Merge branch 'master' into lookup3d

CHANGELOG.md

@@ -6,7 +6,15 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
-- [Fix] Clone ``Canvas3DParams`` when creating a ``Canvas3D`` instance to prevent shared state between multiple instances.
+- [Fix] Clone ``Canvas3DParams`` when creating a ``Canvas3D`` instance to prevent shared state between multiple instances
+- Add ``includeResidueTest`` option to ``alignAndSuperposeWithSIFTSMapping``
+- Add ``parentDisplay`` param for interactions representation.
+- [Experimental] Add support for PyMOL, VMD, and Jmol atom expressions in selection scripts
+- Support for ``failIfMajorPerformanceCaveat`` webgl attribute. Add ``PluginConfig.General.AllowMajorPerformanceCaveat`` and ``allow-major-performance-caveat`` Viewer GET param.
+- Fix handling of PDB TER records (#549)
+- Add support for getting multiple loci from a representation (``.getAllLoci()``)
+- Add ``key`` property to intra- and inter-bonds for referencing source data
+- Fix click event triggered after move
 
 ## [v3.16.0] - 2022-08-25
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.16.0",
+  "version": "3.17.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -90,57 +90,58 @@
     "Michal Malý <michal.maly@ibt.cas.cz>",
     "Jiří Černý <jiri.cerny@ibt.cas.cz>",
     "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>",
-    "Adam Midlik <midlik@gmail.com>"
+    "Adam Midlik <midlik@gmail.com>",
+    "Koya Sakuma <koya.sakuma.work@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
     "@graphql-codegen/add": "^3.2.1",
-    "@graphql-codegen/cli": "^2.11.6",
+    "@graphql-codegen/cli": "^2.12.0",
     "@graphql-codegen/time": "^3.2.1",
     "@graphql-codegen/typescript": "^2.7.3",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.5.3",
+    "@graphql-codegen/typescript-graphql-request": "^4.5.4",
     "@graphql-codegen/typescript-operations": "^2.5.3",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.1",
-    "@types/jest": "^28.1.7",
-    "@types/react": "^18.0.17",
+    "@types/jest": "^29.0.1",
+    "@types/react": "^18.0.19",
     "@types/react-dom": "^18.0.6",
-    "@typescript-eslint/eslint-plugin": "^5.33.1",
-    "@typescript-eslint/parser": "^5.33.1",
+    "@typescript-eslint/eslint-plugin": "^5.36.2",
+    "@typescript-eslint/parser": "^5.36.2",
     "benchmark": "^2.1.4",
-    "concurrently": "^7.3.0",
+    "concurrently": "^7.4.0",
     "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
     "css-loader": "^6.7.1",
-    "eslint": "^8.22.0",
+    "eslint": "^8.23.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.1.0",
     "graphql": "^16.6.0",
     "http-server": "^14.1.1",
-    "jest": "^28.1.3",
+    "jest": "^29.0.3",
     "mini-css-extract-plugin": "^2.6.1",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "sass": "^1.54.5",
+    "sass": "^1.54.9",
     "sass-loader": "^13.0.2",
-    "simple-git": "^3.12.0",
+    "simple-git": "^3.14.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^28.0.8",
-    "typescript": "^4.7.4",
+    "ts-jest": "^29.0.0",
+    "typescript": "^4.8.3",
     "webpack": "^5.74.0",
     "webpack-cli": "^4.10.0"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
-    "@types/benchmark": "^2.1.1",
+    "@types/benchmark": "^2.1.2",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.51",
+    "@types/node": "^16.11.58",
     "@types/node-fetch": "^2.6.2",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",

src/apps/docking-viewer/index.ts

@@ -166,7 +166,7 @@ class Viewer {
             structures.push({ ref: structureProperties?.ref || structure.ref });
         }
 
-        // remove current structuresfrom hierarchy as they will be merged
+        // remove current structures from hierarchy as they will be merged
         // TODO only works with using loadStructuresFromUrlsAndMerge once
         //      need some more API metho to work with the hierarchy
         this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');

src/apps/docking-viewer/viewport.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -202,14 +202,14 @@ const InteractionsPreset = StructureRepresentationPresetProvider({
         const components = {
             ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
             surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
-            interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
+            interactions: await presetStaticComponent(plugin, structureCell, 'ligand'),
         };
 
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
         const representations = {
             ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
             ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, material: CustomMaterial, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
-            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams, material: CustomMaterial, includeParent: true, parentDisplay: 'between' }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
             label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, material: CustomMaterial, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
         };
 

src/apps/viewer/app.ts

@@ -89,6 +89,7 @@ const DefaultViewerOptions = {
     pickPadding: PluginConfig.General.PickPadding.defaultValue,
     enableWboit: PluginConfig.General.EnableWboit.defaultValue,
     preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
+    allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -159,6 +160,7 @@ export class Viewer {
                 [PluginConfig.General.PickPadding, o.pickPadding],
                 [PluginConfig.General.EnableWboit, o.enableWboit],
                 [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+                [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
@@ -497,4 +499,4 @@ export const ViewerAutoPreset = StructureRepresentationPresetProvider({
             return await PresetStructureRepresentations.auto.apply(ref, params, plugin);
         }
     }
-});
+});

src/apps/viewer/index.html

@@ -61,6 +61,7 @@
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
             var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
 
             molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
@@ -76,6 +77,7 @@
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
                 enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
                 preferWebgl1: preferWebgl1,
+                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();
                 if (snapshotId) viewer.setRemoteSnapshot(snapshotId);

src/extensions/geo-export/ui.tsx

@@ -60,6 +60,8 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
     }
 
     componentDidMount() {
+        if (!this.plugin.canvas3d) return;
+
         const merged = merge(
             this.controls.behaviors.params,
             this.plugin.canvas3d!.reprCount

src/extensions/mp4-export/controls.ts

@@ -118,11 +118,13 @@ export class Mp4Controls extends PluginComponent {
     }
 
     private init() {
+        if (!this.plugin.canvas3d) return;
+
         this.subscribe(this.plugin.managers.animation.events.updated.pipe(debounceTime(16)), () => {
             this.sync();
         });
 
-        this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
+        this.subscribe(this.plugin.canvas3d.resized, () => this.syncInfo());
         this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
 
         this.subscribe(this.plugin.behaviors.state.isBusy, b => this.updateCanApply(b));

src/mol-canvas3d/canvas3d.ts

@@ -117,6 +117,7 @@ interface Canvas3DContext {
 
 namespace Canvas3DContext {
     export const DefaultAttribs = {
+        failIfMajorPerformanceCaveat: false,
         /** true by default to avoid issues with Safari (Jan 2021) */
         antialias: true,
         /** true to support multiple Canvas3D objects with a single context */
@@ -132,8 +133,9 @@ namespace Canvas3DContext {
 
     export function fromCanvas(canvas: HTMLCanvasElement, assetManager: AssetManager, attribs: Partial<Attribs> = {}): Canvas3DContext {
         const a = { ...DefaultAttribs, ...attribs };
-        const { antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
+        const { failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
         const gl = getGLContext(canvas, {
+            failIfMajorPerformanceCaveat,
             antialias,
             preserveDrawingBuffer,
             alpha: true, // the renderer requires an alpha channel

src/mol-model-formats/structure/common/component.ts

@@ -32,6 +32,7 @@ const DnaAtomIdsList = [
 /** Used to reduce false positives for atom name-based type guessing */
 const NonPolymerNames = new Set([
     'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // Mononucleotides
+    'LIG'
 ]);
 
 const StandardComponents = (function () {

src/mol-model-formats/structure/pdb/atom-site.ts

@@ -39,7 +39,7 @@ export function getAtomSiteTemplate(data: string, count: number) {
     };
 }
 
-export function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
+export function getAtomSite(sites: AtomSiteTemplate, terIndices: Set<number>): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
     const pdbx_PDB_model_num = CifField.ofStrings(sites.pdbx_PDB_model_num);
     const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
     const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
@@ -67,21 +67,17 @@ export function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): { [K in k
         const seqId = auth_seq_id.int(i);
         let atomId = auth_atom_id.str(i);
 
-        let asymIdChanged = false;
-
         if (modelNum !== currModelNum) {
             asymIdCounts.clear();
             atomIdCounts.clear();
             currModelNum = modelNum;
             currAsymId = asymId;
             currSeqId = seqId;
-            asymIdChanged = true;
             currLabelAsymId = asymId;
         } else if (currAsymId !== asymId) {
             atomIdCounts.clear();
             currAsymId = asymId;
             currSeqId = seqId;
-            asymIdChanged = true;
             currLabelAsymId = asymId;
         } else if (currSeqId !== seqId) {
             atomIdCounts.clear();
@@ -91,7 +87,7 @@ export function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): { [K in k
         if (asymIdCounts.has(asymId)) {
             // only change the chains name if there are TER records
             // otherwise assume repeated chain name use is from interleaved chains
-            if (hasTer && asymIdChanged) {
+            if (terIndices.has(i)) {
                 const asymIdCount = asymIdCounts.get(asymId)! + 1;
                 asymIdCounts.set(asymId, asymIdCount);
                 currLabelAsymId = `${asymId}_${asymIdCount}`;

src/mol-model-formats/structure/pdb/to-cif.ts

@@ -51,7 +51,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
 
     let modelNum = 0, modelStr = '';
     let conectRange: [number, number] | undefined = undefined;
-    let hasTer = false;
+    const terIndices = new Set<number>();
 
     for (let i = 0, _i = lines.count; i < _i; i++) {
         let s = indices[2 * i], e = indices[2 * i + 1];
@@ -164,7 +164,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
                 break;
             case 'T':
                 if (substringStartsWith(data, s, e, 'TER')) {
-                    hasTer = true;
+                    terIndices.add(atomSite.index);
                 }
         }
     }
@@ -183,7 +183,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
         atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
     }
 
-    const atom_site = getAtomSite(atomSite, hasTer);
+    const atom_site = getAtomSite(atomSite, terIndices);
     if (!isPdbqt) delete atom_site.partial_charge;
 
     if (conectRange) {

src/mol-model-formats/structure/property/bonds/chem_comp.ts

@@ -65,7 +65,7 @@ export namespace ComponentBond {
             return e;
         }
 
