283,7 @@ export class DrawPass {
 
         renderer.clear(true);
         if (scene.hasOpaque) {
-            renderer.renderBlendedOpaque(scene.primitives, camera, null);
+            renderer.renderOpaque(scene.primitives, camera);
         }
 
         if (!toDrawingBuffer) {
@@ -270,26 +292,51 @@ export class DrawPass {
             if (this.depthTargetOpaque) {
                 this.depthTargetOpaque.bind();
                 renderer.clearDepth(true);
-                renderer.renderDepthOpaque(scene.primitives, camera, null);
+                renderer.renderDepthOpaque(scene.primitives, camera);
                 this.colorTarget.bind();
             }
 
-            if (PostprocessingPass.isEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isTransparentDepthRequired(scene, postprocessingProps)) {
+                this.depthTargetTransparent.bind();
+                renderer.clearDepth(true);
+                if (scene.opacityAverage < 1) {
+                    renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
+                }
+            }
+
+            // render transparent primitives
+            const isPostprocessingEnabled = PostprocessingPass.isEnabled(postprocessingProps);
+            if (scene.opacityAverage < 1) {
+                if (isPostprocessingEnabled) {
+                    this.transparentColorTarget.bind();
+                    renderer.clear(false, false, true);
+
+                    if (!this.packedDepth) {
+                        this.depthTextureOpaque.attachFramebuffer(this.transparentColorTarget.framebuffer, 'depth');
+                    } else {
+                        this.colorTarget.depthRenderbuffer?.detachFramebuffer(this.transparentColorTarget.framebuffer);
+                    }
+                }
+
+                renderer.renderBlendedTransparent(scene.primitives, camera);
+
+                if (isPostprocessingEnabled) {
+                    if (!this.packedDepth) {
+                        this.depthTextureOpaque.detachFramebuffer(this.transparentColorTarget.framebuffer, 'depth');
+                    } else {
+                        this.colorTarget.depthRenderbuffer?.detachFramebuffer(this.transparentColorTarget.framebuffer);
+                    }
+                }
+            }
+
+            if (isPostprocessingEnabled) {
                 if (!this.packedDepth) {
                     this.depthTextureOpaque.detachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
                 } else {
                     this.colorTarget.depthRenderbuffer?.detachFramebuffer(this.postprocessing.target.framebuffer);
                 }
 
-                if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
-                    this.depthTargetTransparent.bind();
-                    renderer.clearDepth(true);
-                    if (scene.opacityAverage < 1) {
-                        renderer.renderDepthTransparent(scene.primitives, camera, this.depthTextureOpaque);
-                    }
-                }
-
-                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
+                this.postprocessing.render(camera, scene, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light, renderer.ambientColor);
 
                 if (!this.packedDepth) {
                     this.depthTextureOpaque.attachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
@@ -309,7 +356,7 @@ export class DrawPass {
                 }
                 target.bind();
 
-                renderer.renderBlendedVolume(scene.volumes, camera, this.depthTextureOpaque);
+                renderer.renderVolume(scene.volumes, camera, this.depthTextureOpaque);
 
                 if (!this.packedDepth) {
                     this.depthTextureOpaque.attachFramebuffer(target.framebuffer, 'depth');
@@ -318,10 +365,8 @@ export class DrawPass {
                 }
                 target.bind();
             }
-        }
-
-        if (scene.opacityAverage < 1) {
-            renderer.renderBlendedTransparent(scene.primitives, camera, null);
+        } else if (scene.opacityAverage < 1) {
+            renderer.renderBlendedTransparent(scene.primitives, camera);
         }
     }
 
@@ -330,6 +375,7 @@ export class DrawPass {
         const postprocessingEnabled = PostprocessingPass.isEnabled(props.postprocessing);
         const antialiasingEnabled = AntialiasingPass.isEnabled(props.postprocessing);
         const markingEnabled = MarkingPass.isEnabled(props.marking);
+        const dofEnabled = DofPass.isEnabled(props.postprocessing);
 
         const { x, y, width, height } = camera.viewport;
         renderer.setViewport(x, y, width, height);
@@ -362,7 +408,7 @@ export class DrawPass {
             if (markingDepthTest && scene.markerAverage !== 1) {
                 this.marking.depthTarget.bind();
                 renderer.clear(false, true);
-                renderer.renderMarkingDepth(scene.primitives, camera, null);
+                renderer.renderMarkingDepth(scene.primitives, camera);
             }
 
             this.marking.maskTarget.bind();
@@ -388,12 +434,30 @@ export class DrawPass {
             renderer.renderBlended(helper.camera.scene, helper.camera.camera);
         }
 
+        let needsTargetCopy = false;
+
         if (antialiasingEnabled) {
             const input = PostprocessingPass.isEnabled(props.postprocessing)
                 ? this.postprocessing.target.texture
                 : this.colorTarget.texture;
-            this.antialiasing.render(camera, input, toDrawingBuffer, props.postprocessing);
-        } else if (toDrawingBuffer) {
+            this.antialiasing.render(camera, input, toDrawingBuffer && !dofEnabled, props.postprocessing);
+        } else if (toDrawingBuffer && !DofPass.isEnabled(props.postprocessing)) {
+            needsTargetCopy = true;
+        }
+
+        if (props.postprocessing.dof.name === 'on') {
+            const input = AntialiasingPass.isEnabled(props.postprocessing)
+                ? this.antialiasing.target.texture
+                : PostprocessingPass.isEnabled(props.postprocessing)
+                    ? this.postprocessing.target.texture
+                    : this.colorTarget.texture;
+            this.dof.update(camera, input, this.depthTargetOpaque?.texture || this.depthTextureOpaque, this.depthTextureTransparent, props.postprocessing.dof.params, scene.boundingSphereVisible);
+            this.dof.render(camera.viewport, toDrawingBuffer ? undefined : this.getColorTarget(props.postprocessing));
+        } else if (toDrawingBuffer && !AntialiasingPass.isEnabled(props.postprocessing)) {
+            needsTargetCopy = true;
+        }
+
+        if (needsTargetCopy) {
             this.drawTarget.bind();
 
             this.webgl.state.disable(this.webgl.gl.DEPTH_TEST);
@@ -411,7 +475,7 @@ export class DrawPass {
                 this.bloom.emissiveTarget.bind();
                 renderer.clear(false, true);
                 renderer.update(camera, scene);
-                renderer.renderEmissive(scene.primitives, camera, null);
+                renderer.renderEmissive(scene.primitives, camera);
             }
 
             if (!emissiveBloom || scene.emissiveAverage > 0) {
@@ -448,7 +512,9 @@ export class DrawPass {
     }
 
     getColorTarget(postprocessingProps: PostprocessingProps): RenderTarget {
-        if (AntialiasingPass.isEnabled(postprocessingProps)) {
+        if (DofPass.isEnabled(postprocessingProps)) {
+            return this.dof.target;
+        } else if (AntialiasingPass.isEnabled(postprocessingProps)) {
             return this.antialiasing.target;
         } else if (PostprocessingPass.isEnabled(postprocessingProps)) {
             return this.postprocessing.target;

