5.0.0-dev.4

* 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 property `molstar_postprocessing` with the ability to customize outline, depth of field, bloom, shadow, occlusion (SSAO), and fog
   - `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.4",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "5.0.0-dev.2",
+      "version": "5.0.0-dev.4",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.17",
@@ -1171,9 +1171,9 @@
       }
     },
     "node_modules/@eslint/plugin-kit": {
-      "version": "0.3.3",
-      "resolved": "https://registry.npmjs.org/@eslint/plugin-kit/-/plugin-kit-0.3.3.tgz",
-      "integrity": "sha512-1+WqvgNMhmlAambTvT3KPtCl/Ibr68VldY2XY40SL1CE0ZXiakFR/cbTspaF5HsnpDMvcYYoJHfl4980NBjGag==",
+      "version": "0.3.4",
+      "resolved": "https://registry.npmjs.org/@eslint/plugin-kit/-/plugin-kit-0.3.4.tgz",
+      "integrity": "sha512-Ul5l+lHEcw3L5+k8POx6r74mxEYKG5kOb6Xpy2gCRW6zweT6TEhAf8vhxGgjhqrd/VO/Dirhsb+1hNpD1ue9hw==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -2763,7 +2763,7 @@
       "version": "5.0.1",
       "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz",
       "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=8"
       }
@@ -3021,7 +3021,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz",
       "integrity": "sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/basic-auth": {
       "version": "2.0.1",
@@ -3081,7 +3081,7 @@
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
       "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0"
@@ -3494,7 +3494,7 @@
       "version": "0.0.1",
       "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz",
       "integrity": "sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/concurrently": {
       "version": "9.1.2",
@@ -4127,7 +4127,7 @@
       "version": "8.0.0",
       "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
       "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/encodeurl": {
       "version": "2.0.0",
@@ -5012,7 +5012,7 @@
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz",
       "integrity": "sha512-OO0pH2lK6a0hZnAdau5ItzHPI6pUlvI7jMVnxUQRtw4owF2wk8lOSabtGDCTP4Ggrg2MbGnWO9X8K1t4+fGMDw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/fsevents": {
       "version": "2.3.3",
@@ -5170,7 +5170,7 @@
       "version": "7.2.3",
       "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz",
       "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "fs.realpath": "^1.0.0",
         "inflight": "^1.0.4",
@@ -5203,7 +5203,7 @@
       "version": "1.1.12",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.12.tgz",
       "integrity": "sha512-9T9UjW3r0UW5c1Q7GTwllptXwhvYmEzFhzMfZ9H7FQWt+uZePjZPjBP/W1ZEyZ1twGWom5/56TF4lPcqjnDHcg==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0",
@@ -5214,7 +5214,7 @@
       "version": "3.1.2",
       "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz",
       "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "brace-expansion": "^1.1.7"
       },
@@ -5297,7 +5297,7 @@
       "version": "4.2.11",
       "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.11.tgz",
       "integrity": "sha512-RbJ5/jmFcNNCcDV5o9eTnBLJ/HszWV0P73bc+Ff4nS/rJj+YaS6IGyiOL0VoBYX+l1Wrl3k63h/KrH+nhJ0XvQ==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/graphemer": {
       "version": "1.4.0",
@@ -5621,7 +5621,7 @@
       "version": "0.1.4",
       "resolved": "https://registry.npmjs.org/imurmurhash/-/imurmurhash-0.1.4.tgz",
       "integrity": "sha512-JmXMZ6wuvDmLiHEml9ykzqO6lwFbof0GG4IkcGaENdCRDDmMVnny7s5HsIgHCbaq0w2MyPhDqkhTUgS2LU2PHA==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=0.8.19"
       }
@@ -5630,7 +5630,7 @@
       "version": "1.0.6",
       "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz",
       "integrity": "sha512-k92I/b08q4wvFscXCLvqfsHCrjrF7yiXsQuIVvVE7N82W3+aqpzuUdBbfhWcy/FZR3/4IgflMgKLOsvPDrGCJA==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "once": "^1.3.0",
         "wrappy": "1"
@@ -5838,7 +5838,7 @@
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz",
       "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=8"
       }
@@ -6080,7 +6080,7 @@
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/isexe/-/isexe-2.0.0.tgz",
       "integrity": "sha512-RHxMLp9lnKHGHRng9QFhRCMbYAcVpn69smSGcq3f36xjgVVWThj4qqLbTLlq7Ssj8B+fIQ1EuCEGI2lKsyQeIw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/istanbul-lib-coverage": {
       "version": "3.2.2",
@@ -7980,7 +7980,7 @@
       "version": "1.2.8",
       "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz",
       "integrity": "sha512-2yyAR8qBkN3YuheJanUpWC5U3bb5osDywNB8RzDVlDwDHbocAJveqqj1u8+SVD7jkWT4yvsHCpWqqWqAxb0zCA==",
-      "devOptional": true,
+      "dev": true,
       "funding": {
         "url": "https://github.com/sponsors/ljharb"
       }
@@ -8357,7 +8357,7 @@
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/path-is-absolute/-/path-is-absolute-1.0.1.tgz",
       "integrity": "sha512-AVbw3UJ2e9bq64vSaS9Am0fje1Pa8pbGqTTsmXfaIiMpnr5DlDhfJOuLj9Sf95ZPVDAUerDfEk88MPmPe7UCQg==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=0.10.0"
       }
@@ -9162,7 +9162,7 @@
       "version": "5.1.2",
       "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz",
       "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/safe-identifier": {
       "version": "0.4.2",
@@ -9518,7 +9518,7 @@
       "version": "3.0.7",
       "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz",
       "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/simple-git": {
       "version": "3.28.0",
@@ -9639,7 +9639,7 @@
       "version": "4.2.3",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
       "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "emoji-regex": "^8.0.0",
         "is-fullwidth-code-point": "^3.0.0",
@@ -9721,7 +9721,7 @@
       "version": "6.0.1",
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
       "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "ansi-regex": "^5.0.1"
       },
@@ -10454,7 +10454,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
       "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/util.promisify": {
       "version": "1.1.3",
@@ -10577,7 +10577,7 @@
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
       "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "isexe": "^2.0.0"
       },