-        const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount } = data;
+        const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount, pdbx_ordinal } = data;
 
         let entry = addEntry(comp_id.value(0)!);
         for (let i = 0; i < _rowCount; i++) {
@@ -74,6 +74,7 @@ export namespace ComponentBond {
             const nameB = atom_id_2.value(i)!;
             const order = value_order.value(i)!;
             const aromatic = pdbx_aromatic_flag.value(i) === 'y';
+            const key = pdbx_ordinal.value(i);
 
             if (entry.id !== id) {
                 entry = addEntry(id);
@@ -89,29 +90,29 @@ export namespace ComponentBond {
                 case 'quad': ord = 4; break;
             }
 
-            entry.add(nameA, nameB, ord, flags);
+            entry.add(nameA, nameB, ord, flags, key);
         }
 
         return entries;
     }
 
     export class Entry {
-        readonly map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
+        readonly map: Map<string, Map<string, { order: number, flags: number, key: number }>> = new Map();
 
-        add(a: string, b: string, order: number, flags: number, swap = true) {
+        add(a: string, b: string, order: number, flags: number, key: number, swap = true) {
             const e = this.map.get(a);
             if (e !== void 0) {
                 const f = e.get(b);
                 if (f === void 0) {
-                    e.set(b, { order, flags });
+                    e.set(b, { order, flags, key });
                 }
             } else {
-                const map = new Map<string, { order: number, flags: number }>();
-                map.set(b, { order, flags });
+                const map = new Map<string, { order: number, flags: number, key: number }>();
+                map.set(b, { order, flags, key });
                 this.map.set(a, map);
             }
 
-            if (swap) this.add(b, a, order, flags, false);
+            if (swap) this.add(b, a, order, flags, key, false);
         }
 
         constructor(public readonly id: string) { }

src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts

@@ -22,6 +22,8 @@ import { LocationIterator } from '../../../mol-geo/util/location-iterator';
 import { InteractionFlag } from '../interactions/common';
 import { Unit } from '../../../mol-model/structure/structure';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { InteractionsSharedParams } from './shared';
 
 function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InteractionsInterUnitParams>, mesh?: Mesh) {
     if (!structure.hasAtomic) return Mesh.createEmpty(mesh);
@@ -31,7 +33,7 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
     const { contacts, unitsFeatures } = interactions;
 
     const { edgeCount, edges } = contacts;
-    const { sizeFactor } = props;
+    const { sizeFactor, parentDisplay } = props;
 
     if (!edgeCount) return Mesh.createEmpty(mesh);
 
@@ -70,14 +72,48 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
 
             if (child) {
                 const b = edges[edgeIndex];
-                const childUnitA = child.unitMap.get(b.unitA);
-                if (!childUnitA) return true;
-
-                const unitA = structure.unitMap.get(b.unitA);
-                const { offsets, members } = unitsFeatures.get(b.unitA);
-                for (let i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
-                    const eA = unitA.elements[members[i]];
-                    if (!SortedArray.has(childUnitA.elements, eA)) return true;
+
+                if (parentDisplay === 'stub') {
+                    const childUnitA = child.unitMap.get(b.unitA);
+                    if (!childUnitA) return true;
+
+                    const unitA = structure.unitMap.get(b.unitA);
+                    const { offsets, members } = unitsFeatures.get(b.unitA);
+                    for (let i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
+                        const eA = unitA.elements[members[i]];
+                        if (!SortedArray.has(childUnitA.elements, eA)) return true;
+                    }
+                } else if (parentDisplay === 'full' || parentDisplay === 'between') {
+                    let flagA = false;
+                    let flagB = false;
+
+                    const childUnitA = child.unitMap.get(b.unitA);
+                    if (!childUnitA) {
+                        flagA = true;
+                    } else {
+                        const unitA = structure.unitMap.get(b.unitA);
+                        const { offsets, members } = unitsFeatures.get(b.unitA);
+                        for (let i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
+                            const eA = unitA.elements[members[i]];
+                            if (!SortedArray.has(childUnitA.elements, eA)) flagA = true;
+                        }
+                    }
+
+                    const childUnitB = child.unitMap.get(b.unitB);
+                    if (!childUnitB) {
+                        flagB = true;
+                    } else {
+                        const unitB = structure.unitMap.get(b.unitB);
+                        const { offsets, members } = unitsFeatures.get(b.unitB);
+                        for (let i = offsets[b.indexB], il = offsets[b.indexB + 1]; i < il; ++i) {
+                            const eB = unitB.elements[members[i]];
+                            if (!SortedArray.has(childUnitB.elements, eB)) flagB = true;
+                        }
+                    }
+
+                    return parentDisplay === 'full' ? flagA && flagB : flagA === flagB;
+                } else {
+                    assertUnreachable(parentDisplay);
                 }
             }
 
@@ -101,10 +137,7 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
 export const InteractionsInterUnitParams = {
     ...ComplexMeshParams,
     ...LinkCylinderParams,
-    sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
-    dashCount: PD.Numeric(6, { min: 2, max: 10, step: 2 }),
-    dashScale: PD.Numeric(0.4, { min: 0, max: 2, step: 0.1 }),
-    includeParent: PD.Boolean(false),
+    ...InteractionsSharedParams,
 };
 export type InteractionsInterUnitParams = typeof InteractionsInterUnitParams
 
@@ -121,7 +154,8 @@ export function InteractionsInterUnitVisual(materialId: number): ComplexVisual<I
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.dashScale !== currentProps.dashScale ||
                 newProps.dashCap !== currentProps.dashCap ||
-                newProps.radialSegments !== currentProps.radialSegments
+                newProps.radialSegments !== currentProps.radialSegments ||
+                newProps.parentDisplay !== currentProps.parentDisplay
             );
 
             const interactionsHash = InteractionsProvider.get(newStructure).version;

src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts

@@ -22,6 +22,8 @@ import { Interactions } from '../interactions/interactions';
 import { InteractionFlag } from '../interactions/common';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
+import { InteractionsSharedParams } from './shared';
 
 async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<InteractionsIntraUnitParams>, mesh?: Mesh) {
     if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
@@ -38,7 +40,7 @@ async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit:
 
     const { x, y, z, members, offsets } = features;
     const { edgeCount, a, b, edgeProps: { flag } } = contacts;
-    const { sizeFactor } = props;
+    const { sizeFactor, parentDisplay } = props;
 
     if (!edgeCount) return Mesh.createEmpty(mesh);
 
@@ -60,10 +62,31 @@ async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit:
             if (flag[edgeIndex] === InteractionFlag.Filtered) return true;
 
             if (childUnit) {
-                const f = a[edgeIndex];
-                for (let i = offsets[f], jl = offsets[f + 1]; i < jl; ++i) {
-                    const e = unit.elements[members[offsets[i]]];
-                    if (!SortedArray.has(childUnit.elements, e)) return true;
+                if (parentDisplay === 'stub') {
+                    const f = a[edgeIndex];
+                    for (let i = offsets[f], il = offsets[f + 1]; i < il; ++i) {
+                        const e = unit.elements[members[offsets[i]]];
+                        if (!SortedArray.has(childUnit.elements, e)) return true;
+                    }
+                } else if (parentDisplay === 'full' || parentDisplay === 'between') {
+                    let flagA = false;
+                    let flagB = false;
+
+                    const fA = a[edgeIndex];
+                    for (let i = offsets[fA], il = offsets[fA + 1]; i < il; ++i) {
+                        const eA = unit.elements[members[offsets[i]]];
+                        if (!SortedArray.has(childUnit.elements, eA)) flagA = true;
+                    }
+
+                    const fB = b[edgeIndex];
+                    for (let i = offsets[fB], il = offsets[fB + 1]; i < il; ++i) {
+                        const eB = unit.elements[members[offsets[i]]];
+                        if (!SortedArray.has(childUnit.elements, eB)) flagB = true;
+                    }
+
+                    return parentDisplay === 'full' ? flagA && flagB : flagA === flagB;
+                } else {
+                    assertUnreachable(parentDisplay);
                 }
             }
 
@@ -86,10 +109,7 @@ async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit:
 export const InteractionsIntraUnitParams = {
     ...UnitsMeshParams,
     ...LinkCylinderParams,
-    sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
-    dashCount: PD.Numeric(6, { min: 2, max: 10, step: 2 }),
-    dashScale: PD.Numeric(0.4, { min: 0, max: 2, step: 0.1 }),
-    includeParent: PD.Boolean(false),
+    ...InteractionsSharedParams,
 };
 export type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams
 
@@ -106,7 +126,8 @@ export function InteractionsIntraUnitVisual(materialId: number): UnitsVisual<Int
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.dashScale !== currentProps.dashScale ||
                 newProps.dashCap !== currentProps.dashCap ||
-                newProps.radialSegments !== currentProps.radialSegments
+                newProps.radialSegments !== currentProps.radialSegments ||
+                newProps.parentDisplay !== currentProps.parentDisplay
             );
 
             const interactionsHash = InteractionsProvider.get(newStructureGroup.structure).version;

src/mol-model-props/computed/representations/shared.ts

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+export const InteractionsSharedParams = {
+    sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
+    dashCount: PD.Numeric(6, { min: 2, max: 10, step: 2 }),
+    dashScale: PD.Numeric(0.4, { min: 0, max: 2, step: 0.1 }),
+    includeParent: PD.Boolean(false),
+    parentDisplay: PD.Select('stub', PD.arrayToOptions(['stub', 'full', 'between'] as const), { description: 'Only has an effect when "includeParent" is enabled. "Stub" shows just the child side of interactions to the parent. "Full" shows both sides of interactions to the parent. "Between" shows only interactions to the parent.' }),
+};
+export type InteractionsSharedParams = typeof InteractionsSharedParams

src/mol-model/structure/query.ts

@@ -12,6 +12,7 @@ import * as modifiers from './query/queries/modifiers';
 import * as filters from './query/queries/filters';
 import * as combinators from './query/queries/combinators';
 import * as internal from './query/queries/internal';
+import * as atomset from './query/queries/atom-set';
 import { Predicates as pred } from './query/predicates';
 
 export const Queries = {
@@ -20,7 +21,8 @@ export const Queries = {
     modifiers,
     combinators,
     pred,
-    internal
+    internal,
+    atomset
 };
 
