5.0.0-dev.3

* add query command to markdown extensions

* fix typo

* better postprocessing param support in MVS

* molstar_mesh/label/line_params

CHANGELOG.md

@@ -19,8 +19,9 @@ Note that since we don't clearly distinguish between a public and private interf
 - MolViewSpec extension:
   - Generic color schemes (`palette` parameter for color_from_* nodes)
   - Annotation field remapping (`field_remapping` parameter for color_from_* nodes)
-  - Representation node: support custom property `molstar_reprepresentation_params`,
-  - Canvas node: support custom properties `molstar_enable_outline`, `molstar_enable_shadow`, `molstar_enable_ssao`
+  - Representation node: support custom property `molstar_reprepresentation_params`
+  - Primitives node: support custom property `molstar_mesh/label/line_params`
+  - Canvas node: support custom properties `molstar_enable_outline/shadow/ssao`, `molstar_outline/shadow/ssao_params`
   - `clip` node support for structure and volume representations
   - `grid_slice` representation support for volumes
   - Support tethers and background for primitive labels

docs/docs/plugin/managers/markdown-extensions.md

@@ -14,12 +14,20 @@ The main use case of this is enriching [MolViewSpec](`https://molstar.org/mol-vi
 
 Extends Markdown Hyperlink syntax to support expressions of the form `[title](!c1=v1&c2=v2&...)` into an executable command. The command can be executed either on click, mouse enter, or mouse leave.
 
+Generally, the command should be URL encoded, e.g., `a b` => `a%20b` (in JS, `encodeURIComponent`, in Python `urllib.parse.quote_plus/urlencode`).
+
 ### Built-in Commands
 
 - `center-camera` - Centers the camera
 - `apply-snapshot=key` - Loads snapshots with the provided key
 - `focus-refs=ref1,ref2,...` - On click, focuses nodes with the provided refs
 - `highlight-refs=ref1,ref2,...` - On mouse over, highlights the provided refs
+- `query=...&lang=...&action=highlight,focus&focus-radius=...`
+  - `query` is an expression (e.g., `resn HEM` when using PyMol syntax)
+  - (optional) `lang` is one of `mol-script` (default), `pymol`, `vmd`, `jmol`
+  - (optional) `action` is an array of `highlight` (default), `focus` (multiple actions can be specified)
+  - (optional) `focus-radius` is extra distance applied when focusing the selection (default is `3`)
+  - Example: `[HEM](!query%3Dresn%20HEM%26lang%3Dpymol%26action%3Dhighlight%2Cfocus)` highlights or focuses the HEM residue (the command must be URL encoded because it contains spaces and possibly other special characters)
 
 ## Custom Content
 
@@ -28,7 +36,7 @@ Extends Markdown Image syntax to support expressions of the form `![alt](!c1=v1&
 ### Built-in Custom Content
 - `color-swatch=color` - Renders a box with the provided color
 -  Color palettes:
-  - `color-palette-name=name` - Renders a gradient with the provivided named color palette (see `mol-util/color/lists.ts` for supported color schemes)
+  - `color-palette-name=name` - Renders a gradient with the provided named color palette (see `mol-util/color/lists.ts` for supported color schemes)
   - `color-palette-colors=color1,color2` - Renders a gradient with the provided colors
   - `color-palette-width=CCS-value` - Specifies the width of the element, defaults to `150px`
   - `color-palette-height=CCS-value` - Specified the height of the element, defaults to `0.5em`

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.2",
+  "version": "5.0.0-dev.3",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "5.0.0-dev.2",
+      "version": "5.0.0-dev.3",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.17",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.2",
+  "version": "5.0.0-dev.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/extensions/mvs/camera.ts