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.2",
+  "version": "5.0.0-dev.4",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/extensions/mvs/camera.ts

@@ -6,7 +6,9 @@
  */
 
 import { Camera } from '../../mol-canvas3d/camera';
-import { Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { CameraFogParams, Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { BloomParams } from '../../mol-canvas3d/passes/bloom';
+import { DofParams } from '../../mol-canvas3d/passes/dof';
 import { OutlineParams } from '../../mol-canvas3d/passes/outline';
 import { ShadowParams } from '../../mol-canvas3d/passes/shadow';
 import { SsaoParams } from '../../mol-canvas3d/passes/ssao';
@@ -129,24 +131,49 @@ export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: Mol
     const params = canvasNode?.params;
     const backgroundColor = decodeColor(params?.background_color) ?? DefaultCanvasBackgroundColor;
 
-    const outline = !!canvasNode?.custom?.molstar_enable_outline;
-    const shadow = !!canvasNode?.custom?.molstar_enable_shadow;
-    const occlusion = !!canvasNode?.custom?.molstar_enable_ssao;
+    const molstar_postprocessing = canvasNode?.custom?.molstar_postprocessing;
+
+    const outline = !!molstar_postprocessing?.enable_outline;
+    const outlineParams = molstar_postprocessing?.outline_params;
+
+    const shadow = !!molstar_postprocessing?.enable_shadow;
+    const shadowParams = molstar_postprocessing?.shadow_params;
+
+    const occlusion = !!molstar_postprocessing?.enable_ssao;
+    const occlusionParams = molstar_postprocessing?.ssao_params;
+
+    const fog = !!molstar_postprocessing?.enable_fog;
+    const fogParams = molstar_postprocessing?.fog_params;
+
+    const dof = !!molstar_postprocessing?.enable_depth_of_field;
+    const dofParams = molstar_postprocessing?.depth_of_field_params;
+
+    const bloom = !!molstar_postprocessing?.enable_bloom;
+    const bloomParams = molstar_postprocessing?.bloom_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), ...occlusionParams } }
                 : oldCanvasProps.postprocessing.occlusion,
+            dof: dof
+                ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(DofParams), ...dofParams } }
+                : oldCanvasProps.postprocessing.dof,
+            bloom: bloom
+                ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(BloomParams), ...bloomParams } }
+                : oldCanvasProps.postprocessing.bloom,
         },
+        cameraFog: fog
+            ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(CameraFogParams), ...fogParams } }
+            : oldCanvasProps.cameraFog,
         renderer: {
             ...oldCanvasProps.renderer,
             backgroundColor: backgroundColor,