src/mol-canvas3d/passes/illumination.ts

@@ -0,0 +1,671 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CopyRenderable, QuadSchema, QuadValues, createCopyRenderable } from '../../mol-gl/compute/util';
+import { DefineSpec, TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { ValueCell } from '../../mol-util';
+import { isDebugMode, isTimingMode } from '../../mol-util/debug';
+import { Renderer, RendererProps } from '../../mol-gl/renderer';
+import { Camera, ICamera } from '../camera';
+import { Scene } from '../../mol-gl/scene';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { compose_frag } from '../../mol-gl/shader/illumination/compose.frag';
+import { Vec2 } from '../../mol-math/linear-algebra/3d/vec2';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Color } from '../../mol-util/color/color';
+import { AntialiasingPass, PostprocessingPass, PostprocessingProps } from './postprocessing';
+import { DrawPass } from './draw';
+import { MarkingPass, MarkingProps } from './marking';
+import { Helper } from '../helper/helper';
+import { DofPass } from './dof';
+import { TracingParams, TracingPass } from './tracing';
+import { JitterVectors, MultiSampleProps } from './multi-sample';
+import { compose_frag as multiSample_compose_frag } from '../../mol-gl/shader/compose.frag';
+import { clamp, lerp } from '../../mol-math/interpolate';
+import { SsaoProps } from './ssao';
+
+type Props = {
+    transparentBackground: boolean;
+    dpoitIterations: number;
+    illumination: IlluminationProps;
+    renderer: RendererProps;
+    postprocessing: PostprocessingProps;
+    marking: MarkingProps;
+    multiSample: MultiSampleProps;
+}
+
+type RenderContext = {
+    renderer: Renderer;
+    camera: Camera;
+    scene: Scene;
+    helper: Helper;
+}
+
+export const IlluminationParams = {
+    enabled: PD.Boolean(false),
+    maxIterations: PD.Numeric(5, { min: 0, max: 16, step: 1 }, { description: 'Maximum number of tracing iterations. Final iteration count is 2^x.' }),
+    denoise: PD.Boolean(true),
+    denoiseThreshold: PD.Interval([0.15, 1], { min: 0, max: 4, step: 0.01 }, { description: 'Threshold for denoising. Automatically adjusted within given interval based on current iteration.' }),
+    ignoreOutline: PD.Boolean(true, { description: 'Ignore outline in illumination pass where it is generally not needed for visual clarity. Useful when illumination is often toggled on/off.' }),
+    ...TracingParams,
+};
+export type IlluminationProps = PD.Values<typeof IlluminationParams>
+
+export class IlluminationPass {
+    private readonly tracing: TracingPass;
+
+    private readonly transparentTarget: RenderTarget;
+    private readonly outputTarget: RenderTarget;
+
+    readonly packedDepth: boolean;
+
+    private readonly copyRenderable: CopyRenderable;
+    private readonly composeRenderable: ComposeRenderable;
+
+    private multiSampleComposeTarget: RenderTarget;
+    private multiSampleHoldTarget: RenderTarget;
+    private multiSampleAccumulateTarget: RenderTarget;
+    private multiSampleCompose: MultiSampleComposeRenderable;
+
+    private _iteration = 0;
+    get iteration() { return this._iteration; }
+
+    private _colorTarget: RenderTarget;
+    get colorTarget() { return this._colorTarget; }
+
+    private _supported = false;
+    get supported() {
+        return this._supported;
+    }
+
+    getMaxIterations(props: Props) {
+        return Math.pow(2, props.illumination.maxIterations);
+    }
+
+    static isSupported(webgl: WebGLContext) {
+        const { drawBuffers, textureFloat, colorBufferFloat, depthTexture } = webgl.extensions;
+        if (!textureFloat || !colorBufferFloat || !depthTexture || !drawBuffers) {
+            if (isDebugMode) {
+                const missing: string[] = [];
+                if (!textureFloat) missing.push('textureFloat');
+                if (!colorBufferFloat) missing.push('colorBufferFloat');
+                if (!depthTexture) missing.push('depthTexture');
+                if (!drawBuffers) missing.push('drawBuffers');
+                console.log(`Missing "${missing.join('", "')}" extensions required for "illumination"`);
+            }
+            return false;
+        } else {
+            return true;
+        }
+    }
+
+    constructor(private readonly webgl: WebGLContext, private readonly drawPass: DrawPass) {
+        if (!IlluminationPass.isSupported(webgl)) return;
+
+        const { colorTarget } = drawPass;
+        const width = colorTarget.getWidth();
+        const height = colorTarget.getHeight();
+
+        this.tracing = new TracingPass(webgl, this.drawPass);
+
+        this.transparentTarget = webgl.createRenderTarget(width, height, false, 'uint8', 'nearest');
+        this.outputTarget = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
+
+        this.copyRenderable = createCopyRenderable(webgl, this.transparentTarget.texture);
+
+        this.composeRenderable = getComposeRenderable(webgl, this.tracing.accumulateTarget.texture, this.tracing.normalTextureOpaque, this.tracing.colorTextureOpaque, this.drawPass.depthTextureOpaque, this.drawPass.depthTargetTransparent.texture, this.drawPass.postprocessing.outline.target.texture, this.transparentTarget.texture, this.drawPass.postprocessing.ssao.ssaoDepthTexture, this.drawPass.postprocessing.ssao.ssaoDepthTransparentTexture, false);
+
+        this.multiSampleComposeTarget = webgl.createRenderTarget(width, height, false, 'float32');
+        this.multiSampleHoldTarget = webgl.createRenderTarget(width, height, false);
+        this.multiSampleAccumulateTarget = webgl.createRenderTarget(width, height, false, 'float32');
+        this.multiSampleCompose = getMultiSampleComposeRenderable(webgl, this.outputTarget.texture);
+
+        this._supported = true;
+    }
+
+    private renderInput(renderer: Renderer, camera: ICamera, scene: Scene, props: Props) {
+        if (isTimingMode) this.webgl.timer.mark('IlluminationPass.renderInput');
+        const { gl, state } = this.webgl;
+
+        const markingEnabled = MarkingPass.isEnabled(props.marking);
+        const hasTransparent = scene.opacityAverage < 1;
+        const hasMarking = markingEnabled && scene.markerAverage > 0;
+
+        this.transparentTarget.bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        if (hasTransparent) {
+            if (this.drawPass.transparency === 'wboit') {
+                this.drawPass.wboit.bind();
+                renderer.renderWboitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque);
+
+                if (scene.volumes.renderables.length > 0) {
+                    renderer.renderWboitTransparent(scene.volumes, camera, this.drawPass.depthTextureOpaque);
+                }
+
+                this.transparentTarget.bind();
+                this.drawPass.wboit.render();
+            } else if (this.drawPass.transparency === 'dpoit') {
+                const dpoitTextures = this.drawPass.dpoit.bind();
+                renderer.renderDpoitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque, dpoitTextures);
+
+                for (let i = 0, il = props.dpoitIterations; i < il; i++) {
+                    if (isTimingMode) this.webgl.timer.mark('DpoitPass.layer');
+                    const dpoitTextures = this.drawPass.dpoit.bindDualDepthPeeling();
+                    renderer.renderDpoitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque, dpoitTextures);
+
+                    this.transparentTarget.bind();
+                    this.drawPass.dpoit.renderBlendBack();
+                    if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.layer');
+                }
+
+                // evaluate dpoit
+                this.transparentTarget.bind();
+                this.drawPass.dpoit.render();
+
+                if (scene.volumes.renderables.length > 0) {
+                    renderer.renderVolume(scene.volumes, camera, this.drawPass.depthTextureOpaque);
+                }
+            } else {
+                this.transparentTarget.bind();
+                this.drawPass.depthTextureOpaque.attachFramebuffer(this.transparentTarget.framebuffer, 'depth');
+                renderer.renderBlendedTransparent(scene.primitives, camera);
+                this.drawPass.depthTextureOpaque.detachFramebuffer(this.transparentTarget.framebuffer, 'depth');
+
+                if (scene.volumes.renderables.length > 0) {
+                    renderer.renderVolume(scene.volumes, camera, this.drawPass.depthTextureOpaque);
+                }
+            }
+
+            const outlineEnabled = PostprocessingPass.isTransparentOutlineEnabled(props.postprocessing) && !props.illumination.ignoreOutline;
+            const dofEnabled = DofPass.isEnabled(props.postprocessing);
+            const ssaoEnabled = PostprocessingPass.isTransparentSsaoEnabled(scene, props.postprocessing);
+
+            if (outlineEnabled || dofEnabled || ssaoEnabled) {
+                this.drawPass.depthTargetTransparent.bind();
+                renderer.clearDepth(true);
+                if (scene.opacityAverage < 1) {
+                    renderer.renderDepthTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque);
+                }
+            }
+
+            if (ssaoEnabled) {
+                this.drawPass.postprocessing.ssao.update(camera, scene, props.postprocessing.occlusion.params as SsaoProps, true);
+                this.drawPass.postprocessing.ssao.render(camera);
+            }
+        }
+
+        //
+
+        if (hasMarking) {
+            const markingDepthTest = props.marking.ghostEdgeStrength < 1;
+            if (markingDepthTest && scene.markerAverage !== 1) {
+                this.drawPass.marking.depthTarget.bind();
+                renderer.clear(false, true);
+                renderer.renderMarkingDepth(scene.primitives, camera);
+            }
+
+            this.drawPass.marking.maskTarget.bind();
+            renderer.clear(false, true);
+            renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.drawPass.marking.depthTarget.texture : null);
+
+            this.drawPass.marking.update(props.marking);
+            this.drawPass.marking.render(camera.viewport, this.transparentTarget);
+        }
+
+        //
+
+        this.tracing.composeTarget.bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+        if (isTimingMode) this.webgl.timer.markEnd('IlluminationPass.renderInput');
+    }
+
+    shouldRender(props: Props) {
+        return this._supported && props.illumination.enabled && this._iteration < this.getMaxIterations(props);
+    }
+
+    setSize(width: number, height: number) {
+        if (!this._supported) return;
+
+        const w = this.outputTarget.getWidth();
+        const h = this.outputTarget.getHeight();
+
+        if (width !== w || height !== h) {
+            this.tracing.setSize(width, height);
+
+            this.transparentTarget.setSize(width, height);
+            this.outputTarget.setSize(width, height);
+
+            ValueCell.update(this.copyRenderable.values.uTexSize, Vec2.set(this.copyRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.composeRenderable.values.uTexSize, Vec2.set(this.composeRenderable.values.uTexSize.ref.value, width, height));
+
+            this.multiSampleComposeTarget.setSize(width, height);
+            this.multiSampleHoldTarget.setSize(width, height);
+            this.multiSampleAccumulateTarget.setSize(width, height);
+            ValueCell.update(this.multiSampleCompose.values.uTexSize, Vec2.set(this.multiSampleCompose.values.uTexSize.ref.value, width, height));
+        }
+
+        this.drawPass.setSize(width, height);
+    }
+
+    reset(clearAdjustedProps = false) {
+        if (!this._supported) return;
+
+        this.tracing.reset(clearAdjustedProps);
+        this._iteration = 0;
+        this.prevSampleIndex = -1;
+    }
+
+    private renderInternal(ctx: RenderContext, props: Props, toDrawingBuffer: boolean, forceRenderInput: boolean) {
+        if (!this.shouldRender(props)) return;
+
+        if (isTimingMode) {
+            this.webgl.timer.mark('IlluminationPass.render', {
+                note: `iteration ${this._iteration + 1} of ${this.getMaxIterations(props)}`
+            });
+        }
+        this.tracing.render(ctx, props.transparentBackground, props.illumination, this._iteration, forceRenderInput);
+
+        const { renderer, camera, scene, helper } = ctx;
+        const { gl, state } = this.webgl;
+        const { x, y, width, height } = camera.viewport;
+
+        if (this._iteration === 0 || forceRenderInput) {
+            // render color & depth
+            renderer.setTransparentBackground(props.transparentBackground);
+            renderer.setDrawingBufferSize(this.tracing.composeTarget.getWidth(), this.tracing.composeTarget.getHeight());
+            renderer.setPixelRatio(this.webgl.pixelRatio);
+            renderer.setViewport(x, y, width, height);
+            renderer.update(camera, scene);
+            this.renderInput(renderer, camera, scene, props);
+        }
+
+        state.disable(gl.BLEND);
+        state.disable(gl.DEPTH_TEST);
+        state.disable(gl.CULL_FACE);
+        state.depthMask(false);
+        state.viewport(x, y, width, height);
+        state.scissor(x, y, width, height);
+
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+
+        const outlinesEnabled = props.postprocessing.outline.name === 'on' && !props.illumination.ignoreOutline;
+        const occlusionEnabled = PostprocessingPass.isTransparentSsaoEnabled(scene, props.postprocessing);
+
+        const markingEnabled = MarkingPass.isEnabled(props.marking);
+        const hasTransparent = scene.opacityAverage < 1;
+        const hasMarking = markingEnabled && scene.markerAverage > 0;
+
+        let needsUpdateCompose = false;
+
+        if (this.composeRenderable.values.dOutlineEnable.ref.value !== outlinesEnabled) {
+            needsUpdateCompose = true;
+            ValueCell.update(this.composeRenderable.values.dOutlineEnable, outlinesEnabled);
+        }
+
+        if (props.postprocessing.outline.name === 'on') {
+            const { transparentOutline, outlineScale } = this.drawPass.postprocessing.outline.update(camera, props.postprocessing.outline.params, this.drawPass.depthTargetTransparent.texture, this.drawPass.depthTextureOpaque);
+            this.drawPass.postprocessing.outline.render();
+
+            ValueCell.update(this.composeRenderable.values.uOutlineColor, Color.toVec3Normalized(this.composeRenderable.values.uOutlineColor.ref.value, props.postprocessing.outline.params.color));
+
+            if (this.composeRenderable.values.dOutlineScale.ref.value !== outlineScale) {
+                needsUpdateCompose = true;
+                ValueCell.update(this.composeRenderable.values.dOutlineScale, outlineScale);
+            }
+            if (this.composeRenderable.values.dTransparentOutline.ref.value !== transparentOutline) {
+                needsUpdateCompose = true;
+                ValueCell.update(this.composeRenderable.values.dTransparentOutline, transparentOutline);
+            }
+        }
+
+        if (this.composeRenderable.values.dOcclusionEnable.ref.value !== occlusionEnabled) {
+            needsUpdateCompose = true;
+            ValueCell.update(this.composeRenderable.values.dOcclusionEnable, occlusionEnabled);
+        }
+
+        if (props.postprocessing.occlusion.name === 'on') {
+            ValueCell.update(this.composeRenderable.values.uOcclusionColor, Color.toVec3Normalized(this.composeRenderable.values.uOcclusionColor.ref.value, props.postprocessing.occlusion.params.color));
+        }
+
+        const blendTransparency = hasTransparent || hasMarking;
+        if (this.composeRenderable.values.dBlendTransparency.ref.value !== blendTransparency) {
+            needsUpdateCompose = true;
+            ValueCell.update(this.composeRenderable.values.dBlendTransparency, blendTransparency);
+        }
+
+        ValueCell.updateIfChanged(this.composeRenderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.composeRenderable.values.uFar, camera.far);
+        ValueCell.updateIfChanged(this.composeRenderable.values.uFogFar, camera.fogFar);
+        ValueCell.updateIfChanged(this.composeRenderable.values.uFogNear, camera.fogNear);
+        ValueCell.update(this.composeRenderable.values.uFogColor, Color.toVec3Normalized(this.composeRenderable.values.uFogColor.ref.value, renderer.props.backgroundColor));
+        if (this.composeRenderable.values.dOrthographic.ref.value !== orthographic) {
+            ValueCell.update(this.composeRenderable.values.dOrthographic, orthographic);
+            needsUpdateCompose = true;
+        }
+
+        // background
+
+        const _toDrawingBuffer = toDrawingBuffer && !AntialiasingPass.isEnabled(props.postprocessing) && props.postprocessing.dof.name === 'off';
+        if (_toDrawingBuffer) {
+            this.webgl.unbindFramebuffer();
+        } else {
+            this.tracing.composeTarget.bind();
+        }
+        this._colorTarget = this.tracing.composeTarget;
+
+        this.drawPass.postprocessing.background.update(camera, props.postprocessing.background);
+        this.drawPass.postprocessing.background.clear(props.postprocessing.background, props.transparentBackground, renderer.props.backgroundColor);
+        this.drawPass.postprocessing.background.render(props.postprocessing.background);
+
+        // compose
+
+        ValueCell.updateIfChanged(this.composeRenderable.values.uTransparentBackground, props.transparentBackground || this.drawPass.postprocessing.background.isEnabled(props.postprocessing.background));
+        if (this.composeRenderable.values.dDenoise.ref.value !== props.illumination.denoise) {
+            ValueCell.update(this.composeRenderable.values.dDenoise, props.illumination.denoise);
+            needsUpdateCompose = true;
+        }
+        const denoiseThreshold = props.multiSample.mode === 'on'
+            ? props.illumination.denoiseThreshold[0]
+            : lerp(props.illumination.denoiseThreshold[1], props.illumination.denoiseThreshold[0], clamp(this.iteration / (this.getMaxIterations(props) / 2), 0, 1));
+        ValueCell.updateIfChanged(this.composeRenderable.values.uDenoiseThreshold, denoiseThreshold);
+        if (needsUpdateCompose) this.composeRenderable.update();
+        this.composeRenderable.render();
+
+        //
+
+        renderer.setDrawingBufferSize(this.tracing.composeTarget.getWidth(), this.tracing.composeTarget.getHeight());
+        renderer.setPixelRatio(this.webgl.pixelRatio);
+        renderer.setViewport(x, y, width, height);
+        renderer.update(camera, scene);
+
+        if (helper.debug.isEnabled) {
+            helper.debug.syncVisibility();
+            renderer.renderBlended(helper.debug.scene, camera);
+        }
+        if (helper.handle.isEnabled) {
+            renderer.renderBlended(helper.handle.scene, camera);
+        }
+        if (helper.camera.isEnabled) {
+            helper.camera.update(camera);
+            renderer.update(helper.camera.camera, helper.camera.scene);
+            renderer.renderBlended(helper.camera.scene, helper.camera.camera);
+        }
+
+        //
+
+        let targetIsDrawingbuffer = false;
+        let swapTarget = this.outputTarget;
+
+        if (AntialiasingPass.isEnabled(props.postprocessing)) {
+            const _toDrawingBuffer = toDrawingBuffer && props.postprocessing.dof.name === 'off';
+            this.drawPass.antialiasing.render(camera, this.tracing.composeTarget.texture, _toDrawingBuffer ? true : this.outputTarget, props.postprocessing);
+
+            if (_toDrawingBuffer) {
+                targetIsDrawingbuffer = true;
+            } else {
+                this._colorTarget = this.outputTarget;
+                swapTarget = this.tracing.composeTarget;
+            }
+        }
+
+        if (props.postprocessing.bloom.name === 'on') {
+            const _toDrawingBuffer = (toDrawingBuffer && props.postprocessing.dof.name === 'off') || targetIsDrawingbuffer;
+            this.drawPass.bloom.update(this.tracing.colorTextureOpaque, this.tracing.normalTextureOpaque, this.drawPass.depthTextureOpaque, props.postprocessing.bloom.params);
+            this.drawPass.bloom.render(camera.viewport, _toDrawingBuffer ? undefined : this._colorTarget);
+        }
+
+        if (props.postprocessing.dof.name === 'on') {
+            const _toDrawingBuffer = toDrawingBuffer || targetIsDrawingbuffer;
+            this.drawPass.dof.update(camera, this._colorTarget.texture, this.drawPass.depthTextureOpaque, this.drawPass.depthTargetTransparent.texture, props.postprocessing.dof.params, scene.boundingSphereVisible);
+            this.drawPass.dof.render(camera.viewport, _toDrawingBuffer ? undefined : swapTarget);
+
+            if (!_toDrawingBuffer) {
+                this._colorTarget = swapTarget;
+            }
+        }
+
+        this._iteration += 1;
+        if (isTimingMode) this.webgl.timer.markEnd('IlluminationPass.render');
+
+        this.webgl.gl.flush();
+    }
+
+    private prevSampleIndex = -1;
+
+    private renderMultiSample(ctx: RenderContext, props: Props, toDrawingBuffer: boolean) {
+        const { camera } = ctx;
+        const { multiSampleCompose, multiSampleComposeTarget, multiSampleHoldTarget, webgl } = this;
+        const { gl, state } = webgl;
+
+        // based on the Multisample Anti-Aliasing Render Pass
+        // contributed to three.js by bhouston / http://clara.io/
+        //
+        // This manual approach to MSAA re-renders the scene once for
+        // each sample with camera jitter and accumulates the results.
+        const offsetList = JitterVectors[Math.max(0, Math.min(props.multiSample.sampleLevel, 5))];
+
+        const maxIterations = this.getMaxIterations(props);
+        const iteration = Math.min(this._iteration, maxIterations);
+
+        const sampleIndex = Math.floor((iteration / maxIterations) * offsetList.length);
+
+        if (isTimingMode) {
+            webgl.timer.mark('IlluminationPass.renderMultiSample', {
+                note: `sampleIndex ${sampleIndex + 1} of ${offsetList.length}`
+            });
+        }
+
+        const { x, y, width, height } = camera.viewport;
+        const sampleWeight = 1.0 / maxIterations;
+
+        if (iteration === 0) {
+            this.renderInternal(ctx, props, false, true);
+            ValueCell.update(multiSampleCompose.values.uWeight, 1.0);
+            ValueCell.update(multiSampleCompose.values.tColor, this._colorTarget.texture);
+            multiSampleCompose.update();
+
+            multiSampleHoldTarget.bind();
+            state.disable(gl.BLEND);
+            state.disable(gl.DEPTH_TEST);
+            state.depthMask(false);
+            state.viewport(x, y, width, height);
+            state.scissor(x, y, width, height);
+            multiSampleCompose.render();
+        } else {
+            camera.viewOffset.enabled = true;
+            ValueCell.update(multiSampleCompose.values.tColor, this._colorTarget.texture);
+            ValueCell.update(multiSampleCompose.values.uWeight, sampleWeight);
+            multiSampleCompose.update();
+
+            // render the scene multiple times, each slightly jitter offset
+            // from the last and accumulate the results.
+            const offset = offsetList[sampleIndex];
+            Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height);
+            camera.update();
+
+            // render scene
+            this.renderInternal(ctx, props, false, this.prevSampleIndex !== sampleIndex);
+
+            // compose rendered scene with compose target
+            multiSampleComposeTarget.bind();
+            state.enable(gl.BLEND);
+            state.blendEquationSeparate(gl.FUNC_ADD, gl.FUNC_ADD);
+            state.blendFuncSeparate(gl.ONE, gl.ONE, gl.ONE, gl.ONE);
+            state.disable(gl.DEPTH_TEST);
+            state.depthMask(false);
+            state.viewport(x, y, width, height);
+            state.scissor(x, y, width, height);
+            if (iteration === 1) {
+                state.clearColor(0, 0, 0, 0);
+                gl.clear(gl.COLOR_BUFFER_BIT);
+            }
+            multiSampleCompose.render();
+        }
+
+        this.prevSampleIndex = sampleIndex;
+
+        if (toDrawingBuffer) {
+            this.webgl.unbindFramebuffer();
+        } else {
+            this.multiSampleAccumulateTarget.bind();
+        }
+        state.viewport(x, y, width, height);
+        state.scissor(x, y, width, height);
+
+        const accumulationWeight = iteration * sampleWeight;
+        if (accumulationWeight > 0) {
+            ValueCell.update(multiSampleCompose.values.uWeight, 1.0);
+            ValueCell.update(multiSampleCompose.values.tColor, multiSampleComposeTarget.texture);
+            multiSampleCompose.update();
+            state.disable(gl.BLEND);
+            multiSampleCompose.render();
+        }
+        if (accumulationWeight < 1.0) {
+            ValueCell.update(multiSampleCompose.values.uWeight, 1.0 - accumulationWeight);
+            ValueCell.update(multiSampleCompose.values.tColor, multiSampleHoldTarget.texture);
+            multiSampleCompose.update();
+            if (accumulationWeight === 0) state.disable(gl.BLEND);
+            else state.enable(gl.BLEND);
+            multiSampleCompose.render();
+        }
+
+        if (!toDrawingBuffer) {
+            state.disable(gl.BLEND);
+            this.colorTarget.bind();
+            if (this.copyRenderable.values.tColor.ref.value !== this.multiSampleAccumulateTarget.texture) {
+                ValueCell.update(this.copyRenderable.values.tColor, this.multiSampleAccumulateTarget.texture);
+                this.copyRenderable.update();
+            }
+            this.copyRenderable.render();
+        }
+
+        camera.viewOffset.enabled = false;
+        camera.update();
+        if (isTimingMode) webgl.timer.markEnd('IlluminationPass.renderMultiSample');
+    }
+
+    render(ctx: RenderContext, props: Props, toDrawingBuffer: boolean) {
+        if (!this._supported) return;
+
+        if (props.multiSample.mode === 'on') {
+            this.renderMultiSample(ctx, props, toDrawingBuffer);
+        } else {
+            this.renderInternal(ctx, props, toDrawingBuffer, false);
+        }
+    }
+}
+
+//
+
+const ComposeSchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tNormal: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tShaded: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tTransparentColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    dBlendTransparency: DefineSpec('boolean'),
+    tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tSsaoDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tOutlines: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    dDenoise: DefineSpec('boolean'),
+    uDenoiseThreshold: UniformSpec('f'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+    uFogNear: UniformSpec('f'),
+    uFogFar: UniformSpec('f'),
+    uFogColor: UniformSpec('v3'),
+    uOutlineColor: UniformSpec('v3'),
+    uOcclusionColor: UniformSpec('v3'),
+    uTransparentBackground: UniformSpec('b'),
+
+    dOcclusionEnable: DefineSpec('boolean'),
+    dOutlineEnable: DefineSpec('boolean'),
+    dOutlineScale: DefineSpec('number'),
+    dTransparentOutline: DefineSpec('boolean'),
+};
+const ComposeShaderCode = ShaderCode('compose', quad_vert, compose_frag);
+type ComposeRenderable = ComputeRenderable<Values<typeof ComposeSchema>>
+
+function getComposeRenderable(ctx: WebGLContext, colorTexture: Texture, normalTexture: Texture, shadedTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, outlinesTexture: Texture, transparentColorTexture: Texture, ssaoDepthOpaqueTexture: Texture, ssaoDepthTransparentTexture: Texture, transparentOutline: boolean): ComposeRenderable {
+    const values: Values<typeof ComposeSchema> = {
+        ...QuadValues,
+        tColor: ValueCell.create(colorTexture),
+        tNormal: ValueCell.create(normalTexture),
+        tShaded: ValueCell.create(shadedTexture),
+        tTransparentColor: ValueCell.create(transparentColorTexture),
+        dBlendTransparency: ValueCell.create(true),
+        tSsaoDepth: ValueCell.create(ssaoDepthOpaqueTexture),
+        tSsaoDepthTransparent: ValueCell.create(ssaoDepthTransparentTexture),
+        tDepthOpaque: ValueCell.create(depthTextureOpaque),
+        tDepthTransparent: ValueCell.create(depthTextureTransparent),
+        tOutlines: ValueCell.create(outlinesTexture),
+        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+
+        dDenoise: ValueCell.create(true),
+        uDenoiseThreshold: ValueCell.create(0.1),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+        uFogNear: ValueCell.create(10000),
+        uFogFar: ValueCell.create(10000),
+        uFogColor: ValueCell.create(Vec3.create(1, 1, 1)),
+        uOutlineColor: ValueCell.create(Vec3.create(0, 0, 0)),
+        uOcclusionColor: ValueCell.create(Vec3.create(0, 0, 0)),
+        uTransparentBackground: ValueCell.create(false),
+
+        dOcclusionEnable: ValueCell.create(false),
+        dOutlineEnable: ValueCell.create(false),
+        dOutlineScale: ValueCell.create(1),
+        dTransparentOutline: ValueCell.create(transparentOutline),
+    };
+
+    const schema = { ...ComposeSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', ComposeShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+//
+
+const MultiSampleComposeSchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+    uWeight: UniformSpec('f'),
+};
+const MultiSampleComposeShaderCode = ShaderCode('compose', quad_vert, multiSample_compose_frag);
+type MultiSampleComposeRenderable = ComputeRenderable<Values<typeof MultiSampleComposeSchema>>
+
+function getMultiSampleComposeRenderable(ctx: WebGLContext, colorTexture: Texture): MultiSampleComposeRenderable {
+    const values: Values<typeof MultiSampleComposeSchema> = {
+        ...QuadValues,
+        tColor: ValueCell.create(colorTexture),
+        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+        uWeight: ValueCell.create(1.0),
+    };
+
+    const schema = { ...MultiSampleComposeSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', MultiSampleComposeShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-canvas3d/passes/image.ts

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
-import { Renderer } from '../../mol-gl/renderer';
+import { Renderer, RendererParams } from '../../mol-gl/renderer';
 import { Scene } from '../../mol-gl/scene';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { DrawPass } from './draw';
@@ -19,6 +19,10 @@ import { Helper } from '../helper/helper';
 import { CameraHelper, CameraHelperParams } from '../helper/camera-helper';
 import { MarkingParams } from './marking';
 import { AssetManager } from '../../mol-util/assets';
+import { IlluminationParams, IlluminationPass } from './illumination';
+import { RuntimeContext } from '../../mol-task';
+import { isTimingMode } from '../../mol-util/debug';
+import { printTimerResults } from '../../mol-gl/webgl/timer';
 
 export const ImageParams = {
     transparentBackground: PD.Boolean(false),
@@ -26,8 +30,10 @@ export const ImageParams = {
     multiSample: PD.Group(MultiSampleParams),
     postprocessing: PD.Group(PostprocessingParams),
     marking: PD.Group(MarkingParams),
+    illumination: PD.Group(IlluminationParams),
 
     cameraHelper: PD.Group(CameraHelperParams),
+    renderer: PD.Group(RendererParams),
 };
 export type ImageProps = PD.Values<typeof ImageParams>
 
@@ -42,6 +48,7 @@ export class ImagePass {
     get colorTarget() { return this._colorTarget; }
 
     private readonly drawPass: DrawPass;
+    private readonly illuminationPass: IlluminationPass;
     private readonly multiSamplePass: MultiSamplePass;
     private readonly multiSampleHelper: MultiSampleHelper;
     private readonly helper: Helper;
@@ -53,6 +60,7 @@ export class ImagePass {
         this.props = { ...PD.getDefaultValues(ImageParams), ...props };
 
         this.drawPass = new DrawPass(webgl, assetManager, 128, 128, transparency);
+        this.illuminationPass = new IlluminationPass(webgl, this.drawPass);
         this.multiSamplePass = new MultiSamplePass(webgl, this.drawPass);
         this.multiSampleHelper = new MultiSampleHelper(this.multiSamplePass);
 
@@ -80,6 +88,7 @@ export class ImagePass {
         this._height = height;
 
         this.drawPass.setSize(width, height);
+        this.illuminationPass.setSize(width, height);
         this.multiSamplePass.syncSize();
     }
 
@@ -88,24 +97,59 @@ export class ImagePass {
         if (props.cameraHelper) this.helper.camera.setProps(props.cameraHelper);
     }
 