@@ -130,21 +130,26 @@ export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: Mol
     const backgroundColor = decodeColor(params?.background_color) ?? DefaultCanvasBackgroundColor;
 
     const outline = !!canvasNode?.custom?.molstar_enable_outline;
+    const outlineParams = canvasNode?.custom?.molstar_outline_params;
+
     const shadow = !!canvasNode?.custom?.molstar_enable_shadow;
+    const shadowParams = canvasNode?.custom?.molstar_shadow_params;
+
     const occlusion = !!canvasNode?.custom?.molstar_enable_ssao;
+    const ssaoParams = canvasNode?.custom?.molstar_ssao_params;
 
     return {
         ...oldCanvasProps,
         postprocessing: {
             ...oldCanvasProps.postprocessing,
             outline: outline
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(OutlineParams) }
+                ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(OutlineParams), ...outlineParams } }
                 : oldCanvasProps.postprocessing.outline,
             shadow: shadow
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(ShadowParams) }
+                ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(ShadowParams), ...shadowParams } }
                 : oldCanvasProps.postprocessing.shadow,
             occlusion: occlusion
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(SsaoParams) }
+                ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(SsaoParams), ...ssaoParams } }
                 : oldCanvasProps.postprocessing.occlusion,
         },
         renderer: {

src/extensions/mvs/components/primitives.ts

@@ -140,11 +140,13 @@ export const MVSBuildPrimitiveShape = MVSTransform({
         if (params.kind === 'mesh') {
             if (!hasPrimitiveKind(a.data, 'mesh')) return StateObject.Null;
 
+            const customMeshParams = a.data.node.custom?.molstar_mesh_params;
             return new SO.Shape.Provider({
                 label,
                 data: context,
                 params: {
                     ...PD.withDefaults(Mesh.Params, { alpha: a.data.options?.opacity ?? 1 }),
+                    ...customMeshParams,
                     ...snapshotKey,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveMesh(data, prev?.geometry),
@@ -155,6 +157,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
 
             const options = a.data.options;
             const bgColor = options?.label_background_color;
+            const customLabelParams = a.data.node.custom?.molstar_label_params;
             return new SO.Shape.Provider({
                 label,
                 data: context,
@@ -167,6 +170,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
                         background: isDefined(bgColor),
                         backgroundColor: isDefined(bgColor) ? decodeColor(bgColor) : undefined,
                     }),
+                    ...customLabelParams,
                     ...snapshotKey,
                 },
                 getShape: (_, data, props, prev: any) => buildPrimitiveLabels(data, prev?.geometry, props),
@@ -175,11 +179,13 @@ export const MVSBuildPrimitiveShape = MVSTransform({
         } else if (params.kind === 'lines') {
             if (!hasPrimitiveKind(a.data, 'line')) return StateObject.Null;
 
+            const customLineParams = a.data.node.custom?.molstar_line_params;
             return new SO.Shape.Provider({
                 label,
                 data: context,
                 params: {
                     ...PD.withDefaults(Lines.Params, { alpha: a.data.options?.opacity ?? 1 }),
+                    ...customLineParams,
                     ...snapshotKey,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveLines(data, prev?.geometry),

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

@@ -6,10 +6,8 @@
  */
 
 import * as iots from 'io-ts';
-import { PathReporter } from "io-ts/lib/PathReporter.js";
 import { onelinerJsonString } from '../../../../mol-util/json';
 