-export { StructureSelection, StructureQuery };
+export { StructureSelection, StructureQuery };

src/mol-model/structure/query/context.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Structure, StructureElement, Unit } from '../structure';
@@ -113,6 +114,7 @@ class QueryContextBondInfo<U extends Unit = Unit> {
     bIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
     type: BondType = BondType.Flag.None;
     order: number = 0;
+    key: number = -1;
 
     private testFn: QueryPredicate = defaultBondTest;
 

src/mol-model/structure/query/queries/atom-set.ts

@@ -0,0 +1,36 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Koya Sakuma
+ * Adapted from MolQL implemtation of atom-set.ts
+ *
+ * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureQuery } from '../query';
+import { StructureSelection } from '../selection';
+import { getCurrentStructureProperties } from './filters';
+import { QueryContext, QueryFn } from '../context';
+
+
+export function atomCount(ctx: QueryContext) {
+    return ctx.currentStructure.elementCount;
+}
+
+
+export function countQuery(query: StructureQuery) {
+    return (ctx: QueryContext) => {
+        const sel = query(ctx);
+        return StructureSelection.structureCount(sel);
+    };
+}
+
+export function propertySet(prop: QueryFn<any>) {
+    return (ctx: QueryContext) => {
+        const set = new Set();
+        return getCurrentStructureProperties(ctx, prop, set);
+    };
+}
+

src/mol-model/structure/query/queries/filters.ts

@@ -1,12 +1,13 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { SetUtils } from '../../../../mol-util/set';
 import { Unit } from '../../structure';
-import { QueryContext, QueryFn, QueryPredicate } from '../context';
+import { QueryContext, QueryFn } from '../context';
 import { StructureQuery } from '../query';
 import { StructureSelection } from '../selection';
 import { structureAreIntersecting } from '../utils/structure-set';
@@ -16,7 +17,7 @@ import { Structure } from '../../structure/structure';
 import { StructureElement } from '../../structure/element';
 import { SortedArray } from '../../../../mol-data/int';
 
-export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuery {
+export function pick(query: StructureQuery, pred: QueryFn<any>): StructureQuery {
     return ctx => {
         const sel = query(ctx);
         const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
@@ -50,9 +51,7 @@ export function first(query: StructureQuery): StructureQuery {
     };
 }
 
-export interface UnitTypeProperties { atomic?: QueryFn, coarse?: QueryFn }
-
-export function getCurrentStructureProperties(ctx: QueryContext, props: UnitTypeProperties, set: Set<any>) {
+export function getCurrentStructureProperties(ctx: QueryContext, props: QueryFn<any>, set: Set<any>) {
     const { units } = ctx.currentStructure;
     const l = ctx.pushCurrentElement();
 
@@ -61,9 +60,9 @@ export function getCurrentStructureProperties(ctx: QueryContext, props: UnitType
         l.unit = unit;
         const elements = unit.elements;
 
-        let fn;
-        if (Unit.isAtomic(unit)) fn = props.atomic;
-        else fn = props.coarse;
+        const fn = props;
+        //        if (Unit.isAtomic(unit)) fn = props.atomic;
+        //        else fn = props.coarse;
         if (!fn) continue;
 
         for (let j = 0, _j = elements.length; j < _j; j++) {
@@ -77,7 +76,7 @@ export function getCurrentStructureProperties(ctx: QueryContext, props: UnitType
     return set;
 }
 
-function getSelectionProperties(ctx: QueryContext, query: StructureQuery, props: UnitTypeProperties) {
+function getSelectionProperties(ctx: QueryContext, query: StructureQuery, props: QueryFn<any>) {
     const set = new Set();
 
     const sel = query(ctx);
@@ -92,7 +91,7 @@ function getSelectionProperties(ctx: QueryContext, query: StructureQuery, props:
     return set;
 }
 
-export function withSameAtomProperties(query: StructureQuery, propertySource: StructureQuery, props: UnitTypeProperties): StructureQuery {
+export function withSameAtomProperties(query: StructureQuery, propertySource: StructureQuery, props: QueryFn<any>): StructureQuery {
     return ctx => {
         const sel = query(ctx);
         const propSet = getSelectionProperties(ctx, propertySource, props);
@@ -102,7 +101,7 @@ export function withSameAtomProperties(query: StructureQuery, propertySource: St
         StructureSelection.forEach(sel, (s, i) => {
             ctx.currentStructure = s;
             const currentProps = getCurrentStructureProperties(ctx, props, new Set());
-            if (SetUtils.isSuperset(currentProps, propSet)) {
+            if (SetUtils.isSuperset(propSet, currentProps)) {
                 ret.add(s);
             }
 
@@ -248,7 +247,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
 
         const inputUnit = input.unitMap.get(unit.id) as Unit.Atomic;
 
-        const { offset, b, edgeProps: { flags, order } } = inputUnit.bonds;
+        const { offset, b, edgeProps: { flags, order, key } } = inputUnit.bonds;
         const bondedUnits = interBonds.getConnectedUnits(unit.id);
         const buCount = bondedUnits.length;
 
@@ -273,6 +272,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
                 atomicBond.bIndex = b[l] as StructureElement.UnitIndex;
                 atomicBond.type = flags[l];
                 atomicBond.order = order[l];
+                atomicBond.key = key[l];
                 if (atomicBond.test(queryCtx, true)) return true;
             }
 
@@ -295,6 +295,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
                     atomicBond.bIndex = bond.indexB;
                     atomicBond.type = bond.props.flag;
                     atomicBond.order = bond.props.order;
+                    atomicBond.key = bond.props.key;
                     if (atomicBond.test(queryCtx, true)) return true;
                 }
             }
@@ -342,4 +343,4 @@ export function isConnectedTo({ query, target, disjunct, invert, bondTest }: IsC
 
         return ret.getSelection();
     };
-}
+}

src/mol-model/structure/query/queries/generators.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -322,7 +322,7 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
         for (const unit of structure.units) {
             if (unit.kind !== Unit.Kind.Atomic) continue;
 
-            const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order } } = unit.bonds;
+            const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order, key } } = unit.bonds;
             atomicBond.a.unit = unit;
             atomicBond.b.unit = unit;
             for (let i = 0 as StructureElement.UnitIndex, _i = unit.elements.length; i < _i; i++) {
@@ -335,6 +335,7 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
                     atomicBond.b.element = unit.elements[intraBondB[lI]];
                     atomicBond.type = flags[lI];
                     atomicBond.order = order[lI];
+                    atomicBond.key = key[lI];
                     // No need to "swap test" because each bond direction will be visited eventually.
                     if (atomicBond.test(ctx, false)) {
                         const b = structure.subsetBuilder(false);
@@ -358,6 +359,7 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
             atomicBond.bIndex = bond.indexB;
             atomicBond.order = bond.props.order;
             atomicBond.type = bond.props.flag;
+            atomicBond.key = bond.props.key;
 
             // No need to "swap test" because each bond direction will be visited eventually.
             if (atomicBond.test(ctx, false)) {

src/mol-model/structure/query/queries/modifiers.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Segmentation, SortedArray } from '../../../../mol-data/int';
@@ -370,7 +371,7 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
         }
 
         const inputUnitA = inputStructure.unitMap.get(unit.id) as Unit.Atomic;
-        const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order } } = inputUnitA.bonds;
+        const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order, key } } = inputUnitA.bonds;
 
         atomicBond.setStructure(inputStructure);
 
@@ -397,6 +398,7 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
                 atomicBond.b.element = bElement;
                 atomicBond.type = flags[lI];
                 atomicBond.order = order[lI];
+                atomicBond.key = key[lI];
 
                 if (atomicBond.test(ctx, true)) {
                     builder.addToUnit(unit.id, bElement);
@@ -427,6 +429,7 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
                     atomicBond.b.element = bElement;
                     atomicBond.type = bond.props.flag;
                     atomicBond.order = bond.props.order;
+                    atomicBond.key = bond.props.key;
 
                     if (atomicBond.test(ctx, true)) {
                         builder.addToUnit(bondedUnit.unitB, bElement);

src/mol-model/structure/structure/unit/bonds/data.ts

@@ -15,16 +15,17 @@ import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
 type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
     readonly order: ArrayLike<number>,
     readonly flags: ArrayLike<BondType.Flag>
+    readonly key: ArrayLike<number>,
 }, {
     /** can remap even with dynamicBonds on, e.g., for water molecules */
     readonly canRemap?: boolean
 }>
 
 namespace IntraUnitBonds {
-    export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });
+    export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [], key: [] });
 }
 
-type InterUnitEdgeProps = { readonly order: number, readonly flag: BondType.Flag }
+type InterUnitEdgeProps = { readonly order: number, readonly flag: BondType.Flag, readonly key: number }
 
 class InterUnitBonds extends InterUnitGraph<number, StructureElement.UnitIndex, InterUnitEdgeProps> {
     /** Get inter-unit bond given a bond-location */

src/mol-model/structure/structure/unit/bonds/inter-compute.ts

@@ -80,7 +80,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
 
         if (!props.forceCompute && indexPairs) {
             const { maxDistance } = indexPairs;
-            const { offset, b, edgeProps: { order, distance, flag } } = indexPairs.bonds;
+            const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;
 
             const srcA = sourceIndex.value(aI);
             const aeI = getElementIdx(type_symbolA.value(aI));
@@ -113,7 +113,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
                 }
 
                 if (add) {
-                    builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
+                    builder.add(_aI, _bI, { order: order[i], flag: flag[i], key: key[i] });
                 }
             }
             continue; // assume `indexPairs` supplies all bonds
@@ -131,7 +131,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
                 // check if the bond is within MAX_RADIUS for this pair of units
                 if (getDistance(unitA, aI, unitB, p.atomIndex) > maxRadius) continue;
 
-                builder.add(_aI, _bI, { order: se.order, flag: se.flags });
+                builder.add(_aI, _bI, { order: se.order, flag: se.flags, key: se.rowIndex });
                 added = true;
             }
             // assume, for an atom, that if any inter unit bond is given
@@ -187,7 +187,8 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
                 const compIdB = label_comp_idB.value(residueIndexB[bI]);
                 builder.add(_aI, _bI, {
                     order: getInterBondOrderFromTable(compIdA, compIdB, atomIdA, atomIdB),
-                    flag: (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed
+                    flag: (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed,
+                    key: -1
                 });
             }
         }