-    render() {
+    async render(runtime: RuntimeContext) {
         Camera.copySnapshot(this._camera.state, this.camera.state);
         Viewport.set(this._camera.viewport, 0, 0, this._width, this._height);
         this._camera.update();
 
         const ctx = { renderer: this.renderer, camera: this._camera, scene: this.scene, helper: this.helper };
-        if (MultiSamplePass.isEnabled(this.props.multiSample)) {
-            this.multiSampleHelper.render(ctx, this.props, false);
-            this._colorTarget = this.multiSamplePass.colorTarget;
+        if (this.illuminationPass.supported && this.props.illumination.enabled) {
+            await runtime.update({ message: 'Tracing...', current: 1, max: this.illuminationPass.getMaxIterations(this.props) });
+            this.illuminationPass.reset(true);
+            while (this.illuminationPass.shouldRender(this.props)) {
+                if (isTimingMode) this.webgl.timer.mark('ImagePass.render', { captureStats: true });
+                this.illuminationPass.render(ctx, this.props, false);
+                if (isTimingMode) this.webgl.timer.markEnd('ImagePass.render');
+                if (runtime.shouldUpdate) {
+                    await runtime.update({ current: this.illuminationPass.iteration });
+                }
+                await this.webgl.waitForGpuCommandsComplete();
+            }
+            this._colorTarget = this.illuminationPass.colorTarget;
         } else {
-            this.drawPass.render(ctx, this.props, false);
-            this._colorTarget = this.drawPass.getColorTarget(this.props.postprocessing);
+            if (isTimingMode) this.webgl.timer.mark('ImagePass.render', { captureStats: true });
+            if (MultiSamplePass.isEnabled(this.props.multiSample)) {
+                this.multiSampleHelper.render(ctx, this.props, false);
+                this._colorTarget = this.multiSamplePass.colorTarget;
+            } else {
+                this.drawPass.render(ctx, this.props, false);
+                this._colorTarget = this.drawPass.getColorTarget(this.props.postprocessing);
+            }
+            if (isTimingMode) this.webgl.timer.markEnd('ImagePass.render');
+        }
+
+        if (isTimingMode) {
+            const timerResults = this.webgl.timer.resolve();
+            if (timerResults) {
+                for (const result of timerResults) {
+                    printTimerResults([result]);
+                }
+            }
+        }
+
+        if (isTimingMode) {
+            const timerResults = this.webgl.timer.resolve();
+            if (timerResults) {
+                for (const result of timerResults) {
+                    printTimerResults([result]);
+                }
+            }
         }
     }
 
-    getImageData(width: number, height: number, viewport?: Viewport) {
+    async getImageData(runtime: RuntimeContext, width: number, height: number, viewport?: Viewport) {
         this.setSize(width, height);
-        this.render();
+        await this.render(runtime);
         this.colorTarget.bind();
 
         const w = viewport?.width ?? width, h = viewport?.height ?? height;

src/mol-canvas3d/passes/multi-sample.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -54,6 +54,7 @@ export const MultiSampleParams = {
     mode: PD.Select('temporal', [['off', 'Off'], ['on', 'On'], ['temporal', 'Temporal']]),
     sampleLevel: PD.Numeric(2, { min: 0, max: 5, step: 1 }, { description: 'Take level^2 samples.' }),
     reduceFlicker: PD.Boolean(true, { description: 'Reduce flicker in "temporal" mode.' }),
+    reuseOcclusion: PD.Boolean(true, { description: 'Reuse occlusion data. It is faster but has some artefacts.' }),
 };
 export type MultiSampleProps = PD.Values<typeof MultiSampleParams>
 
@@ -161,7 +162,7 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, sampleWeight);
 
             // render scene
-            if (i === 0) {
+            if (i === 0 || !props.multiSample.reuseOcclusion) {
                 drawPass.postprocessing.setOcclusionOffset(0, 0);
             } else {
                 drawPass.postprocessing.setOcclusionOffset(
@@ -252,7 +253,7 @@ export class MultiSamplePass {
                 camera.update();
 
                 // render scene
-                if (sampleIndex === 0) {
+                if (sampleIndex === 0 || !props.multiSample.reuseOcclusion) {
                     drawPass.postprocessing.setOcclusionOffset(0, 0);
                 } else {
                     drawPass.postprocessing.setOcclusionOffset(
@@ -313,7 +314,7 @@ export class MultiSamplePass {
     }
 }
 
-const JitterVectors = [
+export const JitterVectors = [
     [
         [0, 0]
     ],

src/mol-canvas3d/passes/outline.ts

@@ -0,0 +1,147 @@
+/**
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { ValueCell } from '../../mol-util';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
+import { Mat4, Vec2 } from '../../mol-math/linear-algebra';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { ICamera } from '../../mol-canvas3d/camera';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { outlines_frag } from '../../mol-gl/shader/outlines.frag';
+import { isTimingMode } from '../../mol-util/debug';
+import { Color } from '../../mol-util/color';
+import { PostprocessingProps } from './postprocessing';
+
+export const OutlineParams = {
+    scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
+    threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
+    color: PD.Color(Color(0x000000)),
+    includeTransparent: PD.Boolean(true, { description: 'Whether to show outline for transparent objects' }),
+};
+
+export type OutlineProps = PD.Values<typeof OutlineParams>
+
+export class OutlinePass {
+    static isEnabled(props: PostprocessingProps) {
+        return props.outline.name !== 'off';
+    }
+
+    readonly target: RenderTarget;
+    private readonly renderable: OutlinesRenderable;
+
+    constructor(private readonly webgl: WebGLContext, width: number, height: number, depthTextureTransparent: Texture, depthTextureOpaque: Texture) {
+        this.target = webgl.createRenderTarget(width, height, false);
+        this.renderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent, true);
+    }
+
+    setSize(width: number, height: number) {
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        if (width !== w || height !== h) {
+            this.target.setSize(width, height);
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    update(camera: ICamera, props: OutlineProps, depthTextureTransparent: Texture, depthTextureOpaque: Texture) {
+        let needsUpdate = false;
+
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+
+        const invProjection = this.renderable.values.uInvProjection.ref.value;
+        Mat4.invert(invProjection, camera.projection);
+
+        const transparentOutline = props.includeTransparent ?? true;
+        const outlineScale = Math.max(1, Math.round(props.scale * this.webgl.pixelRatio)) - 1;
+        const outlineThreshold = 50 * props.threshold * this.webgl.pixelRatio;
+
+        ValueCell.updateIfChanged(this.renderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.renderable.values.uFar, camera.far);
+        ValueCell.update(this.renderable.values.uInvProjection, invProjection);
+        if (this.renderable.values.dTransparentOutline.ref.value !== transparentOutline) {
+            needsUpdate = true;
+            ValueCell.update(this.renderable.values.dTransparentOutline, transparentOutline);
+        }
+        if (this.renderable.values.dOrthographic.ref.value !== orthographic) {
+            needsUpdate = true;
+            ValueCell.update(this.renderable.values.dOrthographic, orthographic);
+        }
+        ValueCell.updateIfChanged(this.renderable.values.uOutlineThreshold, outlineThreshold);
+
+        if (this.renderable.values.tDepthTransparent.ref.value !== depthTextureTransparent) {
+            needsUpdate = true;
+            ValueCell.update(this.renderable.values.tDepthTransparent, depthTextureTransparent);
+        }
+        if (this.renderable.values.tDepthOpaque.ref.value !== depthTextureOpaque) {
+            needsUpdate = true;
+            ValueCell.update(this.renderable.values.tDepthOpaque, depthTextureOpaque);
+        }
+
+        if (needsUpdate) {
+            this.renderable.update();
+        }
+
+        return { transparentOutline, outlineScale };
+    }
+
+    render() {
+        if (isTimingMode) this.webgl.timer.mark('OutlinePass.render');
+        this.target.bind();
+        this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('OutlinePass.render');
+    }
+}
+
+export const OutlinesSchema = {
+    ...QuadSchema,
+    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+    uInvProjection: UniformSpec('m4'),
+
+    uOutlineThreshold: UniformSpec('f'),
+    dTransparentOutline: DefineSpec('boolean'),
+};
+export type OutlinesRenderable = ComputeRenderable<Values<typeof OutlinesSchema>>
+
+export function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture, transparentOutline: boolean): OutlinesRenderable {
+    const width = depthTextureOpaque.getWidth();
+    const height = depthTextureOpaque.getHeight();
+
+    const values: Values<typeof OutlinesSchema> = {
+        ...QuadValues,
+        tDepthOpaque: ValueCell.create(depthTextureOpaque),
+        tDepthTransparent: ValueCell.create(depthTextureTransparent),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+
+        uOutlineThreshold: ValueCell.create(0.33),
+        dTransparentOutline: ValueCell.create(transparentOutline),
+    };
+
+    const schema = { ...OutlinesSchema };
+    const shaderCode = ShaderCode('outlines', quad_vert, outlines_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-canvas3d/passes/passes.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,17 +9,20 @@ import { PickPass } from './pick';
 import { MultiSamplePass } from './multi-sample';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { AssetManager } from '../../mol-util/assets';
+import { IlluminationPass } from './illumination';
 
 export class Passes {
     readonly draw: DrawPass;
     readonly pick: PickPass;
     readonly multiSample: MultiSamplePass;
+    readonly illumination: IlluminationPass;
 
     constructor(private webgl: WebGLContext, assetManager: AssetManager, attribs: Partial<{ pickScale: number, transparency: 'wboit' | 'dpoit' | 'blended' }> = {}) {
         const { gl } = webgl;
         this.draw = new DrawPass(webgl, assetManager, gl.drawingBufferWidth, gl.drawingBufferHeight, attribs.transparency || 'blended');
         this.pick = new PickPass(webgl, this.draw, attribs.pickScale || 0.25);
         this.multiSample = new MultiSamplePass(webgl, this.draw);
+        this.illumination = new IlluminationPass(webgl, this.draw);
     }
 
     setPickScale(pickScale: number) {
@@ -38,5 +41,6 @@ export class Passes {
         this.draw.setSize(width, height);
         this.pick.syncSize();
         this.multiSample.syncSize();
+        this.illumination.setSize(width, height);
     }
 }

src/mol-canvas3d/passes/pick.ts

@@ -182,16 +182,16 @@ export class PickPass {
     private renderVariant(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, variant: 'pick' | 'depth', pickType: number) {
         renderer.clear(false);
         renderer.update(camera, scene);
-        renderer.renderPick(scene.primitives, camera, variant, null, pickType);
+        renderer.renderPick(scene.primitives, camera, variant, pickType);
 
         if (helper.handle.isEnabled) {
-            renderer.renderPick(helper.handle.scene, camera, variant, null, pickType);
+            renderer.renderPick(helper.handle.scene, camera, variant, pickType);
         }
 
         if (helper.camera.isEnabled) {
             helper.camera.update(camera);
             renderer.update(helper.camera.camera, helper.camera.scene);
-            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, null, pickType);
+            renderer.renderPick(helper.camera.scene, helper.camera.camera, variant, pickType);
         }
     }
 
@@ -300,7 +300,7 @@ export class PickHelper {
     }
 
     private render(camera: Camera | StereoCamera) {
-        if (isTimingMode) this.webgl.timer.mark('PickHelper.render', true);
+        if (isTimingMode) this.webgl.timer.mark('PickHelper.render', { captureStats: true });
         const { pickX, pickY, pickWidth, pickHeight, halfPickWidth } = this;
         const { renderer, scene, helper } = this;
 

src/mol-canvas3d/passes/postprocessing.ts

@@ -4,27 +4,25 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
-import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
 import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
 import { ShaderCode } from '../../mol-gl/shader-code';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Texture } from '../../mol-gl/webgl/texture';
-import { deepEqual, ValueCell } from '../../mol-util';
+import { ValueCell } from '../../mol-util';
 import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
 import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
-import { Mat4, Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
+import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { DrawPass } from './draw';
 import { ICamera } from '../../mol-canvas3d/camera';
+import { Scene } from '../../mol-gl/scene';
 import { quad_vert } from '../../mol-gl/shader/quad.vert';
-import { outlines_frag } from '../../mol-gl/shader/outlines.frag';
-import { ssao_frag } from '../../mol-gl/shader/ssao.frag';
-import { ssaoBlur_frag } from '../../mol-gl/shader/ssao-blur.frag';
 import { postprocessing_frag } from '../../mol-gl/shader/postprocessing.frag';
-import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
 import { Color } from '../../mol-util/color';
 import { FxaaParams, FxaaPass } from './fxaa';
 import { SmaaParams, SmaaPass } from './smaa';
@@ -32,259 +30,21 @@ import { isTimingMode } from '../../mol-util/debug';
 import { BackgroundParams, BackgroundPass } from './background';
 import { AssetManager } from '../../mol-util/assets';
 import { Light } from '../../mol-gl/renderer';
-import { shadows_frag } from '../../mol-gl/shader/shadows.frag';
 import { CasParams, CasPass } from './cas';
+import { DofPass, DofParams } from './dof';
 import { BloomParams } from './bloom';
+import { OutlinePass, OutlineProps, OutlineParams } from './outline';
+import { ShadowPass, ShadowProps, ShadowParams } from './shadow';
+import { SsaoPass, SsaoProps, SsaoParams } from './ssao';
 
-export const OutlinesSchema = {
-    ...QuadSchema,
-    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    uTexSize: UniformSpec('v2'),
-
-    dOrthographic: DefineSpec('number'),
-    uNear: UniformSpec('f'),
-    uFar: UniformSpec('f'),
-    uInvProjection: UniformSpec('m4'),
-
-    uOutlineThreshold: UniformSpec('f'),
-    dTransparentOutline: DefineSpec('boolean'),
-};
-export type OutlinesRenderable = ComputeRenderable<Values<typeof OutlinesSchema>>
-
-export function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture, transparentOutline: boolean): OutlinesRenderable {
-    const width = depthTextureOpaque.getWidth();
-    const height = depthTextureOpaque.getHeight();
-
-    const values: Values<typeof OutlinesSchema> = {
-        ...QuadValues,
-        tDepthOpaque: ValueCell.create(depthTextureOpaque),
-        tDepthTransparent: ValueCell.create(depthTextureTransparent),
-        uTexSize: ValueCell.create(Vec2.create(width, height)),
-
-        dOrthographic: ValueCell.create(0),
-        uNear: ValueCell.create(1),
-        uFar: ValueCell.create(10000),
-        uInvProjection: ValueCell.create(Mat4.identity()),
-
-        uOutlineThreshold: ValueCell.create(0.33),
-        dTransparentOutline: ValueCell.create(transparentOutline),
-    };
-
-    const schema = { ...OutlinesSchema };
-    const shaderCode = ShaderCode('outlines', quad_vert, outlines_frag);
-    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
-
-const ShadowsSchema = {
-    ...QuadSchema,
-    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    uTexSize: UniformSpec('v2'),
-
-    uProjection: UniformSpec('m4'),
-    uInvProjection: UniformSpec('m4'),
-    uBounds: UniformSpec('v4'),
-
-    dOrthographic: DefineSpec('number'),
-    uNear: UniformSpec('f'),
-    uFar: UniformSpec('f'),
-
-    dSteps: DefineSpec('number'),
-    uMaxDistance: UniformSpec('f'),
-    uTolerance: UniformSpec('f'),
-    uBias: UniformSpec('f'),
-
-    uLightDirection: UniformSpec('v3[]'),
-    uLightColor: UniformSpec('v3[]'),
-    dLightCount: DefineSpec('number'),
-};
-type ShadowsRenderable = ComputeRenderable<Values<typeof ShadowsSchema>>
-
-function getShadowsRenderable(ctx: WebGLContext, depthTexture: Texture): ShadowsRenderable {
-    const width = depthTexture.getWidth();
-    const height = depthTexture.getHeight();
-
-    const values: Values<typeof ShadowsSchema> = {
-        ...QuadValues,
-        tDepth: ValueCell.create(depthTexture),
-        uTexSize: ValueCell.create(Vec2.create(width, height)),
-
-        uProjection: ValueCell.create(Mat4.identity()),
-        uInvProjection: ValueCell.create(Mat4.identity()),
-        uBounds: ValueCell.create(Vec4()),
-
-        dOrthographic: ValueCell.create(0),
-        uNear: ValueCell.create(1),
-        uFar: ValueCell.create(10000),
-
-        dSteps: ValueCell.create(1),
-        uMaxDistance: ValueCell.create(3.0),
-        uTolerance: ValueCell.create(1.0),
-        uBias: ValueCell.create(0.6),
-
-        uLightDirection: ValueCell.create([]),
-        uLightColor: ValueCell.create([]),
-        dLightCount: ValueCell.create(0),
-    };
-
-    const schema = { ...ShadowsSchema };
-    const shaderCode = ShaderCode('shadows', quad_vert, shadows_frag);
-    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
-
-const SsaoSchema = {
-    ...QuadSchema,
-    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    tDepthHalf: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    tDepthQuarter: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-
-    uSamples: UniformSpec('v3[]'),
-    dNSamples: DefineSpec('number'),
-
-    uProjection: UniformSpec('m4'),
-    uInvProjection: UniformSpec('m4'),
-    uBounds: UniformSpec('v4'),
-
-    uTexSize: UniformSpec('v2'),
-
-    uRadius: UniformSpec('f'),
-    uBias: UniformSpec('f'),
-
-    dMultiScale: DefineSpec('boolean'),
-    dLevels: DefineSpec('number'),
-    uLevelRadius: UniformSpec('f[]'),
-    uLevelBias: UniformSpec('f[]'),
-    uNearThreshold: UniformSpec('f'),
-    uFarThreshold: UniformSpec('f'),
-};
-
-type SsaoRenderable = ComputeRenderable<Values<typeof SsaoSchema>>
-
-function getSsaoRenderable(ctx: WebGLContext, depthTexture: Texture, depthHalfTexture: Texture, depthQuarterTexture: Texture): SsaoRenderable {
-    const values: Values<typeof SsaoSchema> = {
-        ...QuadValues,
-        tDepth: ValueCell.create(depthTexture),
-        tDepthHalf: ValueCell.create(depthHalfTexture),
-        tDepthQuarter: ValueCell.create(depthQuarterTexture),
-
-        uSamples: ValueCell.create(getSamples(32)),
-        dNSamples: ValueCell.create(32),
-
-        uProjection: ValueCell.create(Mat4.identity()),
-        uInvProjection: ValueCell.create(Mat4.identity()),
-        uBounds: ValueCell.create(Vec4()),
-
-        uTexSize: ValueCell.create(Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)),
-
-        uRadius: ValueCell.create(Math.pow(2, 5)),
-        uBias: ValueCell.create(0.8),
-
-        dMultiScale: ValueCell.create(false),
-        dLevels: ValueCell.create(3),
-        uLevelRadius: ValueCell.create([Math.pow(2, 2), Math.pow(2, 5), Math.pow(2, 8)]),
-        uLevelBias: ValueCell.create([0.8, 0.8, 0.8]),
-        uNearThreshold: ValueCell.create(10.0),
-        uFarThreshold: ValueCell.create(1500.0),
-    };
-
-    const schema = { ...SsaoSchema };
-    const shaderCode = ShaderCode('ssao', quad_vert, ssao_frag);
-    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
-
-const SsaoBlurSchema = {
-    ...QuadSchema,
-    tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    uTexSize: UniformSpec('v2'),
-
-    uKernel: UniformSpec('f[]'),
-    dOcclusionKernelSize: DefineSpec('number'),
-
-    uBlurDirectionX: UniformSpec('f'),
-    uBlurDirectionY: UniformSpec('f'),
-
-    uInvProjection: UniformSpec('m4'),
-    uNear: UniformSpec('f'),
-    uFar: UniformSpec('f'),
-    uBounds: UniformSpec('v4'),
-    dOrthographic: DefineSpec('number'),
-};
-
-type SsaoBlurRenderable = ComputeRenderable<Values<typeof SsaoBlurSchema>>
-
-function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, direction: 'horizontal' | 'vertical'): SsaoBlurRenderable {
-    const values: Values<typeof SsaoBlurSchema> = {
-        ...QuadValues,
-        tSsaoDepth: ValueCell.create(ssaoDepthTexture),
-        uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())),
-
-        uKernel: ValueCell.create(getBlurKernel(15)),
-        dOcclusionKernelSize: ValueCell.create(15),
-
-        uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0),
-        uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0),
-
-        uInvProjection: ValueCell.create(Mat4.identity()),
-        uNear: ValueCell.create(0.0),
-        uFar: ValueCell.create(10000.0),
-        uBounds: ValueCell.create(Vec4()),
-        dOrthographic: ValueCell.create(0),
-    };
-
-    const schema = { ...SsaoBlurSchema };
-    const shaderCode = ShaderCode('ssao_blur', quad_vert, ssaoBlur_frag);
-    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
-
-function getBlurKernel(kernelSize: number): number[] {
-    const sigma = kernelSize / 3.0;
-    const halfKernelSize = Math.floor((kernelSize + 1) / 2);
-
-    const kernel = [];
-    for (let x = 0; x < halfKernelSize; x++) {
-        kernel.push((1.0 / ((Math.sqrt(2 * Math.PI)) * sigma)) * Math.exp(-x * x / (2 * sigma * sigma)));
-    }
-
-    return kernel;
-}
-
-const RandomHemisphereVector: Vec3[] = [];
-for (let i = 0; i < 256; i++) {
-    const v = Vec3();
-    v[0] = Math.random() * 2.0 - 1.0;
-    v[1] = Math.random() * 2.0 - 1.0;
-    v[2] = Math.random();
-    Vec3.normalize(v, v);
-    Vec3.scale(v, v, Math.random());
-    RandomHemisphereVector.push(v);
-}
-
-function getSamples(nSamples: number): number[] {
-    const samples = [];
-    for (let i = 0; i < nSamples; i++) {
-        let scale = (i * i + 2.0 * i + 1) / (nSamples * nSamples);
-        scale = 0.1 + scale * (1.0 - 0.1);
-
-        samples.push(RandomHemisphereVector[i][0] * scale);
-        samples.push(RandomHemisphereVector[i][1] * scale);
-        samples.push(RandomHemisphereVector[i][2] * scale);
-    }
-
-    return samples;
-}
 
 const PostprocessingSchema = {
     ...QuadSchema,
     tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tSsaoDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tTransparentColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    dBlendTransparency: DefineSpec('boolean'),
     tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
     tShadows: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
@@ -302,6 +62,9 @@ const PostprocessingSchema = {
     uTransparentBackground: UniformSpec('b'),
 
     dOcclusionEnable: DefineSpec('boolean'),
+    dOcclusionSingleDepth: DefineSpec('boolean'),
+    dOcclusionIncludeOpacity: DefineSpec('boolean'),
+    dOcclusionIncludeTransparency: DefineSpec('boolean'),
     uOcclusionOffset: UniformSpec('v2'),
 
     dShadowEnable: DefineSpec('boolean'),
@@ -312,11 +75,14 @@ const PostprocessingSchema = {
 };
 type PostprocessingRenderable = ComputeRenderable<Values<typeof PostprocessingSchema>>
 