src/extensions/mvs/components/primitives.ts

@@ -39,8 +39,9 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { capitalize } from '../../../mol-util/string';
 import { rowsToExpression, rowToExpression } from '../helpers/selections';
 import { collectMVSReferences, decodeColor, isDefined } from '../helpers/utils';
-import { MolstarNode, MolstarSubtree } from '../tree/molstar/molstar-tree';
-import { MVSNode } from '../tree/mvs/mvs-tree';
+import { addParamDefaults } from '../tree/generic/params-schema';
+import { MolstarNode, MolstarNodeParams, MolstarSubtree } from '../tree/molstar/molstar-tree';
+import { MVSNode, MVSTreeSchema } from '../tree/mvs/mvs-tree';
 import { isComponentExpression, isPrimitiveComponentExpressions, isVector3, PrimitivePositionT } from '../tree/mvs/param-types';
 import { MVSTransform } from './annotation-structure-component';
 
@@ -97,6 +98,16 @@ export const MVSDownloadPrimitiveData = MVSTransform({
     },
 });
 
+/* Cannot use MolstarSubtree<'primitives'>> because information about type of children would be lost and cause TypeScript errors in dependent code */
+interface PrimitivesSubtree {
+    kind: 'primitives',
+    params: MolstarNodeParams<'primitives'>,
+    children?: {
+        kind: 'primitive',
+        params: MolstarNodeParams<'primitive'>,
+    }[],
+}
+
 export type MVSInlinePrimitiveData = typeof MVSInlinePrimitiveData
 export const MVSInlinePrimitiveData = MVSTransform({
     name: 'mvs-inline-primitive-data',
@@ -104,7 +115,10 @@ export const MVSInlinePrimitiveData = MVSTransform({
     from: [SO.Root, SO.Molecule.Structure],
     to: MVSPrimitivesData,
     params: {
-        node: PD.Value<MolstarSubtree<'primitives'>>(undefined as any, { isHidden: true }),
+        node: PD.Value<PrimitivesSubtree>({
+            kind: 'primitives',
+            params: addParamDefaults(MVSTreeSchema.nodes.primitives.params, {}),
+        }, { isHidden: true }),
     },
 })({
     apply({ a, params }) {
@@ -140,11 +154,12 @@ 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 }),
+                    ...PD.withDefaults(Mesh.Params, { alpha: a.data.options?.opacity ?? 1, ...customMeshParams }),
                     ...snapshotKey,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveMesh(data, prev?.geometry),
@@ -155,6 +170,7 @@ 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,
@@ -166,6 +182,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
                         tetherLength: options?.label_tether_length ?? 1,
                         background: isDefined(bgColor),
                         backgroundColor: isDefined(bgColor) ? decodeColor(bgColor) : undefined,
+                        ...customLabelParams,
                     }),
                     ...snapshotKey,
                 },
@@ -175,11 +192,12 @@ 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 }),
+                    ...PD.withDefaults(Lines.Params, { alpha: a.data.options?.opacity ?? 1, ...customLineParams }),
                     ...snapshotKey,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveLines(data, prev?.geometry),

src/extensions/mvs/load.ts

@@ -312,7 +312,7 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
     },
     primitives(updateParent: UpdateTarget, tree: MolstarSubtree<'primitives'>, context: MolstarLoadingContext): UpdateTarget {
         const refs = getPrimitiveStructureRefs(tree);
-        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree });
+        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree as any });
         return applyPrimitiveVisuals(data, refs);
     },
     primitives_from_uri(updateParent: UpdateTarget, tree: MolstarNode<'primitives_from_uri'>, context: MolstarLoadingContext): UpdateTarget {

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-canvas3d/canvas3d.ts

@@ -50,6 +50,9 @@ import { isMobileBrowser } from '../mol-util/browser';
 import { Ray3D } from '../mol-math/geometry/primitives/ray3d';
 import { RayHelper } from './helper/ray-helper';
 
+export const CameraFogParams = {
+    intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
+};
 export const Canvas3DParams = {
     camera: PD.Group({
         mode: PD.Select('perspective', PD.arrayToOptions(['perspective', 'orthographic'] as const), { label: 'Camera' }),
@@ -63,9 +66,7 @@ export const Canvas3DParams = {
         manualReset: PD.Boolean(false, { isHidden: true }),
     }, { pivot: 'mode' }),
     cameraFog: PD.MappedStatic('on', {
-        on: PD.Group({
-            intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
-        }),
+        on: PD.Group(CameraFogParams),
         off: PD.Group({})
     }, { cycle: true, description: 'Show fog in the distance' }),
     cameraClipping: PD.Group({

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 {