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -24,17 +24,19 @@ import { Model } from '../../../model/model';
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const v3distance = Vec3.distance;
 
-function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.UnitIndex[], _order: number[], _flags: number[], atomCount: number, canRemap: boolean): IntraUnitBonds {
+function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.UnitIndex[], _order: number[], _flags: number[], _key: number[], atomCount: number, canRemap: boolean): IntraUnitBonds {
     const builder = new IntAdjacencyGraph.EdgeBuilder(atomCount, atomA, atomB);
     const flags = new Uint16Array(builder.slotCount);
     const order = new Int8Array(builder.slotCount);
+    const key = new Uint32Array(builder.slotCount);
     for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
         builder.addNextEdge();
         builder.assignProperty(flags, _flags[i]);
         builder.assignProperty(order, _order[i]);
+        builder.assignProperty(key, _key[i]);
     }
 
-    return builder.createGraph({ flags, order }, { canRemap });
+    return builder.createGraph({ flags, order, key }, { canRemap });
 }
 
 const tmpDistVecA = Vec3();
@@ -53,7 +55,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
     const { type_symbol } = unit.model.atomicHierarchy.atoms;
     const atomCount = unit.elements.length;
     const { maxDistance } = indexPairs;
-    const { offset, b, edgeProps: { order, distance, flag } } = indexPairs.bonds;
+    const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;
 
     const { atomSourceIndex: sourceIndex } = unit.model.atomicHierarchy;
     const { invertedIndex } = Model.getInvertedAtomSourceIndex(unit.model);
@@ -62,6 +64,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
     const atomB: StructureElement.UnitIndex[] = [];
     const flags: number[] = [];
     const orders: number[] = [];
+    const keys: number[] = [];
 
     for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
         const aI = atoms[_aI];
@@ -104,11 +107,12 @@ function findIndexPairBonds(unit: Unit.Atomic) {
                 atomB[atomB.length] = _bI;
                 orders[orders.length] = order[i];
                 flags[flags.length] = flag[i];
+                keys[keys.length] = key[i];
             }
         }
     }
 
-    return getGraph(atomA, atomB, orders, flags, atomCount, false);
+    return getGraph(atomA, atomB, orders, flags, keys, atomCount, false);
 }
 
 function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBonds {
@@ -132,9 +136,10 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
     const atomB: StructureElement.UnitIndex[] = [];
     const flags: number[] = [];
     const order: number[] = [];
+    const key: number[] = [];
 
     let lastResidue = -1;
-    let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
+    let componentMap: Map<string, Map<string, { flags: number, order: number, key: number }>> | undefined = void 0;
 
     let isWatery = true, isDictionaryBased = true, isSequenced = true;
 
@@ -162,6 +167,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
                 atomB[atomB.length] = _bI;
                 flags[flags.length] = se.flags;
                 order[order.length] = se.order;
+                key[key.length] = se.rowIndex;
 
                 if (!hasStructConn) structConnAdded.clear();
                 hasStructConn = true;
@@ -230,6 +236,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
                         flag |= BondType.Flag.MetallicCoordination;
                     }
                     flags[flags.length] = flag;
+                    key[key.length] = e.key;
                 }
                 continue;
             }
@@ -243,6 +250,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
                 atomB[atomB.length] = _bI;
                 order[order.length] = getIntraBondOrderFromTable(compId, atomIdA, label_atom_id.value(bI));
                 flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
+                key[key.length] = -1;
 
                 const seqIdB = label_seq_id.value(rbI);
 
@@ -253,7 +261,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
     }
 
     const canRemap = isWatery || (isDictionaryBased && isSequenced);
-    return getGraph(atomA, atomB, order, flags, atomCount, canRemap);
+    return getGraph(atomA, atomB, order, flags, key, atomCount, canRemap);
 }
 
 function computeIntraUnitBonds(unit: Unit.Atomic, props?: Partial<BondComputationProps>) {

src/mol-model/structure/structure/util/superposition-sifts-mapping.ts

@@ -8,7 +8,8 @@
 import { Segmentation } from '../../../../mol-data/int';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
 import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
-import { ElementIndex } from '../../model/indexing';
+import { ElementIndex, ResidueIndex } from '../../model/indexing';
+import { StructureElement } from '../element';
 import { Structure } from '../structure';
 import { Unit } from '../unit';
 
@@ -24,11 +25,16 @@ export interface AlignmentResult {
     failedPairs: [number, number][]
 }
 
-export function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: { traceOnly?: boolean }): AlignmentResult {
+type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location<Unit.Atomic>, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean
+
+export function alignAndSuperposeWithSIFTSMapping(
+    structures: Structure[],
+    options?: { traceOnly?: boolean, includeResidueTest?: IncludeResidueTest }
+): AlignmentResult {
     const indexMap = new Map<string, IndexEntry>();
 
     for (let i = 0; i < structures.length; i++) {
-        buildIndex(structures[i], indexMap, i, options?.traceOnly ?? true);
+        buildIndex(structures[i], indexMap, i, options?.traceOnly ?? true, options?.includeResidueTest ?? _includeAllResidues);
     }
 
     const index = Array.from(indexMap.values());
@@ -137,11 +143,16 @@ interface IndexEntry {
     pivots: { [i: number]: [unit: Unit.Atomic, start: ElementIndex, end: ElementIndex] | undefined }
 }
 
-function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number, traceOnly: boolean) {
+function _includeAllResidues() { return true; }
+
+function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number, traceOnly: boolean, includeTest: IncludeResidueTest) {
+    const loc = StructureElement.Location.create<Unit.Atomic>(structure);
+
     for (const unit of structure.units) {
         if (unit.kind !== Unit.Kind.Atomic) continue;
 
         const { elements, model } = unit;
+        loc.unit = unit;
 
         const map = SIFTSMapping.Provider.get(model).value;
         if (!map) return;
@@ -161,9 +172,11 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
 
                 if (!dbName[rI]) continue;
 
+                const traceElement = traceElementIndex[rI];
+
                 let start, end;
                 if (traceOnly) {
-                    start = traceElementIndex[rI];
+                    start = traceElement;
                     if (start === -1) continue;
                     end = start + 1 as ElementIndex;
                 } else {
@@ -171,6 +184,9 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
                     end = elements[residueSegment.end - 1] + 1 as ElementIndex;
                 }
 
+                loc.element = (traceElement >= 0 ? traceElement : start) as ElementIndex;
+                if (!includeTest(loc, rI, start, end)) continue;
+
                 const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;
 
                 if (!index.has(key)) {

src/mol-plugin-state/builder/structure/representation.ts

@@ -90,7 +90,7 @@ export class StructureRepresentationBuilder {
     }
 
     applyPreset<K extends keyof PresetStructureRepresentations>(parent: StateObjectRef<PluginStateObject.Molecule.Structure>, preset: K, params?: StructureRepresentationPresetProvider.Params<PresetStructureRepresentations[K]>): Promise<StructureRepresentationPresetProvider.State<PresetStructureRepresentations[K]>> | undefined
-    applyPreset<P = any, S = {}>(parent: StateObjectRef<PluginStateObject.Molecule.Structure>, provider: StructureRepresentationPresetProvider<P, S>, params?: P): Promise<S> | undefined
+    applyPreset<P = any, S extends {} = {}>(parent: StateObjectRef<PluginStateObject.Molecule.Structure>, provider: StructureRepresentationPresetProvider<P, S>, params?: P): Promise<S> | undefined
     applyPreset(parent: StateObjectRef<PluginStateObject.Molecule.Structure>, providerId: string, params?: any): Promise<any> | undefined
     applyPreset(parent: StateObjectRef, providerRef: string | StructureRepresentationPresetProvider, params?: any): Promise<any> | undefined {
         const provider = this.resolveProvider(providerRef);

src/mol-plugin-state/component.ts

@@ -42,7 +42,7 @@ export class PluginComponent {
     }
 }
 
-export class StatefulPluginComponent<State> extends PluginComponent {
+export class StatefulPluginComponent<State extends {}> extends PluginComponent {
     private _state: State;
 
     protected updateState(...states: Partial<State>[]): boolean {

src/mol-plugin-state/formats/trajectory.ts

@@ -75,7 +75,7 @@ export const CifCoreProvider: TrajectoryFormatProvider = {
     visuals: defaultVisuals
 };
 
-function directTrajectory<P>(transformer: StateTransformer<PluginStateObject.Data.String | PluginStateObject.Data.Binary, PluginStateObject.Molecule.Trajectory, P>, transformerParams?: P): TrajectoryFormatProvider['parse'] {
+function directTrajectory<P extends {}>(transformer: StateTransformer<PluginStateObject.Data.String | PluginStateObject.Data.Binary, PluginStateObject.Molecule.Trajectory, P>, transformerParams?: P): TrajectoryFormatProvider['parse'] {
     return async (plugin, data, params) => {
         const state = plugin.state.data;
         const trajectory = await state.build().to(data)

src/mol-plugin-state/transforms/model.ts

@@ -1079,4 +1079,4 @@ const ShapeFromPly = PluginStateTransform.BuiltIn({
             return new SO.Shape.Provider(shape, props);
         });
     }
-});
+});

src/mol-plugin-ui/base.tsx

@@ -13,7 +13,7 @@ import { Icon, ArrowRightSvg, ArrowDropDownSvg } from './controls/icons';
 
 export const PluginReactContext = React.createContext(void 0 as any as PluginUIContext);
 