-function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, shadowsTexture: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture, transparentOutline: boolean): PostprocessingRenderable {
+function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, transparentColorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, shadowsTexture: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture, ssaoDepthTransparentTexture: Texture, transparentOutline: boolean): PostprocessingRenderable {
     const values: Values<typeof PostprocessingSchema> = {
         ...QuadValues,
         tSsaoDepth: ValueCell.create(ssaoDepthTexture),
+        tSsaoDepthTransparent: ValueCell.create(ssaoDepthTransparentTexture),
         tColor: ValueCell.create(colorTexture),
+        tTransparentColor: ValueCell.create(transparentColorTexture),
+        dBlendTransparency: ValueCell.create(true),
         tDepthOpaque: ValueCell.create(depthTextureOpaque),
         tDepthTransparent: ValueCell.create(depthTextureTransparent),
         tShadows: ValueCell.create(shadowsTexture),
@@ -334,6 +100,9 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
         uTransparentBackground: ValueCell.create(false),
 
         dOcclusionEnable: ValueCell.create(true),
+        dOcclusionSingleDepth: ValueCell.create(false),
+        dOcclusionIncludeOpacity: ValueCell.create(true),
+        dOcclusionIncludeTransparency: ValueCell.create(false),
         uOcclusionOffset: ValueCell.create(Vec2.create(0, 0)),
 
         dShadowEnable: ValueCell.create(false),
@@ -352,50 +121,21 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
 
 export const PostprocessingParams = {
     occlusion: PD.MappedStatic('on', {
-        on: PD.Group({
-            samples: PD.Numeric(32, { min: 1, max: 256, step: 1 }),
-            multiScale: PD.MappedStatic('off', {
-                on: PD.Group({
-                    levels: PD.ObjectList({
-                        radius: PD.Numeric(5, { min: 0, max: 20, step: 0.1 }, { description: 'Final occlusion radius is 2^x' }),
-                        bias: PD.Numeric(1, { min: 0, max: 3, step: 0.1 }),
-                    }, o => `${o.radius}, ${o.bias}`, { defaultValue: [
-                        { radius: 2, bias: 1 },
-                        { radius: 5, bias: 1 },
-                        { radius: 8, bias: 1 },
-                        { radius: 11, bias: 1 },
-                    ] }),
-                    nearThreshold: PD.Numeric(10, { min: 0, max: 50, step: 1 }),
-                    farThreshold: PD.Numeric(1500, { min: 0, max: 10000, step: 100 }),
-                }),
-                off: PD.Group({})
-            }, { cycle: true }),
-            radius: PD.Numeric(5, { min: 0, max: 20, step: 0.1 }, { description: 'Final occlusion radius is 2^x', hideIf: p => p?.multiScale.name === 'on' }),
-            bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
-            blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
-            resolutionScale: PD.Numeric(1, { min: 0.1, max: 1, step: 0.05 }, { description: 'Adjust resolution of occlusion calculation' }),
-            color: PD.Color(Color(0x000000)),
-        }),
+        on: PD.Group(SsaoParams),
         off: PD.Group({})
     }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
     shadow: PD.MappedStatic('off', {
-        on: PD.Group({
-            steps: PD.Numeric(1, { min: 1, max: 64, step: 1 }),
-            bias: PD.Numeric(0.6, { min: 0.0, max: 1.0, step: 0.01 }),
-            maxDistance: PD.Numeric(3, { min: 0, max: 256, step: 1 }),
-            tolerance: PD.Numeric(1.0, { min: 0.0, max: 10.0, step: 0.1 }),
-        }),
+        on: PD.Group(ShadowParams),
         off: PD.Group({})
     }, { cycle: true, description: 'Simplistic shadows' }),
     outline: PD.MappedStatic('off', {
-        on: PD.Group({
-            scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
-            threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
-            color: PD.Color(Color(0x000000)),
-            includeTransparent: PD.Boolean(true, { description: 'Whether to show outline for transparent objects' }),
-        }),
+        on: PD.Group(OutlineParams),
         off: PD.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' }),
+    dof: PD.MappedStatic('off', {
+        on: PD.Group(DofParams),
+        off: PD.Group({})
+    }, { cycle: true, description: 'DOF' }),
     antialiasing: PD.MappedStatic('smaa', {
         fxaa: PD.Group(FxaaParams),
         smaa: PD.Group(SmaaParams),
@@ -414,381 +154,95 @@ export const PostprocessingParams = {
 
 export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
 
-type Levels = {
-    count: number
-    radius: number[]
-    bias: number[]
-}
-
-function getLevels(props: { radius: number, bias: number }[], levels?: Levels): Levels {
-    const count = props.length;
-    const { radius, bias } = levels || {
-        radius: (new Array(count * 3)).fill(0),
-        bias: (new Array(count * 3)).fill(0),
-    };
-    props = props.slice().sort((a, b) => a.radius - b.radius);
-    for (let i = 0; i < count; ++i) {
-        const p = props[i];
-        radius[i] = Math.pow(2, p.radius);
-        bias[i] = p.bias;
-    }
-    return { count, radius, bias };
-}
-
 export class PostprocessingPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.occlusion.name === 'on' || props.shadow.name === 'on' || props.outline.name === 'on' || props.background.variant.name !== 'off';
+        return SsaoPass.isEnabled(props) || ShadowPass.isEnabled(props) || OutlinePass.isEnabled(props) || props.background.variant.name !== 'off';
+    }
+
+    static isTransparentDepthRequired(scene: Scene, props: PostprocessingProps) {
+        return DofPass.isEnabled(props) || OutlinePass.isEnabled(props) && PostprocessingPass.isTransparentOutlineEnabled(props) || SsaoPass.isEnabled(props) && PostprocessingPass.isTransparentSsaoEnabled(scene, props);
     }
 
     static isTransparentOutlineEnabled(props: PostprocessingProps) {
-        return props.outline.name === 'on' && props.outline.params.includeTransparent;
+        return OutlinePass.isEnabled(props) && (props.outline.params as OutlineProps).includeTransparent;
+    }
+
+    static isTransparentSsaoEnabled(scene: Scene, props: PostprocessingProps) {
+        return SsaoPass.isEnabled(props) && SsaoPass.isTransparentEnabled(scene, props.occlusion.params as SsaoProps);
+    }
+
+    static isSsaoEnabled(props: PostprocessingProps) {
+        return SsaoPass.isEnabled(props);
     }
 
     readonly target: RenderTarget;
 
-    private readonly outlinesTarget: RenderTarget;
-    private readonly outlinesRenderable: OutlinesRenderable;
-
-    private readonly shadowsTarget: RenderTarget;
-    private readonly shadowsRenderable: ShadowsRenderable;
-
-    private readonly ssaoFramebuffer: Framebuffer;
-    private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
-    private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;
-
-    private readonly downsampledDepthTarget: RenderTarget;
-    private readonly downsampleDepthRenderable: CopyRenderable;
-
-    private readonly depthHalfTarget: RenderTarget;
-    private readonly depthHalfRenderable: CopyRenderable;
-
-    private readonly depthQuarterTarget: RenderTarget;
-    private readonly depthQuarterRenderable: CopyRenderable;
-
-    private readonly ssaoDepthTexture: Texture;
-    private readonly ssaoDepthBlurProxyTexture: Texture;
-
-    private readonly ssaoRenderable: SsaoRenderable;
-    private readonly ssaoBlurFirstPassRenderable: SsaoBlurRenderable;
-    private readonly ssaoBlurSecondPassRenderable: SsaoBlurRenderable;
-
-    private nSamples: number;
-    private blurKernelSize: number;
-
     private readonly renderable: PostprocessingRenderable;
 
-    private ssaoScale: number;
-    private calcSsaoScale(resolutionScale: number) {
-        // downscale ssao for high pixel-ratios
-        return Math.min(1, 1 / this.webgl.pixelRatio) * resolutionScale;
-    }
-
-    private levels: { radius: number, bias: number }[];
-
-    private readonly bgColor = Vec3();
+    readonly ssao: SsaoPass;
+    readonly shadow: ShadowPass;
+    readonly outline: OutlinePass;
     readonly background: BackgroundPass;
 
-    constructor(private readonly webgl: WebGLContext, assetManager: AssetManager, private readonly drawPass: DrawPass) {
-        const { colorTarget, depthTextureTransparent, depthTextureOpaque } = drawPass;
+    constructor(private readonly webgl: WebGLContext, assetManager: AssetManager, readonly drawPass: DrawPass) {
+        const { colorTarget, transparentColorTarget, depthTextureOpaque, depthTextureTransparent, packedDepth } = drawPass;
         const width = colorTarget.getWidth();
         const height = colorTarget.getHeight();
 
-        this.nSamples = 1;
-        this.blurKernelSize = 1;
-        this.ssaoScale = this.calcSsaoScale(1);
-        this.levels = [];
-
         // needs to be linear for anti-aliasing pass
         this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
 
-        this.outlinesTarget = webgl.createRenderTarget(width, height, false);
-        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent, true);
+        this.ssao = new SsaoPass(webgl, width, height, packedDepth, depthTextureOpaque, depthTextureTransparent);
+        this.shadow = new ShadowPass(webgl, width, height, depthTextureOpaque);
+        this.outline = new OutlinePass(webgl, width, height, depthTextureTransparent, depthTextureOpaque);
 
-        this.shadowsTarget = webgl.createRenderTarget(width, height, false);
-        this.shadowsRenderable = getShadowsRenderable(webgl, depthTextureOpaque);
-
-        this.ssaoFramebuffer = webgl.resources.framebuffer();
-        this.ssaoBlurFirstPassFramebuffer = webgl.resources.framebuffer();
-        this.ssaoBlurSecondPassFramebuffer = webgl.resources.framebuffer();
-
-        const sw = Math.floor(width * this.ssaoScale);
-        const sh = Math.floor(height * this.ssaoScale);
-
-        const hw = Math.max(1, Math.floor(sw * 0.5));
-        const hh = Math.max(1, Math.floor(sh * 0.5));
-
-        const qw = Math.max(1, Math.floor(sw * 0.25));
-        const qh = Math.max(1, Math.floor(sh * 0.25));
-
-        this.downsampledDepthTarget = drawPass.packedDepth
-            ? webgl.createRenderTarget(sw, sh, false, 'uint8', 'nearest', 'rgba')
-            : webgl.createRenderTarget(sw, sh, false, 'float32', 'nearest', webgl.isWebGL2 ? 'alpha' : 'rgba');
-        this.downsampleDepthRenderable = createCopyRenderable(webgl, depthTextureOpaque);
-
-        const depthTexture = this.ssaoScale === 1 ? depthTextureOpaque : this.downsampledDepthTarget.texture;
-
-        this.depthHalfTarget = drawPass.packedDepth
-            ? webgl.createRenderTarget(hw, hh, false, 'uint8', 'nearest', 'rgba')
-            : webgl.createRenderTarget(hw, hh, false, 'float32', 'nearest', webgl.isWebGL2 ? 'alpha' : 'rgba');
-        this.depthHalfRenderable = createCopyRenderable(webgl, depthTexture);
-
-        this.depthQuarterTarget = drawPass.packedDepth
-            ? webgl.createRenderTarget(qw, qh, false, 'uint8', 'nearest', 'rgba')
-            : webgl.createRenderTarget(qw, qh, false, 'float32', 'nearest', webgl.isWebGL2 ? 'alpha' : 'rgba');
-        this.depthQuarterRenderable = createCopyRenderable(webgl, this.depthHalfTarget.texture);
-
-        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
-        this.ssaoDepthTexture.define(sw, sh);
-        this.ssaoDepthTexture.attachFramebuffer(this.ssaoFramebuffer, 'color0');
-
-        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
-        this.ssaoDepthBlurProxyTexture.define(sw, sh);
-        this.ssaoDepthBlurProxyTexture.attachFramebuffer(this.ssaoBlurFirstPassFramebuffer, 'color0');
-
-        this.ssaoDepthTexture.attachFramebuffer(this.ssaoBlurSecondPassFramebuffer, 'color0');
-
-        this.ssaoRenderable = getSsaoRenderable(webgl, depthTexture, this.depthHalfTarget.texture, this.depthQuarterTarget.texture);
-        this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
-        this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
-        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.shadowsTarget.texture, this.outlinesTarget.texture, this.ssaoDepthTexture, true);
+        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, transparentColorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.shadow.target.texture, this.outline.target.texture, this.ssao.ssaoDepthTexture, this.ssao.ssaoDepthTransparentTexture, true);
 
         this.background = new BackgroundPass(webgl, assetManager, width, height);
     }
 
     setSize(width: number, height: number) {
         const [w, h] = this.renderable.values.uTexSize.ref.value;
-        const ssaoScale = this.calcSsaoScale(1);
-
-        if (width !== w || height !== h || this.ssaoScale !== ssaoScale) {
-            this.ssaoScale = ssaoScale;
 
+        if (width !== w || height !== h) {
             this.target.setSize(width, height);
-            this.outlinesTarget.setSize(width, height);
-            this.shadowsTarget.setSize(width, height);
-
-            const sw = Math.floor(width * this.ssaoScale);
-            const sh = Math.floor(height * this.ssaoScale);
-            this.downsampledDepthTarget.setSize(sw, sh);
-            this.ssaoDepthTexture.define(sw, sh);
-            this.ssaoDepthBlurProxyTexture.define(sw, sh);
-
-            const hw = Math.max(1, Math.floor(sw * 0.5));
-            const hh = Math.max(1, Math.floor(sh * 0.5));
-            this.depthHalfTarget.setSize(hw, hh);
-
-            const qw = Math.max(1, Math.floor(sw * 0.25));
-            const qh = Math.max(1, Math.floor(sh * 0.25));
-            this.depthQuarterTarget.setSize(qw, qh);
-
             ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
-            ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
-            ValueCell.update(this.shadowsRenderable.values.uTexSize, Vec2.set(this.shadowsRenderable.values.uTexSize.ref.value, width, height));
-            ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
-            ValueCell.update(this.depthHalfRenderable.values.uTexSize, Vec2.set(this.depthHalfRenderable.values.uTexSize.ref.value, hw, hh));
-            ValueCell.update(this.depthQuarterRenderable.values.uTexSize, Vec2.set(this.depthQuarterRenderable.values.uTexSize.ref.value, qw, qh));
-            ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
-            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
-            ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
-
-            const depthTexture = this.ssaoScale === 1 ? this.drawPass.depthTextureOpaque : this.downsampledDepthTarget.texture;
-            ValueCell.update(this.depthHalfRenderable.values.tColor, depthTexture);
-            ValueCell.update(this.ssaoRenderable.values.tDepth, depthTexture);
-
-            this.depthHalfRenderable.update();
-            this.ssaoRenderable.update();
-
-            this.background.setSize(width, height);
         }
+
+        this.ssao.setSize(width, height);
+        this.shadow.setSize(width, height);
+        this.outline.setSize(width, height);
+        this.background.setSize(width, height);
     }
 
-    updateState(camera: ICamera, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light) {
-        let needsUpdateShadows = false;
+    updateState(camera: ICamera, scene: Scene, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light, ambientColor: Vec3) {
         let needsUpdateMain = false;
-        let needsUpdateSsao = false;
-        let needsUpdateSsaoBlur = false;
-        let needsUpdateDepthHalf = false;
-        let needsUpdateOutlines = false;
 
         const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
-        const outlinesEnabled = props.outline.name === 'on';
-        const shadowsEnabled = props.shadow.name === 'on';
-        const occlusionEnabled = props.occlusion.name === 'on';
+        const outlinesEnabled = OutlinePass.isEnabled(props);
+        const shadowsEnabled = ShadowPass.isEnabled(props);
+        const occlusionEnabled = SsaoPass.isEnabled(props);
 