-
 /** All types that can be used in tree node params.
  * Can be extended, this is just to list them all in one place and possibly catch some typing errors */
 type AllowedValueTypes = string | number | boolean | null | [number, number, number] | string[] | number[] | {};
@@ -142,6 +140,41 @@ export function fieldValidationIssues<F extends Field>(field: F, value: any): st
     if (validation._tag === 'Right') {
         return undefined;
     } else {
-        return PathReporter.report(validation);
+        return reportErrors(validation.left);
     }
 }
+
+// Inlining `reportErrors` instead of `import { PathReporter } from 'io-ts/PathReporter'`;
+// because it breaks Deno usage.
+
+function reportErrors(errors: iots.Errors): string[] | undefined {
+    if (errors.length === 0) return undefined;
+    return errors.map(getMessage);
+}
+
+function getMessage(e: iots.ValidationError) {
+    return e.message !== undefined
+        ? e.message
+        : `Invalid value ${stringifyError(e.value)} supplied to ${getContextPath(e.context)}`;
+}
+
+function getContextPath(context: iots.ValidationError['context']) {
+    return context.map(a => `${a.key}: ${a.type.name}`).join('/');
+}
+
+function getFunctionName(f: Function & { displayName?: string }) {
+    return f.displayName || f.name || `<function ${f.length}>`;
+}
+
+function stringifyError(v: any) {
+    if (typeof v === 'function') {
+        return getFunctionName(v);
+    }
+    if (typeof v === 'number' && !isFinite(v)) {
+        if (isNaN(v)) {
+            return 'NaN';
+        }
+        return v > 0 ? 'Infinity' : '-Infinity';
+    }
+    return JSON.stringify(v);
+}

src/mol-plugin-state/manager/markdown-extensions.ts

@@ -8,6 +8,8 @@ import { getCellBoundingSphere } from '../../mol-plugin-state/manager/focus-came
 import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { StateObjectCell } from '../../mol-state';
 import { PluginContext } from '../../mol-plugin/context';
+import { Script } from '../../mol-script/script';
+import { QueryContext, QueryFn, StructureElement, StructureSelection } from '../../mol-model/structure';
 
 export type MarkdownExtensionEvent = 'click' | 'mouse-enter' | 'mouse-leave';
 
@@ -82,6 +84,72 @@ export const BuiltInMarkdownExtension: MarkdownExtension[] = [
             }
         }
     },
+    {
+        name: 'query',
+        execute: ({ event, args, manager }) => {
+            const expression = args['query'];
+            if (!expression?.length) return;
+
+            // supported languages: mol-script, pymol, vmd, jmol
+            const language = args['lang'] || 'mol-script';
+            // supported actions: highlight, focus
+            const action = parseArray(args['action'] || 'highlight');
+            const focusRadius = parseFloat(args['focus-radius'] || '3');
+
+            if (event === 'mouse-leave') {
+                if (action.includes('highlight')) {
+                    manager.plugin.managers.interactivity.lociHighlights.clearHighlights();
+                }
+                return;
+            }
+
+            let query: QueryFn<StructureSelection>;
+            try {
+                query = Script.toQuery({
+                    language: language as Script.Language,
+                    expression
+                });
+            } catch (e) {
+                console.warn(`Failed to parse query '${expression}' (${language})`, e);
+                return;
+            }
+
+            const structures = manager.plugin.state.data.selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Structure));
+
+            if (event === 'mouse-enter') {
+                if (!action.includes('focus')) {
+                    return;
+                }
+                manager.plugin.managers.interactivity.lociHighlights.clearHighlights();
+                for (const structure of structures) {
+                    if (!structure.obj?.data) continue;
+                    const selection = query(new QueryContext(structure.obj.data));
+                    const loci = StructureSelection.toLociWithSourceUnits(selection);
+                    manager.plugin.managers.interactivity.lociHighlights.highlight({
+                        loci,
+                    }, false);
+                }
+            }
+
+            if (event === 'click') {
+                if (!action.includes('focus')) {
+                    return;
+                }
+                const spheres = structures.map(s => {
+                    if (!s.obj?.data) return undefined;
+                    const selection = query(new QueryContext(s.obj.data));
+                    if (StructureSelection.isEmpty(selection)) return;
+
+                    const loci = StructureSelection.toLociWithSourceUnits(selection);
+                    return StructureElement.Loci.getBoundary(loci).sphere;
+                }).filter(s => !!s);
+
+                if (spheres.length) {
+                    manager.plugin.managers.camera.focusSpheres(spheres, s => s, { extraRadius: focusRadius });
+                }
+            }
+        },
+    },
 ];
 
 export class MarkdownExtensionManager {