-export abstract class PluginUIComponent<P = {}, S = {}, SS = {}> extends React.Component<P & { children?: any }, S, SS> {
+export abstract class PluginUIComponent<P extends {} = {}, S = {}, SS = {}> extends React.Component<P & { children?: any }, S, SS> {
     static contextType = PluginReactContext;
     readonly plugin: PluginUIContext;
 

src/mol-plugin-ui/controls/parameters.tsx

@@ -7,6 +7,7 @@
 
 import * as React from 'react';
 import { Mat4, Vec2, Vec3 } from '../../mol-math/linear-algebra';
+import { Script } from '../../mol-script/script';
 import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
 import { ColorListEntry } from '../../mol-util/color/color';
@@ -22,7 +23,7 @@ import { PluginUIContext } from '../context';
 import { ActionMenu } from './action-menu';
 import { ColorOptions, ColorValueOption, CombinedColorControl } from './color';
 import { Button, ControlGroup, ControlRow, ExpandGroup, IconButton, TextInput, ToggleButton } from './common';
-import { ArrowDownwardSvg, ArrowDropDownSvg, ArrowRightSvg, ArrowUpwardSvg, BookmarksOutlinedSvg, CheckSvg, ClearSvg, DeleteOutlinedSvg, HelpOutlineSvg, Icon, MoreHorizSvg } from './icons';
+import { ArrowDownwardSvg, ArrowDropDownSvg, ArrowRightSvg, ArrowUpwardSvg, BookmarksOutlinedSvg, CheckSvg, ClearSvg, DeleteOutlinedSvg, HelpOutlineSvg, Icon, MoreHorizSvg, WarningSvg } from './icons';
 import { legendFor } from './legend';
 import { LineGraphComponent } from './line-graph/line-graph-component';
 import { Slider, Slider2 } from './slider';
@@ -1466,31 +1467,38 @@ export class ConvertedControl extends React.PureComponent<ParamProps<PD.Converte
     }
 }
 
-export class ScriptControl extends SimpleParam<PD.Script> {
-    onChange = (e: React.ChangeEvent<HTMLInputElement>) => {
-        const value = e.target.value;
-        if (value !== this.props.value.expression) {
-            this.update({ language: this.props.value.language, expression: value });
-        }
-    };
-
-    onKeyPress = (e: React.KeyboardEvent<HTMLInputElement>) => {
-        if ((e.keyCode === 13 || e.charCode === 13 || e.key === 'Enter')) {
-            if (this.props.onEnter) this.props.onEnter();
+export class ScriptControl extends React.PureComponent<ParamProps<PD.Script>> {
+    onChange: ParamOnChange = ({ name, value }) => {
+        const k = name as 'language' | 'expression';
+        if (value !== this.props.value[k]) {
+            this.props.onChange({ param: this.props.param, name: this.props.name, value: { ...this.props.value, [k]: value } });
         }
-        e.stopPropagation();
     };
 
-    renderControl() {
+    render() {
         // TODO: improve!
 
-        const placeholder = this.props.param.label || camelCaseToWords(this.props.name);
-        return <input type='text'
-            value={this.props.value.expression || ''}
-            placeholder={placeholder}
-            onChange={this.onChange}
-            onKeyPress={this.props.onEnter ? this.onKeyPress : void 0}
-            disabled={this.props.isDisabled}
-        />;
+        const selectParam: PD.Select<PD.Script['defaultValue']['language']> = {
+            defaultValue: this.props.value.language,
+            options: PD.objectToOptions(Script.Info),
+            type: 'select',
+        };
+        const select = <SelectControl param={selectParam}
+            isDisabled={this.props.isDisabled} onChange={this.onChange} onEnter={this.props.onEnter}
+            name='language' value={this.props.value.language} />;
+
+        const textParam: PD.Text = {
+            defaultValue: this.props.value.language,
+            type: 'text',
+        };
+        const text = <TextControl param={textParam} isDisabled={this.props.isDisabled} onChange={this.onChange} name='expression' value={this.props.value.expression} />;
+
+        return <>
+            {select}
+            {this.props.value.language !== 'mol-script' && <div className='msp-help-text' style={{ padding: '10px' }}>
+                <Icon svg={WarningSvg} /> Support for PyMOL, VMD, and Jmol selections is an experimental feature and may not always work as intended.
+            </div>}
+            {text}
+        </>;
     }
-}
+}

src/mol-plugin-ui/controls/screenshot.tsx

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import * as React from 'react';
@@ -25,7 +26,7 @@ export interface ScreenshotPreviewProps {
 const _ScreenshotPreview = (props: ScreenshotPreviewProps) => {
     const { plugin, cropFrameColor } = props;
 
-    const helper = plugin.helpers.viewportScreenshot!;
+    const helper = plugin.helpers.viewportScreenshot;
     const [currentCanvas, setCurrentCanvas] = useState<HTMLCanvasElement | null>(null);
     const canvasRef = useRef<HTMLCanvasElement | null>(null);
     const propsRef = useRef(props);
@@ -70,8 +71,8 @@ const _ScreenshotPreview = (props: ScreenshotPreviewProps) => {
         subscribe(plugin.state.data.behaviors.isUpdating, v => {
             if (!v) isDirty = true;
         });
-        subscribe(helper.behaviors.values, () => isDirty = true);
-        subscribe(helper.behaviors.cropParams, () => isDirty = true);
+        subscribe(helper?.behaviors.values, () => isDirty = true);
+        subscribe(helper?.behaviors.cropParams, () => isDirty = true);
 
         let resizeObserver: any = void 0;
         if (typeof ResizeObserver !== 'undefined') {
@@ -108,7 +109,9 @@ export const ScreenshotPreview = React.memo(_ScreenshotPreview, (prev, next) =>
 
 declare const ResizeObserver: any;
 
-function drawPreview(helper: ViewportScreenshotHelper, target: HTMLCanvasElement, customBackground?: string, borderColor?: string, borderWidth?: number) {
+function drawPreview(helper: ViewportScreenshotHelper | undefined, target: HTMLCanvasElement, customBackground?: string, borderColor?: string, borderWidth?: number) {
+    if (!helper) return;
+
     const { canvas, width, height } = helper.getPreview()!;
     const ctx = target.getContext('2d');
     if (!ctx) return;
@@ -151,9 +154,9 @@ function drawPreview(helper: ViewportScreenshotHelper, target: HTMLCanvasElement
 
 function ViewportFrame({ plugin, canvas, color = 'rgba(255, 87, 45, 0.75)' }: { plugin: PluginContext, canvas: HTMLCanvasElement | null, color?: string }) {
     const helper = plugin.helpers.viewportScreenshot;
-    const params = useBehavior(helper?.behaviors.values!);
-    const cropParams = useBehavior(helper?.behaviors.cropParams!);
-    const crop = useBehavior(helper?.behaviors.relativeCrop!);
+    const params = useBehavior(helper?.behaviors.values);
+    const cropParams = useBehavior(helper?.behaviors.cropParams);
+    const crop = useBehavior(helper?.behaviors.relativeCrop);
     const cropFrameRef = useRef<Viewport>({ x: 0, y: 0, width: 0, height: 0 });
     useBehavior(params?.resolution.name === 'viewport' ? plugin.canvas3d?.resized : void 0);
 
@@ -161,7 +164,7 @@ function ViewportFrame({ plugin, canvas, color = 'rgba(255, 87, 45, 0.75)' }: {
     const [start, setStart] = useState([0, 0]);
     const [current, setCurrent] = useState([0, 0]);
 
-    if (!helper || !canvas) return null;
+    if (!helper || !canvas || !crop) return null;
 
     const { width, height } = helper.getSizeAndViewport();
 
@@ -267,7 +270,7 @@ function ViewportFrame({ plugin, canvas, color = 'rgba(255, 87, 45, 0.75)' }: {
 
     function finish() {
         const cropFrame = cropFrameRef.current;
-        if (cropParams.auto) {
+        if (cropParams?.auto) {
             helper?.behaviors.cropParams.next({ ...cropParams, auto: false });
         }
         helper?.behaviors.relativeCrop.next({

src/mol-plugin-ui/left-panel.tsx

@@ -141,11 +141,13 @@ class FullSettings extends PluginUIComponent {
         this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
         this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
 
-        this.subscribe(this.plugin.canvas3d!.camera.stateChanged, state => {
-            if (state.radiusMax !== undefined || state.radius !== undefined) {
-                this.forceUpdate();
-            }
-        });
+        if (this.plugin.canvas3d) {
+            this.subscribe(this.plugin.canvas3d.camera.stateChanged, state => {
+                if (state.radiusMax !== undefined || state.radius !== undefined) {
+                    this.forceUpdate();
+                }
+            });
+        }
     }
 
     render() {

src/mol-plugin-ui/structure/measurements.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
@@ -288,7 +288,12 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
         for (const loci of this.lociArray) {
             this.plugin.managers.interactivity.lociHighlights.highlight({ loci }, false);
         }
-        this.plugin.managers.interactivity.lociHighlights.highlight({ loci: this.props.cell.obj?.data.repr.getLoci()! }, false);
+        const reprLocis = this.props.cell.obj?.data.repr.getAllLoci();
+        if (reprLocis) {
+            for (const loci of reprLocis) {
+                this.plugin.managers.interactivity.lociHighlights.highlight({ loci }, false);
+            }
+        }
     };
 
     clearHighlight = () => {

src/mol-plugin-ui/viewport/canvas.tsx

@@ -59,7 +59,7 @@ export class ViewportCanvas extends PluginUIComponent<ViewportCanvasParams, View
         return <div className='msp-no-webgl'>
             <div>
                 <p><b>WebGL does not seem to be available.</b></p>
-                <p>This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps.</p>
+                <p>This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps. Also, make sure hardware acceleration is enabled in your browser.</p>
                 <p>For a list of supported browsers, refer to <a href='http://caniuse.com/#feat=webgl' target='_blank'>http://caniuse.com/#feat=webgl</a>.</p>
             </div>
         </div>;

src/mol-plugin-ui/viewport/screenshot.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 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>
@@ -96,18 +96,21 @@ export class DownloadScreenshotControls extends PluginUIComponent<{ close: () =>
 }
 
 function ScreenshotParams({ plugin, isDisabled }: { plugin: PluginContext, isDisabled: boolean }) {
-    const helper = plugin.helpers.viewportScreenshot!;
-    const values = useBehavior(helper.behaviors.values);
+    const helper = plugin.helpers.viewportScreenshot;
+
+    const values = useBehavior(helper?.behaviors.values);
+    if (!helper) return null;
 
     return <ParameterControls params={helper.params} values={values} onChangeValues={v => helper.behaviors.values.next(v)} isDisabled={isDisabled} />;
 }
 
 function CropControls({ plugin }: { plugin: PluginContext }) {
     const helper = plugin.helpers.viewportScreenshot;
-    const cropParams = useBehavior(helper?.behaviors.cropParams!);
+
+    const cropParams = useBehavior(helper?.behaviors.cropParams);
     useBehavior(helper?.behaviors.relativeCrop);
 