-        const invProjection = Mat4.identity();
-        Mat4.invert(invProjection, camera.projection);
-
-        const [w, h] = this.renderable.values.uTexSize.ref.value;
-        const v = camera.viewport;
-
-        if (props.occlusion.name === 'on') {
-            ValueCell.update(this.ssaoRenderable.values.uProjection, camera.projection);
-            ValueCell.update(this.ssaoRenderable.values.uInvProjection, invProjection);
-
-            const b = this.ssaoRenderable.values.uBounds;
-            const s = this.ssaoScale;
-            Vec4.set(b.ref.value,
-                Math.floor(v.x * s) / (w * s),
-                Math.floor(v.y * s) / (h * s),
-                Math.ceil((v.x + v.width) * s) / (w * s),
-                Math.ceil((v.y + v.height) * s) / (h * s)
-            );
-            ValueCell.update(b, b.ref.value);
-            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uBounds, b.ref.value);
-            ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uBounds, b.ref.value);
-
-            ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.uNear, camera.near);
-            ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.uNear, camera.near);
-
-            ValueCell.updateIfChanged(this.ssaoBlurFirstPassRenderable.values.uFar, camera.far);
-            ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.uFar, camera.far);
-
-            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uInvProjection, invProjection);
-            ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uInvProjection, invProjection);
-
-            if (this.ssaoBlurFirstPassRenderable.values.dOrthographic.ref.value !== orthographic) {
-                needsUpdateSsaoBlur = true;
-                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.dOrthographic, orthographic);
-                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.dOrthographic, orthographic);
+        if (occlusionEnabled) {
+            const params = props.occlusion.params as SsaoProps;
+            this.ssao.update(camera, scene, params);
+            const includeTransparency = SsaoPass.isTransparentEnabled(scene, params);
+            if (this.renderable.values.dOcclusionIncludeTransparency.ref.value !== includeTransparency) {
+                needsUpdateMain = true;
+                ValueCell.update(this.renderable.values.dOcclusionIncludeTransparency, includeTransparency);
             }
-
-            if (this.nSamples !== props.occlusion.params.samples) {
-                needsUpdateSsao = true;
-
-                this.nSamples = props.occlusion.params.samples;
-                ValueCell.update(this.ssaoRenderable.values.uSamples, getSamples(this.nSamples));
-                ValueCell.updateIfChanged(this.ssaoRenderable.values.dNSamples, this.nSamples);
-            }
-
-            const multiScale = props.occlusion.params.multiScale.name === 'on';
-            if (this.ssaoRenderable.values.dMultiScale.ref.value !== multiScale) {
-                needsUpdateSsao = true;
-                ValueCell.update(this.ssaoRenderable.values.dMultiScale, multiScale);
-            }
-
-            if (props.occlusion.params.multiScale.name === 'on') {
-                const mp = props.occlusion.params.multiScale.params;
-                if (!deepEqual(this.levels, mp.levels)) {
-                    needsUpdateSsao = true;
-
-                    this.levels = mp.levels;
-                    const levels = getLevels(mp.levels);
-                    ValueCell.updateIfChanged(this.ssaoRenderable.values.dLevels, levels.count);
-
-                    ValueCell.update(this.ssaoRenderable.values.uLevelRadius, levels.radius);
-                    ValueCell.update(this.ssaoRenderable.values.uLevelBias, levels.bias);
-                }
-                ValueCell.updateIfChanged(this.ssaoRenderable.values.uNearThreshold, mp.nearThreshold);
-                ValueCell.updateIfChanged(this.ssaoRenderable.values.uFarThreshold, mp.farThreshold);
-            } else {
-                ValueCell.updateIfChanged(this.ssaoRenderable.values.uRadius, Math.pow(2, props.occlusion.params.radius));
-            }
-            ValueCell.updateIfChanged(this.ssaoRenderable.values.uBias, props.occlusion.params.bias);
-
-            if (this.blurKernelSize !== props.occlusion.params.blurKernelSize) {
-                needsUpdateSsaoBlur = true;
-
-                this.blurKernelSize = props.occlusion.params.blurKernelSize;
-                const kernel = getBlurKernel(this.blurKernelSize);
-
-                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uKernel, kernel);
-                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uKernel, kernel);
-                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
-                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
-            }
-
-            const ssaoScale = this.calcSsaoScale(props.occlusion.params.resolutionScale);
-            if (this.ssaoScale !== ssaoScale) {
-                needsUpdateSsao = true;
-                needsUpdateDepthHalf = true;
-
-                this.ssaoScale = ssaoScale;
-
-                const sw = Math.floor(w * this.ssaoScale);
-                const sh = Math.floor(h * this.ssaoScale);
-                this.downsampledDepthTarget.setSize(sw, sh);
-                this.ssaoDepthTexture.define(sw, sh);
-                this.ssaoDepthBlurProxyTexture.define(sw, sh);
-
-                const hw = Math.floor(sw * 0.5);
-                const hh = Math.floor(sh * 0.5);
-                this.depthHalfTarget.setSize(hw, hh);
-
-                const qw = Math.floor(sw * 0.25);
-                const qh = Math.floor(sh * 0.25);
-                this.depthQuarterTarget.setSize(qw, qh);
-
-                const depthTexture = this.ssaoScale === 1 ? this.drawPass.depthTextureOpaque : this.downsampledDepthTarget.texture;
-                ValueCell.update(this.depthHalfRenderable.values.tColor, depthTexture);
-                ValueCell.update(this.ssaoRenderable.values.tDepth, depthTexture);
-
-                ValueCell.update(this.ssaoRenderable.values.tDepthHalf, this.depthHalfTarget.texture);
-                ValueCell.update(this.ssaoRenderable.values.tDepthQuarter, this.depthQuarterTarget.texture);
-
-                ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
-                ValueCell.update(this.depthHalfRenderable.values.uTexSize, Vec2.set(this.depthHalfRenderable.values.uTexSize.ref.value, hw, hh));
-                ValueCell.update(this.depthQuarterRenderable.values.uTexSize, Vec2.set(this.depthQuarterRenderable.values.uTexSize.ref.value, qw, qh));
-                ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
-                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
-                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
-            }
-
-            ValueCell.update(this.renderable.values.uOcclusionColor, Color.toVec3Normalized(this.renderable.values.uOcclusionColor.ref.value, props.occlusion.params.color));
+            ValueCell.update(this.renderable.values.uOcclusionColor, Color.toVec3Normalized(this.renderable.values.uOcclusionColor.ref.value, params.color));
         }
 
-        if (props.shadow.name === 'on') {
-            ValueCell.update(this.shadowsRenderable.values.uProjection, camera.projection);
-            ValueCell.update(this.shadowsRenderable.values.uInvProjection, invProjection);
-
-            Vec4.set(this.shadowsRenderable.values.uBounds.ref.value,
-                v.x / w,
-                v.y / h,
-                (v.x + v.width) / w,
-                (v.y + v.height) / h
-            );
-            ValueCell.update(this.shadowsRenderable.values.uBounds, this.shadowsRenderable.values.uBounds.ref.value);
-
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uNear, camera.near);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uFar, camera.far);
-            if (this.shadowsRenderable.values.dOrthographic.ref.value !== orthographic) {
-                ValueCell.update(this.shadowsRenderable.values.dOrthographic, orthographic);
-                needsUpdateShadows = true;
-            }
-
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uMaxDistance, props.shadow.params.maxDistance);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uTolerance, props.shadow.params.tolerance);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uBias, props.shadow.params.bias);
-            if (this.shadowsRenderable.values.dSteps.ref.value !== props.shadow.params.steps) {
-                ValueCell.update(this.shadowsRenderable.values.dSteps, props.shadow.params.steps);
-                needsUpdateShadows = true;
-            }
-
-            ValueCell.update(this.shadowsRenderable.values.uLightDirection, light.direction);
-            ValueCell.update(this.shadowsRenderable.values.uLightColor, light.color);
-            if (this.shadowsRenderable.values.dLightCount.ref.value !== light.count) {
-                ValueCell.update(this.shadowsRenderable.values.dLightCount, light.count);
-                needsUpdateShadows = true;
-            }
+        if (shadowsEnabled) {
+            this.shadow.update(camera, light, ambientColor, props.shadow.params as ShadowProps);
         }
 
-        if (props.outline.name === 'on') {
-            const transparentOutline = props.outline.params.includeTransparent ?? true;
-            const outlineScale = Math.max(1, Math.round(props.outline.params.scale * this.webgl.pixelRatio)) - 1;
-            const outlineThreshold = 50 * props.outline.params.threshold * this.webgl.pixelRatio;
+        if (outlinesEnabled) {
+            const outlineProps = props.outline.params as OutlineProps;
+            const { transparentOutline, outlineScale } = this.outline.update(camera, outlineProps, this.drawPass.depthTextureTransparent, this.drawPass.depthTextureOpaque);
 
-            ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
-            ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
-            ValueCell.update(this.outlinesRenderable.values.uInvProjection, invProjection);
-            if (this.outlinesRenderable.values.dTransparentOutline.ref.value !== transparentOutline) {
-                needsUpdateOutlines = true;
-                ValueCell.update(this.outlinesRenderable.values.dTransparentOutline, transparentOutline);
-            }
-            if (this.outlinesRenderable.values.dOrthographic.ref.value !== orthographic) {
-                needsUpdateOutlines = true;
-                ValueCell.update(this.outlinesRenderable.values.dOrthographic, orthographic);
-            }
-            ValueCell.updateIfChanged(this.outlinesRenderable.values.uOutlineThreshold, outlineThreshold);
-
-            ValueCell.update(this.renderable.values.uOutlineColor, Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, props.outline.params.color));
+            ValueCell.update(this.renderable.values.uOutlineColor, Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, outlineProps.color));
 
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) {
                 needsUpdateMain = true;
@@ -806,6 +260,7 @@ export class PostprocessingPass {
         ValueCell.updateIfChanged(this.renderable.values.uFogNear, camera.fogNear);
         ValueCell.update(this.renderable.values.uFogColor, Color.toVec3Normalized(this.renderable.values.uFogColor.ref.value, backgroundColor));
         ValueCell.updateIfChanged(this.renderable.values.uTransparentBackground, transparentBackground);
+
         if (this.renderable.values.dOrthographic.ref.value !== orthographic) {
             needsUpdateMain = true;
             ValueCell.update(this.renderable.values.dOrthographic, orthographic);
@@ -824,25 +279,10 @@ export class PostprocessingPass {
             ValueCell.update(this.renderable.values.dOcclusionEnable, occlusionEnabled);
         }
 
-        if (needsUpdateOutlines) {
-            this.outlinesRenderable.update();
-        }
-
-        if (needsUpdateShadows) {
-            this.shadowsRenderable.update();
-        }
-
-        if (needsUpdateSsao) {
-            this.ssaoRenderable.update();
-        }
-
-        if (needsUpdateSsaoBlur) {
-            this.ssaoBlurFirstPassRenderable.update();
-            this.ssaoBlurSecondPassRenderable.update();
-        }
-
-        if (needsUpdateDepthHalf) {
-            this.depthHalfRenderable.update();
+        const blendTransparency = scene.opacityAverage < 1;
+        if (this.renderable.values.dBlendTransparency.ref.value !== blendTransparency) {
+            needsUpdateMain = true;
+            ValueCell.update(this.renderable.values.dBlendTransparency, blendTransparency);
         }
 
         if (needsUpdateMain) {
@@ -869,64 +309,28 @@ export class PostprocessingPass {
         this.transparentBackground = value;
     }
 
-    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light) {
+    render(camera: ICamera, scene: Scene, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light, ambientColor: Vec3) {
         if (isTimingMode) this.webgl.timer.mark('PostprocessingPass.render');
-        this.updateState(camera, transparentBackground, backgroundColor, props, light);
+        this.updateState(camera, scene, transparentBackground, backgroundColor, props, light, ambientColor);
 
-        const { gl, state } = this.webgl;
+        const { state } = this.webgl;
         const { x, y, width, height } = camera.viewport;
 
         // don't render occlusion if offset is given,
         // which will reuse the existing occlusion
         if (props.occlusion.name === 'on' && this.occlusionOffset[0] === 0 && this.occlusionOffset[1] === 0) {
-            if (isTimingMode) this.webgl.timer.mark('SSAO.render');
-            const sx = Math.floor(x * this.ssaoScale);
-            const sy = Math.floor(y * this.ssaoScale);
-            const sw = Math.ceil(width * this.ssaoScale);
-            const sh = Math.ceil(height * this.ssaoScale);
-
-            state.viewport(sx, sy, sw, sh);
-            state.scissor(sx, sy, sw, sh);
-
-            if (this.ssaoScale < 1) {
-                if (isTimingMode) this.webgl.timer.mark('SSAO.downsample');
-                this.downsampledDepthTarget.bind();
-                this.downsampleDepthRenderable.render();
-                if (isTimingMode) this.webgl.timer.markEnd('SSAO.downsample');
-            }
-
-            if (isTimingMode) this.webgl.timer.mark('SSAO.half');
-            this.depthHalfTarget.bind();
-            this.depthHalfRenderable.render();
-            if (isTimingMode) this.webgl.timer.markEnd('SSAO.half');
-
-            if (isTimingMode) this.webgl.timer.mark('SSAO.quarter');
-            this.depthQuarterTarget.bind();
-            this.depthQuarterRenderable.render();
-            if (isTimingMode) this.webgl.timer.markEnd('SSAO.quarter');
-
-            this.ssaoFramebuffer.bind();
-            this.ssaoRenderable.render();
-
-            this.ssaoBlurFirstPassFramebuffer.bind();
-            this.ssaoBlurFirstPassRenderable.render();
-
-            this.ssaoBlurSecondPassFramebuffer.bind();
-            this.ssaoBlurSecondPassRenderable.render();
-            if (isTimingMode) this.webgl.timer.markEnd('SSAO.render');
+            this.ssao.render(camera);
         }
 
         state.viewport(x, y, width, height);
         state.scissor(x, y, width, height);
 
         if (props.outline.name === 'on') {
-            this.outlinesTarget.bind();
-            this.outlinesRenderable.render();
+            this.outline.render();
         }
 
         if (props.shadow.name === 'on') {
-            this.shadowsTarget.bind();
-            this.shadowsRenderable.render();
+            this.shadow.render();
         }
 
         if (toDrawingBuffer) {
@@ -936,21 +340,8 @@ export class PostprocessingPass {
         }
 
         this.background.update(camera, props.background);
-        if (this.background.isEnabled(props.background)) {
-            if (this.transparentBackground) {
-                state.clearColor(0, 0, 0, 0);
-            } else {
-                Color.toVec3Normalized(this.bgColor, backgroundColor);
-                state.clearColor(this.bgColor[0], this.bgColor[1], this.bgColor[2], 1);
-            }
-            gl.clear(gl.COLOR_BUFFER_BIT);
-            state.enable(gl.BLEND);
-            state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
-            this.background.render();
-        } else {
-            state.clearColor(0, 0, 0, 1);
-            gl.clear(gl.COLOR_BUFFER_BIT);
-        }
+        this.background.clear(props.background, this.transparentBackground, backgroundColor);
+        this.background.render(props.background);
 
         this.renderable.render();
         if (isTimingMode) this.webgl.timer.markEnd('PostprocessingPass.render');

src/mol-canvas3d/passes/shadow.ts

@@ -0,0 +1,170 @@
+/**
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { ValueCell } from '../../mol-util';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
+import { Mat4, Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { ICamera } from '../../mol-canvas3d/camera';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { isTimingMode } from '../../mol-util/debug';
+import { Light } from '../../mol-gl/renderer';
+import { shadows_frag } from '../../mol-gl/shader/shadows.frag';
+import { PostprocessingProps } from './postprocessing';
+
+export const ShadowParams = {
+    steps: PD.Numeric(1, { min: 1, max: 64, step: 1 }),
+    maxDistance: PD.Numeric(3, { min: 0, max: 256, step: 1 }),
+    tolerance: PD.Numeric(1.0, { min: 0.0, max: 10.0, step: 0.1 }),
+};
+
+export type ShadowProps = PD.Values<typeof ShadowParams>
+
+export class ShadowPass {
+    static isEnabled(props: PostprocessingProps) {
+        return props.shadow.name !== 'off';
+    }
+
+    readonly target: RenderTarget;
+    private readonly renderable: ShadowsRenderable;
+
+    constructor(readonly webgl: WebGLContext, width: number, height: number, depthTextureOpaque: Texture) {
+        this.target = webgl.createRenderTarget(width, height, false);
+        this.renderable = getShadowsRenderable(webgl, depthTextureOpaque);
+    }
+
+    setSize(width: number, height: number) {
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        if (width !== w || height !== h) {
+            this.target.setSize(width, height);
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    update(camera: ICamera, light: Light, ambientColor: Vec3, props: ShadowProps) {
+        let needsUpdateShadows = false;
+
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+
+        const invProjection = Mat4.identity();
+        Mat4.invert(invProjection, camera.projection);
+
+        const [w, h] = this.renderable.values.uTexSize.ref.value;
+        const v = camera.viewport;
+
+        ValueCell.update(this.renderable.values.uProjection, camera.projection);
+        ValueCell.update(this.renderable.values.uInvProjection, invProjection);
+
+        Vec4.set(this.renderable.values.uBounds.ref.value,
+            v.x / w,
+            v.y / h,
+            (v.x + v.width) / w,
+            (v.y + v.height) / h
+        );
+        ValueCell.update(this.renderable.values.uBounds, this.renderable.values.uBounds.ref.value);
+
+        ValueCell.updateIfChanged(this.renderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.renderable.values.uFar, camera.far);
+        if (this.renderable.values.dOrthographic.ref.value !== orthographic) {
+            ValueCell.update(this.renderable.values.dOrthographic, orthographic);
+            needsUpdateShadows = true;
+        }
+
+        ValueCell.updateIfChanged(this.renderable.values.uMaxDistance, props.maxDistance);
+        ValueCell.updateIfChanged(this.renderable.values.uTolerance, props.tolerance);
+        if (this.renderable.values.dSteps.ref.value !== props.steps) {
+            ValueCell.update(this.renderable.values.dSteps, props.steps);
+            needsUpdateShadows = true;
+        }
+
+        ValueCell.update(this.renderable.values.uLightDirection, light.direction);
+        ValueCell.update(this.renderable.values.uLightColor, light.color);
+        if (this.renderable.values.dLightCount.ref.value !== light.count) {
+            ValueCell.update(this.renderable.values.dLightCount, light.count);
+            needsUpdateShadows = true;
+        }
+        ValueCell.update(this.renderable.values.uAmbientColor, ambientColor);
+
+        if (needsUpdateShadows) {
+            this.renderable.update();
+        }
+    }
+
+    render() {
+        if (isTimingMode) this.webgl.timer.mark('ShadowPass.render');
+        this.target.bind();
+        this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('ShadowPass.render');
+    }
+}
+
+const ShadowsSchema = {
+    ...QuadSchema,
+    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    uProjection: UniformSpec('m4'),
+    uInvProjection: UniformSpec('m4'),
+    uBounds: UniformSpec('v4'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+
+    dSteps: DefineSpec('number'),
+    uMaxDistance: UniformSpec('f'),
+    uTolerance: UniformSpec('f'),
+
+    uLightDirection: UniformSpec('v3[]'),
+    uLightColor: UniformSpec('v3[]'),
+    dLightCount: DefineSpec('number'),
+    uAmbientColor: UniformSpec('v3'),
+};
+type ShadowsRenderable = ComputeRenderable<Values<typeof ShadowsSchema>>
+
+function getShadowsRenderable(ctx: WebGLContext, depthTexture: Texture): ShadowsRenderable {
+    const width = depthTexture.getWidth();
+    const height = depthTexture.getHeight();
+
+    const values: Values<typeof ShadowsSchema> = {
+        ...QuadValues,
+        tDepth: ValueCell.create(depthTexture),
+        uTexSize: ValueCell.create(Vec2.create(width, height)),
+
+        uProjection: ValueCell.create(Mat4.identity()),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+        uBounds: ValueCell.create(Vec4()),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+
+        dSteps: ValueCell.create(1),
+        uMaxDistance: ValueCell.create(3.0),
+        uTolerance: ValueCell.create(1.0),
+
+        uLightDirection: ValueCell.create([]),
+        uLightColor: ValueCell.create([]),
+        dLightCount: ValueCell.create(0),
+        uAmbientColor: ValueCell.create(Vec3()),
+    };
+
+    const schema = { ...ShadowsSchema };
+    const shaderCode = ShaderCode('shadows', quad_vert, shadows_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-canvas3d/passes/ssao.ts