-    if (!helper) return null;
+    if (!helper || !cropParams) return null;
 
     return <div style={{ width: '100%', height: '24px', marginTop: '8px' }}>
         <ToggleButton icon={CropOrginalSvg} title='Auto-crop' inline isSelected={cropParams.auto}

src/mol-plugin-ui/viewport/simple-settings.tsx

@@ -22,6 +22,8 @@ import { ViewportHelpContent } from './help';
 
 export class SimpleSettingsControl extends PluginUIComponent {
     componentDidMount() {
+        if (!this.plugin.canvas3d) return;
+
         this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
 
         this.subscribe(this.plugin.canvas3d!.camera.stateChanged, state => {

src/mol-plugin/behavior/behavior.ts

@@ -40,7 +40,7 @@ namespace PluginBehavior {
         'misc': 'Miscellaneous'
     };
 
-    export interface CreateParams<P> {
+    export interface CreateParams<P extends {}> {
         name: string,
         category: keyof typeof Categories,
         ctor: Ctor<P>,
@@ -73,7 +73,7 @@ namespace PluginBehavior {
         return categoryMap.get(t.id)!;
     }
 
-    export function create<P>(params: CreateParams<P>) {
+    export function create<P extends {}>(params: CreateParams<P>) {
         const t = PluginStateTransform.CreateBuiltIn<Category, Behavior, P>({
             name: params.name,
             display: params.display,
@@ -113,7 +113,7 @@ namespace PluginBehavior {
         };
     }
 
-    export abstract class Handler<P = { }> implements PluginBehavior<P> {
+    export abstract class Handler<P extends {} = {}> implements PluginBehavior<P> {
         private subs: PluginCommand.Subscription[] = [];
         protected subscribeCommand<T>(cmd: PluginCommand<T>, action: PluginCommand.Action<T>) {
             this.subs.push(cmd.subscribe(this.ctx, action));

src/mol-plugin/behavior/static/state.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -119,7 +119,9 @@ export function Highlight(ctx: PluginContext) {
                 ctx.managers.interactivity.lociHighlights.highlight({ loci: Structure.Loci(cell.obj.data) }, false);
             } else if (cell && SO.isRepresentation3D(cell.obj)) {
                 const { repr } = cell.obj.data;
-                ctx.managers.interactivity.lociHighlights.highlight({ loci: repr.getLoci(), repr }, false);
+                for (const loci of repr.getAllLoci()) {
+                    ctx.managers.interactivity.lociHighlights.highlight({ loci, repr }, false);
+                }
             } else if (SO.Molecule.Structure.Selections.is(cell.obj)) {
                 for (const entry of cell.obj.data) {
                     ctx.managers.interactivity.lociHighlights.highlight({ loci: entry.loci }, false);

src/mol-plugin/config.ts

@@ -35,6 +35,7 @@ export const PluginConfig = {
         // as of Oct 1 2021, WebGL 2 doesn't work on iOS 15.
         // TODO: check back in a few weeks to see if it was fixed
         PreferWebGl1: item('plugin-config.prefer-webgl1', PluginFeatureDetection.preferWebGl1),
+        AllowMajorPerformanceCaveat: item('plugin-config.allow-major-performance-caveat', false),
     },
     State: {
         DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),

src/mol-plugin/context.ts

@@ -201,7 +201,8 @@ export class PluginContext {
                 const pickPadding = this.config.get(PluginConfig.General.PickPadding) ?? 1;
                 const enableWboit = this.config.get(PluginConfig.General.EnableWboit) || false;
                 const preferWebGl1 = this.config.get(PluginConfig.General.PreferWebGl1) || false;
-                (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, this.managers.asset, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit, preferWebGl1 });
+                const failIfMajorPerformanceCaveat = !(this.config.get(PluginConfig.General.AllowMajorPerformanceCaveat) ?? false);
+                (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, this.managers.asset, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit, preferWebGl1, failIfMajorPerformanceCaveat });
             }
             (this.canvas3d as Canvas3D) = Canvas3D.create(this.canvas3dContext!);
             this.canvas3dInit.next(true);

src/mol-repr/representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -154,8 +154,8 @@ interface Representation<D, P extends PD.Params = {}, S extends Representation.S
     createOrUpdate: (props?: Partial<PD.Values<P>>, data?: D) => Task<void>
     setState: (state: Partial<S>) => void
     setTheme: (theme: Theme) => void
-    /** If no pickingId is given, returns a Loci for the whole representation */
-    getLoci: (pickingId?: PickingId) => ModelLoci
+    getLoci: (pickingId: PickingId) => ModelLoci
+    getAllLoci: () => ModelLoci[]
     mark: (loci: ModelLoci, action: MarkerAction) => boolean
     destroy: () => void
 }
@@ -227,6 +227,7 @@ namespace Representation {
         setState: () => {},
         setTheme: () => {},
         getLoci: () => EmptyLoci,
+        getAllLoci: () => [],
         mark: () => false,
         destroy: () => {}
     };
@@ -327,7 +328,7 @@ namespace Representation {
             },
             get state() { return currentState; },
             get theme() { return currentTheme; },
-            getLoci: (pickingId?: PickingId) => {
+            getLoci: (pickingId: PickingId) => {
                 const { visuals } = currentProps;
                 for (let i = 0, il = reprList.length; i < il; ++i) {
                     if (!visuals || visuals.includes(reprMap[i])) {
@@ -337,6 +338,16 @@ namespace Representation {
                 }
                 return EmptyLoci;
             },
+            getAllLoci: () => {
+                const loci: ModelLoci[] = [];
+                const { visuals } = currentProps;
+                for (let i = 0, il = reprList.length; i < il; ++i) {
+                    if (!visuals || visuals.includes(reprMap[i])) {
+                        loci.push(...reprList[i].getAllLoci());
+                    }
+                }
+                return loci;
+            },
             mark: (loci: ModelLoci, action: MarkerAction) => {
                 let marked = false;
                 for (let i = 0, il = reprList.length; i < il; ++i) {
@@ -399,6 +410,10 @@ namespace Representation {
                 // TODO
                 return EmptyLoci;
             },
+            getAllLoci: () => {
+                // TODO
+                return [];
+            },
             mark: (loci: ModelLoci, action: MarkerAction) => {
                 // TODO
                 return false;

src/mol-repr/shape/representation.ts

@@ -213,14 +213,16 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
         get geometryVersion() { return geometryVersion; },
         updated,
         createOrUpdate,
-        getLoci(pickingId?: PickingId) {
-            if (pickingId === undefined) return Shape.Loci(_shape);
+        getLoci(pickingId: PickingId) {
             const { objectId, groupId, instanceId } = pickingId;
             if (_renderObject && _renderObject.id === objectId) {
                 return ShapeGroup.Loci(_shape, [{ ids: OrderedSet.ofSingleton(groupId), instance: instanceId }]);
             }
             return EmptyLoci;
         },
+        getAllLoci() {
+            return [Shape.Loci(_shape)];
+        },
         mark(loci: Loci, action: MarkerAction) {
             if (!MarkerActions.is(_state.markerActions, action)) return false;
             if (ShapeGroup.isLoci(loci) || Shape.isLoci(loci)) {

src/mol-repr/structure/complex-representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -72,11 +72,14 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
         });
     }
 
-    function getLoci(pickingId?: PickingId) {
-        if (pickingId === undefined) return Structure.Loci(_structure.target);
+    function getLoci(pickingId: PickingId) {
         return visual ? visual.getLoci(pickingId) : EmptyLoci;
     }
 
+    function getAllLoci() {
+        return [Structure.Loci(_structure.target)];
+    }
+
     function mark(loci: Loci, action: MarkerAction) {
         if (!_structure) return false;
         if (!MarkerActions.is(_state.markerActions, action)) return false;
@@ -157,6 +160,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
         setState,
         setTheme,
         getLoci,
+        getAllLoci,
         mark,
         destroy
     };

src/mol-repr/structure/units-representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -185,8 +185,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
         });
     }
 
-    function getLoci(pickingId?: PickingId) {
-        if (pickingId === undefined) return Structure.Loci(_structure.target);
+    function getLoci(pickingId: PickingId) {
         let loci: Loci = EmptyLoci;
         visuals.forEach(({ visual }) => {
             const _loci = visual.getLoci(pickingId);
@@ -195,6 +194,10 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
         return loci;
     }
 
+    function getAllLoci() {
+        return [Structure.Loci(_structure.target)];
+    }
+
     function mark(loci: Loci, action: MarkerAction) {
         if (!_structure) return false;
         if (!MarkerActions.is(_state.markerActions, action)) return false;
@@ -302,6 +305,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
         setState,
         setTheme,
         getLoci,
+        getAllLoci,
         mark,
         destroy
     };

src/mol-repr/volume/representation.ts

@@ -358,10 +358,12 @@ export function VolumeRepresentation<P extends VolumeParams>(label: string, ctx:
         createOrUpdate,
         setState,
         setTheme,
-        getLoci: (pickingId?: PickingId): Loci => {
-            if (pickingId === undefined) return getLoci(_volume, _props);
+        getLoci: (pickingId: PickingId): Loci => {
             return visual ? visual.getLoci(pickingId) : EmptyLoci;
         },
+        getAllLoci: (): Loci[] => {
+            return [getLoci(_volume, _props)];
+        },
         mark,
         destroy
     };

src/mol-script/language/symbol-table/structure-query.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -333,6 +333,7 @@ const bondProperty = {
 
     flags: bondProp(Types.BondFlags),
     order: bondProp(Type.Num),
+    key: bondProp(Type.Num),
     length: bondProp(Type.Num),
     atomA: bondProp(Types.ElementReference),
     atomB: bondProp(Types.ElementReference)
@@ -356,5 +357,5 @@ export const structureQuery = {
     combinator,
     atomSet,
     atomProperty,
-    bondProperty: bondProperty
+    bondProperty
 };

src/mol-script/runtime/query/table.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -211,21 +211,21 @@ const symbols = [
     // ============= FILTERS ================
     D(MolScript.structureQuery.filter.pick, (ctx, xs) => Queries.filters.pick(xs[0] as any, xs['test'])(ctx)),
     D(MolScript.structureQuery.filter.first, (ctx, xs) => Queries.filters.first(xs[0] as any)(ctx)),
-    D(MolScript.structureQuery.filter.withSameAtomProperties, (ctx, xs) => Queries.filters.withSameAtomProperties(xs[0] as any, xs['source'] as any, xs['property'] as any)(ctx)),
+    D(MolScript.structureQuery.filter.withSameAtomProperties, (ctx, xs) => Queries.filters.withSameAtomProperties(xs[0] as any, xs['source'] as any, xs['property'])(ctx)),
     D(MolScript.structureQuery.filter.intersectedBy, (ctx, xs) => Queries.filters.areIntersectedBy(xs[0] as any, xs['by'] as any)(ctx)),
     D(MolScript.structureQuery.filter.within, (ctx, xs) => Queries.filters.within({
         query: xs[0] as any,
         target: xs['target'] as any,
-        minRadius: xs['min-radius'] as any,
-        maxRadius: xs['max-radius'] as any,
+        minRadius: xs['min-radius']?.(ctx) as any,
+        maxRadius: xs['max-radius']?.(ctx) as any,
         elementRadius: xs['atom-radius'] as any,
-        invert: xs['invert'] as any
+        invert: xs['invert']?.(ctx) as any
     })(ctx)),
     D(MolScript.structureQuery.filter.isConnectedTo, (ctx, xs) => Queries.filters.isConnectedTo({
         query: xs[0] as any,
         target: xs['target'] as any,
-        disjunct: xs['disjunct'] as any,
-        invert: xs['invert'] as any,
+        disjunct: xs['disjunct']?.(ctx) as any,
+        invert: xs['invert']?.(ctx) as any,
         bondTest: xs['bond-test']
     })(ctx)),
 
@@ -248,6 +248,9 @@ const symbols = [
     D(MolScript.structureQuery.generator.rings, function structureQuery_generator_rings(ctx, xs) {
         return Queries.generators.rings(xs?.['fingerprint']?.(ctx) as any, xs?.['only-aromatic']?.(ctx))(ctx);
     }),
+    D(MolScript.structureQuery.generator.queryInSelection, function structureQuery_generator_queryInSelection(ctx, xs) {
+        return Queries.generators.querySelection(xs[0] as any, xs['query'] as any, xs['in-complement']?.(ctx) as any)(ctx);
+    }),
 
     // ============= MODIFIERS ================
 
@@ -278,6 +281,7 @@ const symbols = [
             fixedPoint: xs['fixed-point']?.(ctx) ?? false
         })(ctx);
     }),
+    D(MolScript.structureQuery.modifier.intersectBy, function structureQuery_modifier_intersectBy(ctx, xs) { return Queries.modifiers.intersectBy(xs[0] as any, xs['by'] as any)(ctx); }),
 
     // ============= COMBINATORS ================
 
@@ -353,9 +357,27 @@ const symbols = [
     D(MolScript.structureQuery.atomProperty.macromolecular.secondaryStructureFlags, atomProp(StructureProperties.residue.secondary_structure_type)),
     D(MolScript.structureQuery.atomProperty.macromolecular.chemCompType, atomProp(StructureProperties.residue.chem_comp_type)),
 
+    // ============= ATOM SET ================
+
+    D(MolScript.structureQuery.atomSet.atomCount,
+        function structureQuery_atomset_atomCount(ctx, xs) {
+	    return Queries.atomset.atomCount(ctx);
+        }),
+
+    D(MolScript.structureQuery.atomSet.countQuery,
+        function structureQuery_atomset_countQuery(ctx, xs) {
+	    return Queries.atomset.countQuery(xs[0] as any)(ctx);
+        }),
+
+    D(MolScript.structureQuery.atomSet.propertySet,
+        function structureQuery_atomset_propertySet(ctx, xs) {
+	  return Queries.atomset.propertySet(xs[0] as any)(ctx);
+        }),
+
     // ============= BOND PROPERTIES ================
     D(MolScript.structureQuery.bondProperty.order, (ctx, xs) => ctx.atomicBond.order),
     D(MolScript.structureQuery.bondProperty.flags, (ctx, xs) => ctx.atomicBond.type),
+    D(MolScript.structureQuery.bondProperty.key, (ctx, xs) => ctx.atomicBond.key),
     D(MolScript.structureQuery.bondProperty.atomA, (ctx, xs) => ctx.atomicBond.a),
     D(MolScript.structureQuery.bondProperty.atomB, (ctx, xs) => ctx.atomicBond.b),
     D(MolScript.structureQuery.bondProperty.length, (ctx, xs) => ctx.atomicBond.length),
@@ -406,4 +428,4 @@ function getArray<T = any>(ctx: QueryContext, xs: any): T[] {
     for (const s of symbols) {
         DefaultQueryRuntimeTable.addSymbol(s);
     }
-})();
+})();

src/mol-script/script.ts

@@ -6,10 +6,12 @@
 
 import { transpileMolScript } from './script/mol-script/symbols';
 import { parseMolScript } from './language/parser';
+import { parse } from './transpile';
 import { Expression } from './language/expression';
 import { StructureElement, QueryContext, StructureSelection, Structure, QueryFn, QueryContextOptions } from '../mol-model/structure';
 import { compile } from './runtime/query/compiler';
 import { MolScriptBuilder } from './language/builder';
+import { assertUnreachable } from '../mol-util/type-helpers';
 
 export { Script };
 
@@ -20,7 +22,13 @@ function Script(expression: string, language: Script.Language): Script {
 }
 
 namespace Script {
-    export type Language = 'mol-script'
+    export const Info = {
+        'mol-script': 'Mol-Script',
+        'pymol': 'PyMOL',
+        'vmd': 'VMD',
+        'jmol': 'Jmol',
+    };
+    export type Language = keyof typeof Info;
 
     export function is(x: any): x is Script {
         return !!x && typeof (x as Script).expression === 'string' && !!(x as Script).language;
@@ -36,8 +44,13 @@ namespace Script {
                 const parsed = parseMolScript(script.expression);
                 if (parsed.length === 0) throw new Error('No query');
                 return transpileMolScript(parsed[0]);
+            case 'pymol':
+            case 'jmol':
+            case 'vmd':
+                return parse(script.language, script.expression);
+            default:
+                assertUnreachable(script.language);
         }
-        throw new Error('unsupported script language');
     }
 
     export function toQuery(script: Script): QueryFn<StructureSelection> {
@@ -56,4 +69,4 @@ namespace Script {
         const query = compile<StructureSelection>(e);
         return query(new QueryContext(structure, options));
     }
-}
+}

src/mol-script/transpile.ts

@@ -0,0 +1,27 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ *
+ * Adapted from MolQL src/transpile.ts
+ */
+
+import { Transpiler } from './transpilers/transpiler';
+import { _transpiler } from './transpilers/all';
+import { Expression } from './language/expression';
+import { Script } from './script';
+const transpiler: {[index: string]: Transpiler} = _transpiler;
+
+export function parse(lang: Script.Language, str: string): Expression {
+    try {
+
+        const query = transpiler[lang](str);
+        return query;
+
+    } catch (e) {
+
+        console.error(e.message);
+        throw e;
+
+    }
+}

src/mol-script/transpilers/_spec/examples.spec.ts

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ * Adapted from MolQL project
+**/
+
+import { Transpiler } from '../transpiler';
+import { _transpiler as transpilers } from '../all';
+
+function testTranspilerExamples(name: string, transpiler: Transpiler) {
+    describe(`${name} examples`, () => {
+        const examples = require(`../${name}/examples`).examples;
+        //        console.log(examples);
+        for (const e of examples) {
+
+            it(e.name, () => {
+                // check if it transpiles and compiles/typechecks.
+                transpiler(e.value);
+            });
+        }
+    });
+}
+
+testTranspilerExamples('pymol', transpilers.pymol);
+testTranspilerExamples('vmd', transpilers.vmd);
+testTranspilerExamples('jmol', transpilers.jmol);

src/mol-script/transpilers/_spec/jmol.spec.ts

@@ -0,0 +1,115 @@
+/**
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as u from './utils';
+import { transpiler } from '../jmol/parser';
+import { keywords } from '../jmol/keywords';
+import { properties } from '../jmol/properties';
+import { operators } from '../jmol/operators';
+
+const general = {
+    supported: [
+        // atom expressions
+        '123',
+        '-42',
+        '_C',
+        '.CA',
+        'ALA',
+        '%A',
+        '^B',
+        ':C',
+        '/2',
+        '10^A:F.CA%C/0',
+        '10^A:F.CA%C',
+        '10^A:F.CA',
+        '10^A:F',
+        '10^A',
+        '10:F.CA',
+        '10/0',
+        '32 or 42',
+        '.CA/0 OR 42:A',
+        '!23',
+        'not ASP',
+        '(ASP or .CA)',
+        'ASP and .CA',
+        '123.CA',
+        '(1 or 2) and .CA',
+        '(1 or 2) and (.CA or .N)',
+        '.CA and (2 or 3)',
+        '.CA and (2 or 3) and ^A',
+        '!32 or :A and .CA',
+
+        // trimming
+        '    atomName = CA   ',
+        'atomName = CA   ',
+        '    atomName = CA',
+
+        // value comparison
+        'resno > 10',
+        // atom expression
+        '[LEU]100:A.CA',
+        '[LEU]100:A',
+        '[LEU]100.CA',
+        '[LEU]:A.CA',
+        '[LEU].CA',
+        // comma as OR
+        '100, 42, ALA',
+        // residue numbering
+        '(1-10,15,21-30)',
+        // within
+        'within(5,[HEM])',
+        // within with parentheses
+        '(within(5,[HEM])) and backbone',
+        '( within(5,[HEM]) ) and backbone',
+        // trimming
+        '[ALA] and [VAL]  ',
+        ' [ALA] and [VAL] ',
+        '  [ALA] and [VAL]',
+        // within with whitespaces
+        'within (   5 ,  [HEM] ) ',
+        // un-braketed residue name
+        'LEU and ILE',
+        // un-parenthesized residue index range
+        '100-120,220',
+        // un-parenthesized residue index
+        '20',
+        // within in the head or the middle of sentence
+        'within (   5 ,  [HEM] ) and backbone',
+
+        // atom expressions with ranges
+        '19-32:A',
+        '-2-32:B',
+        '-10--2:C',
+        '[1FO]19-32:A',
+    ],
+    unsupported: [
+        // values outside of comparisons
+        'foobar',
+        'protein or foobar',
+    ]
+};
+
+describe('jmol general', () => {
+    general.supported.forEach(str => {
+        it(str, () => {
+            transpiler(str);
+        });
+    });
+    general.unsupported.forEach(str => {
+        it(str, () => {
+            const transpileStr = () => transpiler(str);
+            expect(transpileStr).toThrow();
+            expect(transpileStr).not.toThrowError(RangeError);
+        });
+    });
+});
+
+describe('jmol keywords', () => u.testKeywords(keywords, transpiler));
+describe('jmol properties', () => u.testProperties(properties, transpiler));
+describe('jmol operators', () => u.testOperators(operators, transpiler));