@@ -0,0 +1,689 @@
+/**
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
+ */
+
+import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { deepEqual, ValueCell } from '../../mol-util';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { createComputeRenderable, ComputeRenderable } from '../../mol-gl/renderable';
+import { Mat4, Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { ICamera } from '../../mol-canvas3d/camera';
+import { Scene } from '../../mol-gl/scene';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { ssao_frag } from '../../mol-gl/shader/ssao.frag';
+import { ssaoBlur_frag } from '../../mol-gl/shader/ssao-blur.frag';
+import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
+import { Color } from '../../mol-util/color';
+import { isTimingMode } from '../../mol-util/debug';
+import { PostprocessingProps } from './postprocessing';
+
+export const SsaoParams = {
+    samples: PD.Numeric(32, { min: 1, max: 256, step: 1 }),
+    multiScale: PD.MappedStatic('off', {
+        on: PD.Group({
+            levels: PD.ObjectList({
+                radius: PD.Numeric(5, { min: 0, max: 20, step: 0.1 }, { description: 'Final occlusion radius is 2^x' }),
+                bias: PD.Numeric(1, { min: 0, max: 3, step: 0.1 }),
+            }, o => `${o.radius}, ${o.bias}`, { defaultValue: [
+                { radius: 2, bias: 1 },
+                { radius: 5, bias: 1 },
+                { radius: 8, bias: 1 },
+                { radius: 11, bias: 1 },
+            ] }),
+            nearThreshold: PD.Numeric(10, { min: 0, max: 50, step: 1 }),
+            farThreshold: PD.Numeric(1500, { min: 0, max: 10000, step: 100 }),
+        }),
+        off: PD.Group({})
+    }, { cycle: true }),
+    radius: PD.Numeric(5, { min: 0, max: 20, step: 0.1 }, { description: 'Final occlusion radius is 2^x', hideIf: p => p?.multiScale.name === 'on' }),
+    bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
+    blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
+    blurDepthBias: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
+    resolutionScale: PD.Numeric(1, { min: 0.1, max: 1, step: 0.05 }, { description: 'Adjust resolution of occlusion calculation' }),
+    color: PD.Color(Color(0x000000)),
+    transparentThreshold: PD.Numeric(0.4, { min: 0, max: 1, step: 0.05 }),
+};
+
+export type SsaoProps = PD.Values<typeof SsaoParams>
+
+type Levels = {
+    count: number
+    radius: number[]
+    bias: number[]
+}
+
+function getLevels(props: { radius: number, bias: number }[], levels?: Levels): Levels {
+    const count = props.length;
+    const { radius, bias } = levels || {
+        radius: (new Array(count * 3)).fill(0),
+        bias: (new Array(count * 3)).fill(0),
+    };
+    props = props.slice().sort((a, b) => a.radius - b.radius);
+    for (let i = 0; i < count; ++i) {
+        const p = props[i];
+        radius[i] = Math.pow(2, p.radius);
+        bias[i] = p.bias;
+    }
+    return { count, radius, bias };
+}
+
+export class SsaoPass {
+    static isEnabled(props: PostprocessingProps) {
+        return props.occlusion.name !== 'off';
+    }
+
+    static isTransparentEnabled(scene: Scene, props: SsaoProps) {
+        return scene.opacityAverage < 1 && scene.transparencyMin < props.transparentThreshold;
+    }
+
+    readonly target: RenderTarget;
+
+    private readonly framebuffer: Framebuffer;
+    private readonly blurFirstPassFramebuffer: Framebuffer;
+    private readonly blurSecondPassFramebuffer: Framebuffer;
+
+    private readonly downsampledDepthTargetOpaque: RenderTarget;
+    private readonly downsampleDepthRenderableOpaque: CopyRenderable;
+
+    private readonly depthHalfTargetOpaque: RenderTarget;
+    private readonly depthHalfRenderableOpaque: CopyRenderable;
+
+    private readonly depthQuarterTargetOpaque: RenderTarget;
+    private readonly depthQuarterRenderableOpaque: CopyRenderable;
+
+    private readonly downsampledDepthTargetTransparent: RenderTarget;
+    private readonly downsampleDepthRenderableTransparent: CopyRenderable;
+
+    private readonly depthHalfTargetTransparent: RenderTarget;
+    private readonly depthHalfRenderableTransparent: CopyRenderable;
+
+    private readonly depthQuarterTargetTransparent: RenderTarget;
+    private readonly depthQuarterRenderableTransparent: CopyRenderable;
+
+    readonly ssaoDepthTexture: Texture;
+    readonly ssaoDepthTransparentTexture: Texture;
+
+    private readonly depthBlurProxyTexture: Texture;
+
+    private depthTextureOpaque: Texture;
+    private depthTextureTransparent: Texture;
+
+    private readonly renderable: SsaoRenderable;
+    private readonly blurFirstPassRenderable: SsaoBlurRenderable;
+    private readonly blurSecondPassRenderable: SsaoBlurRenderable;
+
+    private nSamples: number;
+    private blurKernelSize: number;
+    private texSize: [number, number];
+
+    private ssaoScale: number;
+    private calcSsaoScale(resolutionScale: number) {
+        // downscale ssao for high pixel-ratios
+        return Math.min(1, 1 / this.webgl.pixelRatio) * resolutionScale;
+    }
+
+    private levels: { radius: number, bias: number }[];
+
+    private getDepthTexture() {
+        return this.ssaoScale === 1 ? this.depthTextureOpaque : this.downsampledDepthTargetOpaque.texture;
+    }
+
+    private getTransparentDepthTexture() {
+        return this.ssaoScale === 1 ? this.depthTextureTransparent : this.downsampledDepthTargetTransparent.texture;
+    }
+
+    constructor(private readonly webgl: WebGLContext, width: number, height: number, packedDepth: boolean, depthTextureOpaque: Texture, depthTextureTransparent: Texture) {
+        const { textureFloatLinear } = webgl.extensions;
+
+        this.depthTextureOpaque = depthTextureOpaque;
+        this.depthTextureTransparent = depthTextureTransparent;
+
+        this.nSamples = 1;
+        this.blurKernelSize = 1;
+        this.ssaoScale = this.calcSsaoScale(1);
+        this.texSize = [width, height];
+        this.levels = [];
+
+        this.framebuffer = webgl.resources.framebuffer();
+        this.blurFirstPassFramebuffer = webgl.resources.framebuffer();
+        this.blurSecondPassFramebuffer = webgl.resources.framebuffer();
+
+        const sw = Math.floor(width * this.ssaoScale);
+        const sh = Math.floor(height * this.ssaoScale);
+
+        const hw = Math.max(1, Math.floor(sw * 0.5));
+        const hh = Math.max(1, Math.floor(sh * 0.5));
+
+        const qw = Math.max(1, Math.floor(sw * 0.25));
+        const qh = Math.max(1, Math.floor(sh * 0.25));
+
+        const filter = textureFloatLinear ? 'linear' : 'nearest';
+
+        this.downsampledDepthTargetOpaque = packedDepth
+            ? webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear', 'rgba')
+            : webgl.createRenderTarget(sw, sh, false, 'float32', filter, webgl.isWebGL2 ? 'alpha' : 'rgba');
+        this.downsampleDepthRenderableOpaque = createCopyRenderable(webgl, depthTextureOpaque);
+
+        const depthTexture = this.getDepthTexture();
+        this.depthHalfTargetOpaque = packedDepth
+            ? webgl.createRenderTarget(hw, hh, false, 'uint8', 'linear', 'rgba')
+            : webgl.createRenderTarget(hw, hh, false, 'float32', filter, webgl.isWebGL2 ? 'alpha' : 'rgba');
+        this.depthHalfRenderableOpaque = createCopyRenderable(webgl, depthTexture);
+
+        this.depthQuarterTargetOpaque = packedDepth
+            ? webgl.createRenderTarget(qw, qh, false, 'uint8', 'linear', 'rgba')
+            : webgl.createRenderTarget(qw, qh, false, 'float32', filter, webgl.isWebGL2 ? 'alpha' : 'rgba');
+        this.depthQuarterRenderableOpaque = createCopyRenderable(webgl, this.depthHalfTargetOpaque.texture);
+
+        this.downsampledDepthTargetTransparent = webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear', 'rgba');
+        this.downsampleDepthRenderableTransparent = createCopyRenderable(webgl, depthTextureTransparent);
+
+        const transparentDepthTexture = this.getTransparentDepthTexture();
+        this.depthHalfTargetTransparent = webgl.createRenderTarget(hw, hh, false, 'uint8', 'linear', 'rgba');
+        this.depthHalfRenderableTransparent = createCopyRenderable(webgl, transparentDepthTexture);
+
+        this.depthQuarterTargetTransparent = webgl.createRenderTarget(qw, qh, false, 'uint8', 'linear', 'rgba');
+        this.depthQuarterRenderableTransparent = createCopyRenderable(webgl, this.depthHalfTargetTransparent.texture);
+
+        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+        this.ssaoDepthTexture.define(sw, sh);
+        this.ssaoDepthTexture.attachFramebuffer(this.framebuffer, 'color0');
+
+        this.ssaoDepthTransparentTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+        this.ssaoDepthTransparentTexture.define(sw, sh);
+
+        this.depthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
+        this.depthBlurProxyTexture.define(sw, sh);
+        this.depthBlurProxyTexture.attachFramebuffer(this.blurFirstPassFramebuffer, 'color0');
+
+        this.renderable = getSsaoRenderable(webgl, depthTexture, this.depthHalfTargetOpaque.texture, this.depthQuarterTargetOpaque.texture, transparentDepthTexture, this.depthHalfTargetTransparent.texture, this.depthQuarterTargetTransparent.texture);
+        this.blurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTransparentTexture, 'horizontal');
+        this.blurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.depthBlurProxyTexture, 'vertical');
+    }
+
+    setSize(width: number, height: number) {
+        const [w, h] = this.texSize;
+        const ssaoScale = this.calcSsaoScale(1);
+        if (width !== w || height !== h || this.ssaoScale !== ssaoScale) {
+            this.texSize.splice(0, 2, width, height);
+
+            const sw = Math.floor(width * this.ssaoScale);
+            const sh = Math.floor(height * this.ssaoScale);
+            this.ssaoDepthTexture.define(sw, sh);
+            this.ssaoDepthTransparentTexture.define(sw, sh);
+            this.depthBlurProxyTexture.define(sw, sh);
+
+            const hw = Math.max(1, Math.floor(sw * 0.5));
+            const hh = Math.max(1, Math.floor(sh * 0.5));
+            const qw = Math.max(1, Math.floor(sw * 0.25));
+            const qh = Math.max(1, Math.floor(sh * 0.25));
+
+            this.downsampledDepthTargetOpaque.setSize(sw, sh);
+            this.depthHalfTargetOpaque.setSize(hw, hh);
+            this.depthQuarterTargetOpaque.setSize(qw, qh);
+
+            ValueCell.update(this.downsampleDepthRenderableOpaque.values.uTexSize, Vec2.set(this.downsampleDepthRenderableOpaque.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.depthHalfRenderableOpaque.values.uTexSize, Vec2.set(this.depthHalfRenderableOpaque.values.uTexSize.ref.value, hw, hh));
+            ValueCell.update(this.depthQuarterRenderableOpaque.values.uTexSize, Vec2.set(this.depthQuarterRenderableOpaque.values.uTexSize.ref.value, qw, qh));
+
+            this.downsampledDepthTargetTransparent.setSize(sw, sh);
+            this.depthHalfTargetTransparent.setSize(hw, hh);
+            this.depthQuarterTargetTransparent.setSize(qw, qh);
+
+            ValueCell.update(this.downsampleDepthRenderableTransparent.values.uTexSize, Vec2.set(this.downsampleDepthRenderableTransparent.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.depthHalfRenderableTransparent.values.uTexSize, Vec2.set(this.depthHalfRenderableTransparent.values.uTexSize.ref.value, hw, hh));
+            ValueCell.update(this.depthQuarterRenderableTransparent.values.uTexSize, Vec2.set(this.depthQuarterRenderableTransparent.values.uTexSize.ref.value, qw, qh));
+
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.blurFirstPassRenderable.values.uTexSize, Vec2.set(this.blurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.blurSecondPassRenderable.values.uTexSize, Vec2.set(this.blurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
+
+            const depthTexture = this.getDepthTexture();
+            const transparentDepthTexture = this.getTransparentDepthTexture();
+
+            ValueCell.update(this.depthHalfRenderableOpaque.values.tColor, depthTexture);
+            ValueCell.update(this.depthHalfRenderableTransparent.values.tColor, transparentDepthTexture);
+
+            ValueCell.update(this.renderable.values.tDepth, depthTexture);
+            ValueCell.update(this.renderable.values.tDepthTransparent, transparentDepthTexture);
+
+            this.depthHalfRenderableOpaque.update();
+            this.depthHalfRenderableTransparent.update();
+            this.renderable.update();
+        }
+    }
+
+    update(camera: ICamera, scene: Scene, props: SsaoProps, illuminationMode = false) {
+        let needsUpdateSsao = false;
+        let needsUpdateSsaoBlur = false;
+        let needsUpdateDepthHalf = false;
+
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+
+        const invProjection = Mat4.identity();
+        Mat4.invert(invProjection, camera.projection);
+
+        const [w, h] = this.texSize;
+        const v = camera.viewport;
+
+        ValueCell.update(this.renderable.values.uProjection, camera.projection);
+        ValueCell.update(this.renderable.values.uInvProjection, invProjection);
+
+        const b = this.renderable.values.uBounds;
+        const s = this.ssaoScale;
+        Vec4.set(b.ref.value,
+            Math.floor(v.x * s) / (w * s),
+            Math.floor(v.y * s) / (h * s),
+            Math.ceil((v.x + v.width) * s) / (w * s),
+            Math.ceil((v.y + v.height) * s) / (h * s)
+        );
+        ValueCell.update(b, b.ref.value);
+        ValueCell.update(this.blurFirstPassRenderable.values.uBounds, b.ref.value);
+        ValueCell.update(this.blurSecondPassRenderable.values.uBounds, b.ref.value);
+
+        ValueCell.updateIfChanged(this.blurFirstPassRenderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.blurSecondPassRenderable.values.uNear, camera.near);
+
+        ValueCell.updateIfChanged(this.blurFirstPassRenderable.values.uFar, camera.far);
+        ValueCell.updateIfChanged(this.blurSecondPassRenderable.values.uFar, camera.far);
+
+        ValueCell.update(this.blurFirstPassRenderable.values.uInvProjection, invProjection);
+        ValueCell.update(this.blurSecondPassRenderable.values.uInvProjection, invProjection);
+
+        ValueCell.update(this.blurFirstPassRenderable.values.uBlurDepthBias, props.blurDepthBias);
+        ValueCell.update(this.blurSecondPassRenderable.values.uBlurDepthBias, props.blurDepthBias);
+
+        if (this.blurFirstPassRenderable.values.dOrthographic.ref.value !== orthographic) {
+            needsUpdateSsaoBlur = true;
+            ValueCell.update(this.blurFirstPassRenderable.values.dOrthographic, orthographic);
+            ValueCell.update(this.blurSecondPassRenderable.values.dOrthographic, orthographic);
+        }
+
+        const includeTransparent = SsaoPass.isTransparentEnabled(scene, props);
+        if (this.renderable.values.dIncludeTransparent.ref.value !== includeTransparent) {
+            needsUpdateSsao = true;
+
+            ValueCell.update(this.renderable.values.dIncludeTransparent, includeTransparent);
+        }
+
+        if (this.renderable.values.dIllumination.ref.value !== illuminationMode) {
+            needsUpdateSsao = true;
+
+            ValueCell.update(this.renderable.values.dIllumination, illuminationMode);
+        }
+
+        if (this.nSamples !== props.samples) {
+            needsUpdateSsao = true;
+
+            this.nSamples = props.samples;
+            ValueCell.update(this.renderable.values.uSamples, getSamples(this.nSamples));
+            ValueCell.updateIfChanged(this.renderable.values.dNSamples, this.nSamples);
+        }
+
+        const multiScale = props.multiScale.name === 'on';
+        if (this.renderable.values.dMultiScale.ref.value !== multiScale) {
+            needsUpdateSsao = true;
+
+            ValueCell.update(this.renderable.values.dMultiScale, multiScale);
+        }
+
+        if (props.multiScale.name === 'on') {
+            const mp = props.multiScale.params;
+            if (!deepEqual(this.levels, mp.levels)) {
+                needsUpdateSsao = true;
+
+                this.levels = mp.levels;
+                const levels = getLevels(mp.levels);
+                ValueCell.updateIfChanged(this.renderable.values.dLevels, levels.count);
+
+                ValueCell.update(this.renderable.values.uLevelRadius, levels.radius);
+                ValueCell.update(this.renderable.values.uLevelBias, levels.bias);
+            }
+            ValueCell.updateIfChanged(this.renderable.values.uNearThreshold, mp.nearThreshold);
+            ValueCell.updateIfChanged(this.renderable.values.uFarThreshold, mp.farThreshold);
+        } else {
+            ValueCell.updateIfChanged(this.renderable.values.uRadius, Math.pow(2, props.radius));
+        }
+        ValueCell.updateIfChanged(this.renderable.values.uBias, props.bias);
+
+        if (this.blurKernelSize !== props.blurKernelSize) {
+            needsUpdateSsaoBlur = true;
+
+            this.blurKernelSize = props.blurKernelSize;
+            const kernel = getBlurKernel(this.blurKernelSize);
+
+            ValueCell.update(this.blurFirstPassRenderable.values.uKernel, kernel);
+            ValueCell.update(this.blurSecondPassRenderable.values.uKernel, kernel);
+            ValueCell.update(this.blurFirstPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
+            ValueCell.update(this.blurSecondPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
+        }
+
+        const ssaoScale = this.calcSsaoScale(props.resolutionScale);
+        if (this.ssaoScale !== ssaoScale) {
+            needsUpdateSsao = true;
+            needsUpdateDepthHalf = true;
+
+            this.ssaoScale = ssaoScale;
+
+            const sw = Math.floor(w * this.ssaoScale);
+            const sh = Math.floor(h * this.ssaoScale);
+            this.ssaoDepthTexture.define(sw, sh);
+            this.ssaoDepthTransparentTexture.define(sw, sh);
+            this.depthBlurProxyTexture.define(sw, sh);
+
+            const hw = Math.floor(sw * 0.5);
+            const hh = Math.floor(sh * 0.5);
+            const qw = Math.floor(sw * 0.25);
+            const qh = Math.floor(sh * 0.25);
+
+            this.downsampledDepthTargetOpaque.setSize(sw, sh);
+            this.depthHalfTargetOpaque.setSize(hw, hh);
+            this.depthQuarterTargetOpaque.setSize(qw, qh);
+
+            const depthTexture = this.getDepthTexture();
+            ValueCell.update(this.depthHalfRenderableOpaque.values.tColor, depthTexture);
+            ValueCell.update(this.renderable.values.tDepth, depthTexture);
+
+            ValueCell.update(this.renderable.values.tDepthHalf, this.depthHalfTargetOpaque.texture);
+            ValueCell.update(this.renderable.values.tDepthQuarter, this.depthQuarterTargetOpaque.texture);
+
+            ValueCell.update(this.downsampleDepthRenderableOpaque.values.uTexSize, Vec2.set(this.downsampleDepthRenderableOpaque.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.depthHalfRenderableOpaque.values.uTexSize, Vec2.set(this.depthHalfRenderableOpaque.values.uTexSize.ref.value, hw, hh));
+            ValueCell.update(this.depthQuarterRenderableOpaque.values.uTexSize, Vec2.set(this.depthQuarterRenderableOpaque.values.uTexSize.ref.value, qw, qh));
+
+            this.downsampledDepthTargetTransparent.setSize(sw, sh);
+            this.depthHalfTargetTransparent.setSize(hw, hh);
+            this.depthQuarterTargetTransparent.setSize(qw, qh);
+
+            const transparentDepthTexture = this.getTransparentDepthTexture();
+            ValueCell.update(this.depthHalfRenderableTransparent.values.tColor, transparentDepthTexture);
+            ValueCell.update(this.renderable.values.tDepthTransparent, transparentDepthTexture);
+
+            ValueCell.update(this.renderable.values.tDepthHalfTransparent, this.depthHalfTargetTransparent.texture);
+            ValueCell.update(this.renderable.values.tDepthQuarterTransparent, this.depthQuarterTargetTransparent.texture);
+
+            ValueCell.update(this.downsampleDepthRenderableTransparent.values.uTexSize, Vec2.set(this.downsampleDepthRenderableTransparent.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.depthHalfRenderableTransparent.values.uTexSize, Vec2.set(this.depthHalfRenderableTransparent.values.uTexSize.ref.value, hw, hh));
+            ValueCell.update(this.depthQuarterRenderableTransparent.values.uTexSize, Vec2.set(this.depthQuarterRenderableTransparent.values.uTexSize.ref.value, qw, qh));
+
+            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.blurFirstPassRenderable.values.uTexSize, Vec2.set(this.blurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
+            ValueCell.update(this.blurSecondPassRenderable.values.uTexSize, Vec2.set(this.blurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
+        }
+
+        if (needsUpdateSsao) {
+            this.renderable.update();
+        }
+
+        if (needsUpdateSsaoBlur) {
+            this.blurFirstPassRenderable.update();
+            this.blurSecondPassRenderable.update();
+        }
+
+        if (needsUpdateDepthHalf) {
+            this.depthHalfRenderableOpaque.update();
+            this.depthHalfRenderableTransparent.update();
+        }
+    }
+
+    render(camera: ICamera) {
+        if (isTimingMode) this.webgl.timer.mark('SSAO.render');
+
+        const { state } = this.webgl;
+        const { x, y, width, height } = camera.viewport;
+
+        const includeTransparent = this.renderable.values.dIncludeTransparent.ref.value;
+        const multiScale = this.renderable.values.dMultiScale.ref.value;
+
+        const sx = Math.floor(x * this.ssaoScale);
+        const sy = Math.floor(y * this.ssaoScale);
+        const sw = Math.ceil(width * this.ssaoScale);
+        const sh = Math.ceil(height * this.ssaoScale);
+
+        state.viewport(sx, sy, sw, sh);
+        state.scissor(sx, sy, sw, sh);
+
+        if (this.ssaoScale < 1) {
+            if (isTimingMode) this.webgl.timer.mark('SSAO.downsample');
+            this.downsampledDepthTargetOpaque.bind();
+            this.downsampleDepthRenderableOpaque.render();
+            if (includeTransparent) {
+                this.downsampledDepthTargetTransparent.bind();
+                this.downsampleDepthRenderableTransparent.render();
+            }
+            if (isTimingMode) this.webgl.timer.markEnd('SSAO.downsample');
+        }
+
+        if (isTimingMode) this.webgl.timer.mark('SSAO.half');
+        if (multiScale) {
+            this.depthHalfTargetOpaque.bind();
+            this.depthHalfRenderableOpaque.render();
+        }
+        if (multiScale && includeTransparent) {
+            this.depthHalfTargetTransparent.bind();
+            this.depthHalfRenderableTransparent.render();
+        }
+        if (isTimingMode) this.webgl.timer.markEnd('SSAO.half');
+
+        if (isTimingMode) this.webgl.timer.mark('SSAO.quarter');
+        if (multiScale) {
+            this.depthQuarterTargetOpaque.bind();
+            this.depthQuarterRenderableOpaque.render();
+        }
+        if (multiScale && includeTransparent) {
+            this.depthQuarterTargetTransparent.bind();
+            this.depthQuarterRenderableTransparent.render();
+        }
+        if (isTimingMode) this.webgl.timer.markEnd('SSAO.quarter');
+
+        if (isTimingMode) this.webgl.timer.mark('SSAO.opaque');
+        this.ssaoDepthTexture.attachFramebuffer(this.framebuffer, 'color0');
+        ValueCell.update(this.renderable.values.uTransparencyFlag, 0);
+        this.framebuffer.bind();
+        this.renderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('SSAO.opaque');
+
+        if (isTimingMode) this.webgl.timer.mark('SSAO.blurOpaque');
+        ValueCell.update(this.blurFirstPassRenderable.values.tSsaoDepth, this.ssaoDepthTexture);
+        this.blurFirstPassRenderable.update();
+        this.blurFirstPassFramebuffer.bind();
+        this.blurFirstPassRenderable.render();
+
+        this.ssaoDepthTexture.attachFramebuffer(this.blurSecondPassFramebuffer, 'color0');
+        this.blurSecondPassFramebuffer.bind();
+        this.blurSecondPassRenderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('SSAO.blurOpaque');
+        if (includeTransparent) {
+            if (isTimingMode) this.webgl.timer.mark('SSAO.transparent ');
+            this.ssaoDepthTransparentTexture.attachFramebuffer(this.framebuffer, 'color0');
+            ValueCell.update(this.renderable.values.uTransparencyFlag, 1);
+            this.framebuffer.bind();
+            this.renderable.render();
+            if (isTimingMode) this.webgl.timer.markEnd('SSAO.transparent ');
+
+            if (isTimingMode) this.webgl.timer.mark('SSAO.blurTransparent ');
+            ValueCell.update(this.blurFirstPassRenderable.values.tSsaoDepth, this.ssaoDepthTransparentTexture);
+            this.blurFirstPassRenderable.update();
+            this.blurFirstPassFramebuffer.bind();
+            this.blurFirstPassRenderable.render();
+
+            this.ssaoDepthTransparentTexture.attachFramebuffer(this.blurSecondPassFramebuffer, 'color0');
+            this.blurSecondPassFramebuffer.bind();
+            this.blurSecondPassRenderable.render();
+            if (isTimingMode) this.webgl.timer.markEnd('SSAO.blurTransparent ');
+        }
+        if (isTimingMode) this.webgl.timer.markEnd('SSAO.render');
+    }
+}
+
+const SsaoSchema = {
+    ...QuadSchema,
+    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    tDepthHalf: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    tDepthQuarter: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+
+    dIllumination: DefineSpec('boolean'),
+    uTransparencyFlag: UniformSpec('i'),
+    dIncludeTransparent: DefineSpec('boolean'),
+    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    tDepthHalfTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    tDepthQuarterTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+
+    uSamples: UniformSpec('v3[]'),
+    dNSamples: DefineSpec('number'),
+
+    uProjection: UniformSpec('m4'),
+    uInvProjection: UniformSpec('m4'),
+    uBounds: UniformSpec('v4'),
+
+    uTexSize: UniformSpec('v2'),
+
+    uRadius: UniformSpec('f'),
+    uBias: UniformSpec('f'),
+
+    dMultiScale: DefineSpec('boolean'),
+    dLevels: DefineSpec('number'),
+    uLevelRadius: UniformSpec('f[]'),
+    uLevelBias: UniformSpec('f[]'),
+    uNearThreshold: UniformSpec('f'),
+    uFarThreshold: UniformSpec('f'),
+};
+
+type SsaoRenderable = ComputeRenderable<Values<typeof SsaoSchema>>
+
+function getSsaoRenderable(ctx: WebGLContext, depthTexture: Texture, depthHalfTexture: Texture, depthQuarterTexture: Texture, transparentDepthTexture: Texture, transparentDepthHalfTexture: Texture, transparentDepthQuarterTexture: Texture): SsaoRenderable {
+    const values: Values<typeof SsaoSchema> = {
+        ...QuadValues,
+        tDepth: ValueCell.create(depthTexture),
+        tDepthHalf: ValueCell.create(depthHalfTexture),
+        tDepthQuarter: ValueCell.create(depthQuarterTexture),
+
+        dIllumination: ValueCell.create(false),
+        dIncludeTransparent: ValueCell.create(true),
+        uTransparencyFlag: ValueCell.create(0),
+        tDepthTransparent: ValueCell.create(transparentDepthTexture),
+        tDepthHalfTransparent: ValueCell.create(transparentDepthHalfTexture),
+        tDepthQuarterTransparent: ValueCell.create(transparentDepthQuarterTexture),
+
+        uSamples: ValueCell.create(getSamples(32)),
+        dNSamples: ValueCell.create(32),
+
+        uProjection: ValueCell.create(Mat4.identity()),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+        uBounds: ValueCell.create(Vec4()),
+
+        uTexSize: ValueCell.create(Vec2.create(ctx.gl.drawingBufferWidth, ctx.gl.drawingBufferHeight)),
+
+        uRadius: ValueCell.create(Math.pow(2, 5)),
+        uBias: ValueCell.create(0.8),
+
+        dMultiScale: ValueCell.create(false),
+        dLevels: ValueCell.create(3),
+        uLevelRadius: ValueCell.create([Math.pow(2, 2), Math.pow(2, 5), Math.pow(2, 8)]),
+        uLevelBias: ValueCell.create([0.8, 0.8, 0.8]),
+        uNearThreshold: ValueCell.create(10.0),
+        uFarThreshold: ValueCell.create(1500.0),
+    };
+
+    const schema = { ...SsaoSchema };
+    const shaderCode = ShaderCode('ssao', quad_vert, ssao_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+const SsaoBlurSchema = {
+    ...QuadSchema,
+    tSsaoDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    uKernel: UniformSpec('f[]'),
+    dOcclusionKernelSize: DefineSpec('number'),
+    uBlurDepthBias: UniformSpec('f'),
+
+    uBlurDirectionX: UniformSpec('f'),
+    uBlurDirectionY: UniformSpec('f'),
+
+    uInvProjection: UniformSpec('m4'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+    uBounds: UniformSpec('v4'),
+    dOrthographic: DefineSpec('number'),
+};
+
+type SsaoBlurRenderable = ComputeRenderable<Values<typeof SsaoBlurSchema>>
+
+function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, direction: 'horizontal' | 'vertical'): SsaoBlurRenderable {
+    const values: Values<typeof SsaoBlurSchema> = {
+        ...QuadValues,
+        tSsaoDepth: ValueCell.create(ssaoDepthTexture),
+        uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())),
+
+        uKernel: ValueCell.create(getBlurKernel(15)),
+        dOcclusionKernelSize: ValueCell.create(15),
+        uBlurDepthBias: ValueCell.create(0.5),
+
+        uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0),
+        uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0),
+
+        uInvProjection: ValueCell.create(Mat4.identity()),
+        uNear: ValueCell.create(0.0),
+        uFar: ValueCell.create(10000.0),
+        uBounds: ValueCell.create(Vec4()),
+        dOrthographic: ValueCell.create(0),
+    };
+
+    const schema = { ...SsaoBlurSchema };
+    const shaderCode = ShaderCode('ssao_blur', quad_vert, ssaoBlur_frag);
+    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+function getBlurKernel(kernelSize: number): number[] {
+    const sigma = kernelSize / 3.0;
+    const halfKernelSize = Math.floor((kernelSize + 1) / 2);
+
+    const kernel = [];
+    for (let x = 0; x < halfKernelSize; x++) {
+        kernel.push((1.0 / ((Math.sqrt(2 * Math.PI)) * sigma)) * Math.exp(-x * x / (2 * sigma * sigma)));
+    }
+
+    return kernel;
+}
+
+const RandomHemisphereVector: Vec3[] = [];
+for (let i = 0; i < 256; i++) {
+    const v = Vec3();
+    v[0] = Math.random() * 2.0 - 1.0;
+    v[1] = Math.random() * 2.0 - 1.0;
+    v[2] = Math.random();
+    Vec3.normalize(v, v);
+    Vec3.scale(v, v, Math.random());
+    RandomHemisphereVector.push(v);
+}
+
+function getSamples(nSamples: number): number[] {
+    const samples = [];
+    for (let i = 0; i < nSamples; i++) {
+        let scale = (i * i + 2.0 * i + 1) / (nSamples * nSamples);
+        scale = 0.1 + scale * (1.0 - 0.1);
+
+        samples.push(RandomHemisphereVector[i][0] * scale);
+        samples.push(RandomHemisphereVector[i][1] * scale);
+        samples.push(RandomHemisphereVector[i][2] * scale);
+    }
+
+    return samples;
+}

src/mol-canvas3d/passes/tracing.ts

@@ -0,0 +1,507 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { DefineSpec, TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { ValueCell } from '../../mol-util';
+import { isTimingMode } from '../../mol-util/debug';
+import { Renderer } from '../../mol-gl/renderer';
+import { Camera, ICamera } from '../camera';
+import { Scene } from '../../mol-gl/scene';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { trace_frag } from '../../mol-gl/shader/illumination/trace.frag';
+import { Vec2 } from '../../mol-math/linear-algebra/3d/vec2';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Mat4 } from '../../mol-math/linear-algebra/3d/mat4';
+import { Vec4 } from '../../mol-math/linear-algebra/3d/vec4';
+import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Color } from '../../mol-util/color/color';
+import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
+import { Helper } from '../helper/helper';
+import { accumulate_frag } from '../../mol-gl/shader/illumination/accumulate.frag';
+import { now } from '../../mol-util/now';
+import { clamp } from '../../mol-math/interpolate';
+import { DrawPass } from './draw';
+
+type RenderContext = {
+    renderer: Renderer;
+    camera: Camera;
+    scene: Scene;
+    helper: Helper;
+}
+
+export const TracingParams = {
+    rendersPerFrame: PD.Interval([1, 16], { min: 1, max: 64, step: 1 }, { description: 'Number of rays per pixel each frame. May be adjusted to reach targetFps but will stay within given interval.' }),
+    targetFps: PD.Numeric(30, { min: 0, max: 120, step: 0.1 }, { description: 'Target FPS per frame. If observed FPS is lower or higher, some parameters may get adjusted.' }),
+    steps: PD.Numeric(32, { min: 1, max: 1024, step: 1 }),
+    firstStepSize: PD.Numeric(0.01, { min: 0.001, max: 1, step: 0.001 }),
+    refineSteps: PD.Numeric(4, { min: 0, max: 8, step: 1 }, { description: 'Number of refine steps per ray hit. May be lower to reach targetFps.' }),
+    rayDistance: PD.Numeric(256, { min: 1, max: 8192, step: 1 }, { description: 'Maximum distance a ray can travel (in world units).' }),
+    thicknessMode: PD.Select('auto', PD.arrayToOptions(['auto', 'fixed'] as const)),
+    minThickness: PD.Numeric(0.5, { min: 0.1, max: 16, step: 0.1 }, { hideIf: p => p.thicknessMode === 'fixed' }),
+    thicknessFactor: PD.Numeric(1, { min: 0.1, max: 2, step: 0.05 }, { hideIf: p => p.thicknessMode === 'fixed' }),
+    thickness: PD.Numeric(4, { min: 0.1, max: 512, step: 0.1 }, { hideIf: p => p.thicknessMode === 'auto' }),
+    bounces: PD.Numeric(4, { min: 1, max: 32, step: 1 }, { description: 'Number of bounces for each ray.' }),
+    glow: PD.Boolean(true, { description: 'Bounced rays always get the full light. This produces a slight glowing effect.' }),
+    shadowEnable: PD.Boolean(false),
+    shadowSoftness: PD.Numeric(0.1, { min: 0.01, max: 1.0, step: 0.01 }),
+    shadowThickness: PD.Numeric(0.5, { min: 0.1, max: 32, step: 0.1 }),
+};
+export type TracingProps = PD.Values<typeof TracingParams>
+
+export class TracingPass {
+    private readonly framebuffer: Framebuffer;
+
+    readonly colorTextureOpaque: Texture;
+    readonly normalTextureOpaque: Texture;
+    readonly shadedTextureOpaque: Texture;
+
+    private readonly thicknessTarget: RenderTarget;
+    private readonly holdTarget: RenderTarget;
+    readonly accumulateTarget: RenderTarget;
+    readonly composeTarget: RenderTarget;
+
+    private readonly traceRenderable: TraceRenderable;
+    private readonly accumulateRenderable: AccumulateRenderable;
+
+    constructor(private readonly webgl: WebGLContext, private readonly drawPass: DrawPass) {
+        const { extensions: { drawBuffers, colorBufferHalfFloat, textureHalfFloat }, resources, isWebGL2 } = webgl;
+
+        const { depthTextureOpaque } = drawPass;
+        const width = depthTextureOpaque.getWidth();
+        const height = depthTextureOpaque.getHeight();
+
+        if (isWebGL2) {
+            this.shadedTextureOpaque = resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+            this.shadedTextureOpaque.define(width, height);
+
+            this.normalTextureOpaque = colorBufferHalfFloat && textureHalfFloat
+                ? resources.texture('image-float16', 'rgba', 'fp16', 'nearest')
+                : resources.texture('image-float32', 'rgba', 'float', 'nearest');
+            this.normalTextureOpaque.define(width, height);
+
+            this.colorTextureOpaque = resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+            this.colorTextureOpaque.define(width, height);
+        } else {
+            // webgl1 requires consistent bit plane counts
+
+            this.shadedTextureOpaque = resources.texture('image-float32', 'rgba', 'float', 'nearest');
+            this.shadedTextureOpaque.define(width, height);
+
+            this.normalTextureOpaque = resources.texture('image-float32', 'rgba', 'float', 'nearest');
+            this.normalTextureOpaque.define(width, height);
+
+            this.colorTextureOpaque = resources.texture('image-float32', 'rgba', 'float', 'nearest');
+            this.colorTextureOpaque.define(width, height);
+        }
+
+        this.framebuffer = resources.framebuffer();
+
+        this.framebuffer.bind();
+        drawBuffers!.drawBuffers([
+            drawBuffers!.COLOR_ATTACHMENT0,
+            drawBuffers!.COLOR_ATTACHMENT1,
+            drawBuffers!.COLOR_ATTACHMENT2,
+        ]);
+
+        this.shadedTextureOpaque.attachFramebuffer(this.framebuffer, 'color0');
+        this.normalTextureOpaque.attachFramebuffer(this.framebuffer, 'color1');
+        this.colorTextureOpaque.attachFramebuffer(this.framebuffer, 'color2');
+
+        this.thicknessTarget = webgl.createRenderTarget(width, height, true, 'uint8', 'nearest');
+        this.holdTarget = webgl.createRenderTarget(width, height, false, 'float32');
+        this.accumulateTarget = webgl.createRenderTarget(width, height, false, 'float32');
+        this.composeTarget = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
+
+        this.traceRenderable = getTraceRenderable(webgl, this.colorTextureOpaque, this.normalTextureOpaque, this.shadedTextureOpaque, this.thicknessTarget.texture, this.accumulateTarget.texture, this.drawPass.depthTextureOpaque);
+        this.accumulateRenderable = getAccumulateRenderable(webgl, this.holdTarget.texture);
+    }
+
+    private renderInput(renderer: Renderer, camera: ICamera, scene: Scene, props: TracingProps) {
+        if (isTimingMode) this.webgl.timer.mark('TracePass.renderInput');
+        const { gl, state } = this.webgl;
+
+        this.framebuffer.bind();
+        this.drawPass.depthTextureOpaque.attachFramebuffer(this.framebuffer, 'depth');
+        renderer.clear(true);
+        renderer.renderTracing(scene.primitives, camera);
+
+        //
+
+        if (props.thicknessMode === 'auto') {
+            this.thicknessTarget.bind();
+            state.clearColor(0, 0, 0, 0);
+            gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT);
+            renderer.renderDepthOpaqueBack(scene.primitives, camera);
+        }
+        if (isTimingMode) this.webgl.timer.markEnd('TracePass.renderInput');
+    }
+
+    setSize(width: number, height: number) {
+        const w = this.composeTarget.getWidth();
+        const h = this.composeTarget.getHeight();
+
+        if (width !== w || height !== h) {
+            this.thicknessTarget.setSize(width, height);
+            this.holdTarget.setSize(width, height);
+            this.accumulateTarget.setSize(width, height);
+            this.composeTarget.setSize(width, height);
+
+            this.colorTextureOpaque.define(width, height);
+            this.normalTextureOpaque.define(width, height);
+            this.shadedTextureOpaque.define(width, height);
+
+            ValueCell.update(this.traceRenderable.values.uTexSize, Vec2.set(this.traceRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.accumulateRenderable.values.uTexSize, Vec2.set(this.accumulateRenderable.values.uTexSize.ref.value, width, height));
+        }
+    }
+
+    private clearAdjustedProps = true;
+
+    reset(clearAdjustedProps = false) {
+        const { gl, state } = this.webgl;
+
+        this.accumulateTarget.bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        this.composeTarget.bind();
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+
+        if (clearAdjustedProps) {
+            this.prevTime = 0;
+            this.currTime = 0;
+            this.clearAdjustedProps = true;
+        }
+    }
+
+    private prevTime = 0;
+    private currTime = 0;
+    private rendersPerFrame = 1;
+    private refineSteps = 1;
+    private steps = 16;
+
+    private increaseAdjustedProps(props: TracingProps) {
+        this.steps += 1;
+        if (this.steps > props.steps) {
+            this.refineSteps += 1;
+        }
+        if (this.refineSteps > props.refineSteps) {
+            this.rendersPerFrame += 1;
+        }
+    }
+
+    private decreaseAdjustedProps(props: TracingProps) {
+        const minRefineSteps = Math.min(1, props.refineSteps);
+        this.rendersPerFrame -= 1;
+        if (this.rendersPerFrame < 1) {
+            this.refineSteps -= 1;
+        }
+        if (this.refineSteps < minRefineSteps) {
+            this.steps -= 1;
+        }
+    }
+
+    private getAdjustedProps(props: TracingProps, iteration: number) {
+        this.currTime = now();
+        const minRefineSteps = Math.min(1, props.refineSteps);
+        const minSteps = Math.round(props.steps / 2);
+
+        if (this.clearAdjustedProps) {
+            this.rendersPerFrame = props.rendersPerFrame[0];
+            this.refineSteps = minRefineSteps;
+            this.steps = minSteps;
+            this.clearAdjustedProps = false;
+        }
+
+        if (iteration > 0) {
+            const targetTimeMs = 1000 / props.targetFps;
+            const deltaTime = this.currTime - this.prevTime;
+            let f = Math.round(deltaTime / targetTimeMs);
+            if (f >= 2) {
+                while (f > 0) {
+                    this.decreaseAdjustedProps(props);
+                    f -= 1;
+                }
+            } else if (deltaTime < targetTimeMs) {
+                this.increaseAdjustedProps(props);
+            } else if (deltaTime > targetTimeMs + 0.5) {
+                this.decreaseAdjustedProps(props);
+            }
+        }
+
+        this.prevTime = this.currTime;
+        this.rendersPerFrame = clamp(this.rendersPerFrame, props.rendersPerFrame[0], props.rendersPerFrame[1]);
+        this.refineSteps = clamp(this.refineSteps, minRefineSteps, props.refineSteps);
+        this.steps = clamp(this.steps, minSteps, props.steps);
+
+        return {
+            rendersPerFrame: iteration === 0 ? Math.ceil(this.rendersPerFrame / 2) : this.rendersPerFrame,
+            refineSteps: iteration === 0 ? minRefineSteps : this.refineSteps,
+            steps: iteration === 0 ? minSteps : this.steps,
+        };
+    }
+
+    render(ctx: RenderContext, transparentBackground: boolean, props: TracingProps, iteration: number, forceRenderInput: boolean) {
+        const { rendersPerFrame, refineSteps, steps } = this.getAdjustedProps(props, iteration);
+
+        if (isTimingMode) {
+            this.webgl.timer.mark('TracePass.render', {
+                note: `${rendersPerFrame} rendersPerFrame, ${refineSteps} refineSteps, ${steps} steps`
+            });
+        }
+
+        const { renderer, camera, scene } = ctx;
+        const { gl, state } = this.webgl;
+        const { x, y, width, height } = camera.viewport;
+
+        if (iteration === 0 || forceRenderInput) {
+            // render color & depth
+            renderer.setTransparentBackground(transparentBackground);
+            renderer.setDrawingBufferSize(this.composeTarget.getWidth(), this.composeTarget.getHeight());
+            renderer.setPixelRatio(this.webgl.pixelRatio);
+            renderer.setViewport(x, y, width, height);
+            renderer.update(camera, scene);
+            this.renderInput(renderer, camera, scene, props);
+        }
+
+        state.disable(gl.BLEND);
+        state.disable(gl.DEPTH_TEST);
+        state.disable(gl.CULL_FACE);
+        state.depthMask(false);
+        state.viewport(x, y, width, height);
+        state.scissor(x, y, width, height);
+
+        const invProjection = Mat4.identity();
+        Mat4.invert(invProjection, camera.projection);
+        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
+        const [w, h] = this.traceRenderable.values.uTexSize.ref.value;
+        const v = camera.viewport;
+
+        const ambientColor = Vec3();
+        Vec3.scale(ambientColor, Color.toArrayNormalized(renderer.props.ambientColor, ambientColor, 0), renderer.props.ambientIntensity);
+        const lightStrength = Vec3.clone(ambientColor);
+        for (let i = 0, il = renderer.light.count; i < il; ++i) {
+            const light = Vec3.fromArray(Vec3(), renderer.light.color, i * 3);
+            Vec3.add(lightStrength, lightStrength, light);
+        }
+
+        // trace
+        this.holdTarget.bind();
+        let needsUpdateTrace = false;
+        ValueCell.update(this.traceRenderable.values.uFrameNo, iteration);
+        if (this.traceRenderable.values.dRendersPerFrame.ref.value !== rendersPerFrame) {
+            ValueCell.update(this.traceRenderable.values.dRendersPerFrame, rendersPerFrame);
+            needsUpdateTrace = true;
+        }
+        ValueCell.update(this.traceRenderable.values.uProjection, camera.projection);
+        ValueCell.update(this.traceRenderable.values.uInvProjection, invProjection);
+        Vec4.set(this.traceRenderable.values.uBounds.ref.value,
+            v.x / w,
+            v.y / h,
+            (v.x + v.width) / w,
+            (v.y + v.height) / h
+        );
+        ValueCell.update(this.traceRenderable.values.uBounds, this.traceRenderable.values.uBounds.ref.value);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uNear, camera.near);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uFar, camera.far);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uFogFar, camera.fogFar);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uFogNear, camera.fogNear);
+        ValueCell.update(this.traceRenderable.values.uFogColor, Color.toVec3Normalized(this.traceRenderable.values.uFogColor.ref.value, renderer.props.backgroundColor));
+        if (this.traceRenderable.values.dOrthographic.ref.value !== orthographic) {
+            ValueCell.update(this.traceRenderable.values.dOrthographic, orthographic);
+            needsUpdateTrace = true;
+        }
+        ValueCell.update(this.traceRenderable.values.uLightDirection, renderer.light.direction);
+        ValueCell.update(this.traceRenderable.values.uLightColor, renderer.light.color);
+        if (this.traceRenderable.values.dLightCount.ref.value !== renderer.light.count) {
+            ValueCell.update(this.traceRenderable.values.dLightCount, renderer.light.count);
+            needsUpdateTrace = true;
+        }
+        ValueCell.update(this.traceRenderable.values.uAmbientColor, ambientColor);
+        ValueCell.update(this.traceRenderable.values.uLightStrength, lightStrength);
+        if (this.traceRenderable.values.dGlow.ref.value !== props.glow) {
+            ValueCell.update(this.traceRenderable.values.dGlow, props.glow);
+            needsUpdateTrace = true;
+        }
+        if (this.traceRenderable.values.dBounces.ref.value !== props.bounces) {
+            ValueCell.update(this.traceRenderable.values.dBounces, props.bounces);
+            needsUpdateTrace = true;
+        }
+        if (this.traceRenderable.values.dSteps.ref.value !== steps) {
+            ValueCell.update(this.traceRenderable.values.dSteps, steps);
+            needsUpdateTrace = true;
+        }
+        if (this.traceRenderable.values.dFirstStepSize.ref.value !== props.firstStepSize) {
+            ValueCell.update(this.traceRenderable.values.dFirstStepSize, props.firstStepSize);
+            needsUpdateTrace = true;
+        }
+        if (this.traceRenderable.values.dRefineSteps.ref.value !== refineSteps) {
+            ValueCell.update(this.traceRenderable.values.dRefineSteps, refineSteps);
+            needsUpdateTrace = true;
+        }
+        ValueCell.updateIfChanged(this.traceRenderable.values.uRayDistance, props.rayDistance);
+        if (this.traceRenderable.values.dThicknessMode.ref.value !== props.thicknessMode) {
+            ValueCell.update(this.traceRenderable.values.dThicknessMode, props.thicknessMode);
+            needsUpdateTrace = true;
+        }
+        ValueCell.updateIfChanged(this.traceRenderable.values.uMinThickness, props.minThickness);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uThicknessFactor, props.thicknessFactor);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uThickness, props.thickness);
+        if (this.traceRenderable.values.dShadowEnable.ref.value !== props.shadowEnable) {
+            ValueCell.update(this.traceRenderable.values.dShadowEnable, props.shadowEnable);
+            needsUpdateTrace = true;
+        }
+        ValueCell.updateIfChanged(this.traceRenderable.values.uShadowSoftness, props.shadowSoftness);
+        ValueCell.updateIfChanged(this.traceRenderable.values.uShadowThickness, props.shadowThickness);
+        if (needsUpdateTrace) this.traceRenderable.update();
+        if (isTimingMode) this.webgl.timer.mark('TracePass.renderTrace');
+        this.traceRenderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('TracePass.renderTrace');
+
+        // accumulate
+        this.accumulateTarget.bind();
+        this.accumulateRenderable.render();
+        if (isTimingMode) this.webgl.timer.markEnd('TracePass.render');
+    }
+}
+
+//
+
+const TraceSchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tNormal: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tShaded: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tThickness: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tAccumulate: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+
+    dOrthographic: DefineSpec('number'),
+    uNear: UniformSpec('f'),
+    uFar: UniformSpec('f'),
+    uFogNear: UniformSpec('f'),
+    uFogFar: UniformSpec('f'),
+    uFogColor: UniformSpec('v3'),
+
+    uProjection: UniformSpec('m4'),
+    uInvProjection: UniformSpec('m4'),
+    uBounds: UniformSpec('v4'),
+
+    uLightDirection: UniformSpec('v3[]'),
+    uLightColor: UniformSpec('v3[]'),
+    dLightCount: DefineSpec('number'),
+    uAmbientColor: UniformSpec('v3'),
+    uLightStrength: UniformSpec('v3'),
+
+    uFrameNo: UniformSpec('i'),
+    dRendersPerFrame: DefineSpec('number'),
+
+    dGlow: DefineSpec('boolean'),
+    dBounces: DefineSpec('number'),
+    dSteps: DefineSpec('number'),
+    dFirstStepSize: DefineSpec('number'),
+    dRefineSteps: DefineSpec('number'),
+    uRayDistance: UniformSpec('f'),
+
+    dThicknessMode: DefineSpec('string'),
+    uMinThickness: UniformSpec('f'),
+    uThicknessFactor: UniformSpec('f'),
+    uThickness: UniformSpec('f'),
+
+    dShadowEnable: DefineSpec('boolean'),
+    uShadowSoftness: UniformSpec('f'),
+    uShadowThickness: UniformSpec('f'),
+};
+const TraceShaderCode = ShaderCode('trace', quad_vert, trace_frag);
+type TraceRenderable = ComputeRenderable<Values<typeof TraceSchema>>
+
+function getTraceRenderable(ctx: WebGLContext, colorTexture: Texture, normalTexture: Texture, shadedTexture: Texture, thicknessTexture: Texture, accumulateTexture: Texture, depthTexture: Texture): TraceRenderable {
+    const values: Values<typeof TraceSchema> = {
+        ...QuadValues,
+        tColor: ValueCell.create(colorTexture),
+        tNormal: ValueCell.create(normalTexture),
+        tShaded: ValueCell.create(shadedTexture),
+        tThickness: ValueCell.create(thicknessTexture),
+        tAccumulate: ValueCell.create(accumulateTexture),
+        tDepth: ValueCell.create(depthTexture),
+        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+
+        dOrthographic: ValueCell.create(0),
+        uNear: ValueCell.create(1),
+        uFar: ValueCell.create(10000),
+        uFogNear: ValueCell.create(10000),
+        uFogFar: ValueCell.create(10000),
+        uFogColor: ValueCell.create(Vec3.create(1, 1, 1)),
+
+        uProjection: ValueCell.create(Mat4.identity()),
+        uInvProjection: ValueCell.create(Mat4.identity()),
+        uBounds: ValueCell.create(Vec4()),
+
+        uLightDirection: ValueCell.create([]),
+        uLightColor: ValueCell.create([]),
+        dLightCount: ValueCell.create(0),
+        uAmbientColor: ValueCell.create(Vec3()),
+        uLightStrength: ValueCell.create(Vec3.create(1, 1, 1)),
+
+        uFrameNo: ValueCell.create(0),
+        dRendersPerFrame: ValueCell.create(1),
+
+        dGlow: ValueCell.create(true),
+        dBounces: ValueCell.create(4),
+        dSteps: ValueCell.create(32),
+        dFirstStepSize: ValueCell.create(0.01),
+        dRefineSteps: ValueCell.create(4),
+        uRayDistance: ValueCell.create(256),
+
+        dThicknessMode: ValueCell.create('auto'),
+        uMinThickness: ValueCell.create(0.5),
+        uThicknessFactor: ValueCell.create(1),
+        uThickness: ValueCell.create(4),
+
+        dShadowEnable: ValueCell.create(false),
+        uShadowSoftness: ValueCell.create(0.1),
+        uShadowThickness: ValueCell.create(0.1),
+    };
+
+    const schema = { ...TraceSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', TraceShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+//
+
+const AccumulateSchema = {
+    ...QuadSchema,
+    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
+    uTexSize: UniformSpec('v2'),
+    uWeight: UniformSpec('f'),
+};
+const AccumulateShaderCode = ShaderCode('accumulate', quad_vert, accumulate_frag);
+type AccumulateRenderable = ComputeRenderable<Values<typeof AccumulateSchema>>
+
+function getAccumulateRenderable(ctx: WebGLContext, colorTexture: Texture): AccumulateRenderable {
+    const values: Values<typeof AccumulateSchema> = {
+        ...QuadValues,
+        tColor: ValueCell.create(colorTexture),
+        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),
+        uWeight: ValueCell.create(1.0),
+    };
+
+    const schema = { ...AccumulateSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', AccumulateShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}

src/mol-data/int/_spec/sorted-array.spec.ts

@@ -51,6 +51,12 @@ describe('sortedArray', () => {
     test('predIndex4', SortedArray.findPredecessorIndex(a2468, 3), 1);
     test('predIndexInt', SortedArray.findPredecessorIndexInInterval(a1234, 0, Interval.ofRange(2, 3)), 2);
 
+    const aDuplSmall = SortedArray.ofSortedArray([1, ...new Array(2).fill(3), 3]);
+    test('predIndexDuplSmall', SortedArray.findPredecessorIndex(aDuplSmall, 2), 1);
+
+    const aDuplBig = SortedArray.ofSortedArray([1, ...new Array(333).fill(2), ...new Array(666).fill(3), 4]);
+    test('predIndexDuplBig', SortedArray.findPredecessorIndex(aDuplBig, 3), 334);
+
     testI('findRange', SortedArray.findRange(a2468, 2, 4), Interval.ofRange(0, 1));
 
     it('deduplicate', () => {

src/mol-data/int/impl/sorted-array.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { sortArray, hash3, hash4, createRangeArray } from '../../util';
@@ -71,25 +72,20 @@ export function areEqual(a: Nums, b: Nums) {
 }
 
 /**
- * Returns 0 if `v` is smaller or equal the first element of `xs`
- * Returns length of `xs` if `v` is bigger than the last element of `xs`
- * Otherwise returns the first index where the value of `xs` is equal or bigger than `v`
+ * Returns 0 if `query` is smaller or equal the first element of `xs`.
+ * Returns length of `xs` if `query` is bigger than the last element of `xs`.
+ * Otherwise returns the first index where the value of `xs` is equal or bigger than `query`.
  */
-export function findPredecessorIndex(xs: Nums, v: number) {
-    const len = xs.length;
-    if (v <= xs[0]) return 0;
-    if (v > xs[len - 1]) return len;
-    return binarySearchPredIndexRange(xs, v, 0, len);
+export function findPredecessorIndex(xs: Nums, query: number) {
+    return binarySearchPredIndexRange(xs, query, 0, xs.length);
 }
 
-export function findPredecessorIndexInInterval(xs: Nums, v: number, bounds: Interval) {
-    const s = Interval.start(bounds), e = Interval.end(bounds);
-    const sv = xs[s];
-    if (v <= sv) return s;
-    if (e > s && v > xs[e - 1]) return e;
-    // do a linear search if there are only 10 or less items remaining
-    if (v - sv <= 11) return linearSearchPredInRange(xs, v, s + 1, e);
-    return binarySearchPredIndexRange(xs, v, s, e);
+/**
+ * Return index of the first element of `xs` within range `bounds` which is greater than or equal to `query`.
+ * Return end of `bounds` (exclusive) if all elements in the range are less than `query`.
+*/
+export function findPredecessorIndexInInterval(xs: Nums, query: number, bounds: Interval) {
+    return binarySearchPredIndexRange(xs, query, Interval.start(bounds), Interval.end(bounds));
 }
 
 export function findRange(xs: Nums, min: number, max: number) {
@@ -116,31 +112,29 @@ function binarySearchRange(xs: Nums, value: number, start: number, end: number)
     return -1;
 }
 
-function binarySearchPredIndexRange(xs: Nums, value: number, start: number, end: number) {
-    let min = start, max = end - 1;
-    while (min < max) {
-        // do a linear search if there are only 10 or less items remaining
-        if (min + 11 > max) {
-            for (let i = min; i <= max; i++) {
-                if (value <= xs[i]) return i;
-            }
-            return max + 1;
-        }
+/** Return index of the first element within range [start, end) which is greater than or equal to `query`.
+* Return `end` if all elements in the range are less than `query`. */
+function binarySearchPredIndexRange(xs: Nums, query: number, start: number, end: number): number {
+    if (start === end) return start;
+    if (xs[start] >= query) return start;
+    if (xs[end - 1] < query) return end;
+    // Invariants: xs[i] < query for each i < min, xs[i] >= query for each i >= max
+    let min = start, max = end;
+    while (max - min > 4) {
         const mid = (min + max) >> 1;
-        const v = xs[mid];
-        if (value < v) max = mid - 1;
-        else if (value > v) min = mid + 1;
-        else return mid;
+        if (xs[mid] >= query) {
+            max = mid;
+        } else {
+            min = mid + 1;
+        }
     }
-    if (min > max) return max + 1;
-    return xs[min] >= value ? min : min + 1;
-}
-
-function linearSearchPredInRange(xs: Nums, value: number, start: number, end: number) {
-    for (let i = start; i < end; i++) {
-        if (value <= xs[i]) return i;
+    // Linear search remaining elements:
+    for (let i = min; i < max; i++) {
+        if (xs[i] >= query) {
+            return i;
+        }
     }
-    return end;
+    return max;
 }
 
 export function areIntersecting(a: Nums, b: Nums) {