src/mol-script/transpilers/_spec/pymol.spec.ts

@@ -0,0 +1,73 @@
+/**
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ */
+
+import * as u from './utils';
+import { transpiler } from '../pymol/parser';
+import { keywords } from '../pymol/keywords';
+import { properties } from '../pymol/properties';
+import { operators } from '../pymol/operators';
+
+const general = {
+    supported: [
+        // macros
+        '10/cb',
+        'a/10-12/ca',
+        'lig/b/6+8/c+o',
+
+        // trimming
+        '    name CA   ',
+        'name CA   ',
+        '    name CA',
+    ],
+    unsupported: [
+        // macros
+        'pept/enz/c/3/n',
+        'pept/enz///n',
+
+        '/pept/lig/',
+        '/pept/lig/a',
+        '/pept/lig/a/10',
+        '/pept/lig/a/10/ca',
+        '/pept//a/10',
+
+        // object
+        'foobar',
+        'protein and bazbar',
+    ]
+};
+
+describe('pymol general', () => {
+    general.supported.forEach(str => {
+        it(str, () => {
+            transpiler(str);
+            //          compile(expr);
+        });
+    });
+    general.unsupported.forEach(str => {
+        it(str, () => {
+            const transpileStr = () => transpiler(str);
+            expect(transpileStr).toThrow();
+            expect(transpileStr).not.toThrowError(RangeError);
+        });
+    });
+});
+
+// check against builder output
+// 'not (resi 42 or chain A)'
+// '!resi 42 or chain A'
+// 'b >= 0.3',
+// 'b != 0.3',
+// 'b>0.3',
+// 'b <0.3',
+// 'b <= 0.3',
+// 'b = 1',
+// 'fc.=.1',
+
+describe('pymol keywords', () => u.testKeywords(keywords, transpiler));
+describe('pymol operators', () => u.testOperators(operators, transpiler));
+describe('pymol properties', () => u.testProperties(properties, transpiler));

src/mol-script/transpilers/_spec/utils.ts

@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panangiot_tourlov@hotmail.com>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ */
+
+import { Transpiler } from '../transpiler';
+import { KeywordDict, PropertyDict, OperatorList } from '../types';
+
+export function testKeywords(keywords: KeywordDict, transpiler: Transpiler) {
+    for (const name in keywords) {
+        it(name, () => {
+            const k = keywords[name];
+            if (k.map) {
+                const expr = transpiler(name);
+                expect(expr).toEqual(k.map());
+            } else {
+                const transpile = () => transpiler(name);
+                expect(transpile).toThrow();
+                expect(transpile).not.toThrowError(RangeError);
+            }
+        });
+    }
+}
+
+export function testProperties(properties: PropertyDict, transpiler: Transpiler) {
+    for (const name in properties) {
+        const p = properties[name];
+        p['@examples'].forEach(example => {
+            it(name, () => {
+                if (!p.isUnsupported) {
+                    transpiler(example);
+                } else {
+                    const transpile = () => transpiler(example);
+                    expect(transpile).toThrow();
+                    expect(transpile).not.toThrowError(RangeError);
+                }
+            });
+        });
+        it(name, () => {
+            if (!p['@examples'].length) {
+                throw Error(`'${name}' property has no example(s)`);
+            }
+        });
+    }
+}
+
+export function testOperators(operators: OperatorList, transpiler: Transpiler) {
+    operators.forEach(o => {
+        o['@examples'].forEach(example => {
+            it(o.name, () => {
+                if (!o.isUnsupported) {
+                    transpiler(example);
+                } else {
+                    const transpile = () => transpiler(example);
+                    expect(transpile).toThrow();
+                    expect(transpile).not.toThrowError(RangeError);
+                }
+            });
+        });
+        it(o.name, () => {
+            if (!o['@examples'].length) {
+                throw Error(`'${o.name}' operator has no example(s)`);
+            }
+        });
+    });
+}

src/mol-script/transpilers/_spec/vmd.spec.ts

@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ */
+
+import * as u from './utils';
+import { transpiler } from '../vmd/parser';
+import { keywords } from '../vmd/keywords';
+import { properties } from '../vmd/properties';
+import { operators } from '../vmd/operators';
+
+const general = {
+    supported: [
+        // trimming
+        '    name CA   ',
+        'name CA   ',
+        '    name CA',
+    ],
+    unsupported: [
+        // variables
+        'name $atomname',
+        'protein and @myselection',
+
+        // values outside of comparisons
+        'foobar',
+        '34',
+        'name',
+        'abs(-42)',
+        'abs(21+21)',
+        'sqr(3)',
+        'sqr(x)',
+        'sqr(x+33)',
+        'protein or foobar',
+        '34 and protein',
+        'name or protein',
+    ]
+};
+
+describe('vmd general', () => {
+    general.supported.forEach(str => {
+        it(str, () => {
+            transpiler(str);
+            // compile(expr);
+        });
+    });
+    general.unsupported.forEach(str => {
+        it(str, () => {
+            const transpileStr = () => transpiler(str);
+            expect(transpileStr).toThrow();
+            expect(transpileStr).not.toThrowError(RangeError);
+        });
+    });
+});
+
+describe('vmd keywords', () => u.testKeywords(keywords, transpiler));
+describe('vmd operators', () => u.testOperators(operators, transpiler));
+describe('vmd properties', () => u.testProperties(properties, transpiler));

src/mol-script/transpilers/all.ts

@@ -0,0 +1,17 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { transpiler as jmol } from './jmol/parser';
+import { transpiler as pymol } from './pymol/parser';
+import { transpiler as vmd } from './vmd/parser';
+
+export const _transpiler = {
+    pymol,
+    vmd,
+    jmol,
+};

src/mol-script/transpilers/helper.ts

@@ -0,0 +1,385 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../mol-util/monadic-parser';
+import { MolScriptBuilder } from '../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { Expression } from '../language/expression';
+import { KeywordDict, PropertyDict, FunctionDict, OperatorList } from './types';
+
+export function escapeRegExp(s: String) {
+    return String(s).replace(/[\\^$*+?.()|[\]{}]/g, '\\$&');
+}
+
+// Takes a parser for the prefix operator, and a parser for the base thing being
+// parsed, and parses as many occurrences as possible of the prefix operator.
+// Note that the parser is created using `P.lazy` because it's recursive. It's
+// valid for there to be zero occurrences of the prefix operator.
+export function prefix(opParser: P.MonadicParser<any>, nextParser: P.MonadicParser<any>, mapFn: any) {
+    const parser: P.MonadicParser<any> = P.MonadicParser.lazy(() => {
+        return P.MonadicParser.seq(opParser, parser)
+            .map(x => mapFn(...x))
+            .or(nextParser);
+    });
+    return parser;
+}
+
+// Ideally this function would be just like `PREFIX` but reordered like
+// `P.seq(parser, opParser).or(nextParser)`, but that doesn't work. The
+// reason for that is that Parsimmon will get stuck in infinite recursion, since
+// the very first rule. Inside `parser` is to match parser again. Alternatively,
+// you might think to try `nextParser.or(P.seq(parser, opParser))`, but
+// that won't work either because in a call to `.or` (aka `P.alt`), Parsimmon
+// takes the first possible match, even if subsequent matches are longer, so the
+// parser will never actually look far enough ahead to see the postfix
+// operators.
+export function postfix(opParser: P.MonadicParser<any>, nextParser: P.MonadicParser<any>, mapFn: any) {
+    // Because we can't use recursion like stated above, we just match a flat list
+    // of as many occurrences of the postfix operator as possible, then use
+    // `.reduce` to manually nest the list.
+    //
+    // Example:
+    //
+    // INPUT  :: "4!!!"
+    // PARSE  :: [4, "factorial", "factorial", "factorial"]
+    // REDUCE :: ["factorial", ["factorial", ["factorial", 4]]]
+    return P.MonadicParser.seqMap(
+        nextParser,
+        opParser.many(),
+        (x: any, suffixes: any) =>
+            suffixes.reduce((acc: any, x: any) => {
+                return mapFn(x, acc);
+            }, x)
+    );
+}
+
+// Takes a parser for all the operators at this precedence level, and a parser
+// that parsers everything at the next precedence level, and returns a parser
+// that parses as many binary operations as possible, associating them to the
+// right. (e.g. 1^2^3 is 1^(2^3) not (1^2)^3)
+export function binaryRight(opParser: P.MonadicParser<any>, nextParser: P.MonadicParser<any>, mapFn: any) {
+    const parser: P.MonadicParser<any> = P.MonadicParser.lazy(() =>
+        nextParser.chain(next =>
+            P.MonadicParser.seq(
+                opParser,
+                P.MonadicParser.of(next),
+                parser
+            ).map((x) => {
+                return x;
+            }).or(P.MonadicParser.of(next))
+        )
+    );
+    return parser;
+}
+
+// Takes a parser for all the operators at this precedence level, and a parser
+// that parsers everything at the next precedence level, and returns a parser
+// that parses as many binary operations as possible, associating them to the
+// left. (e.g. 1-2-3 is (1-2)-3 not 1-(2-3))
+export function binaryLeft(opParser: P.MonadicParser<any>, nextParser: P.MonadicParser<any>, mapFn: any) {
+    // We run into a similar problem as with the `POSTFIX` parser above where we
+    // can't recurse in the direction we want, so we have to resort to parsing an
+    // entire list of operator chunks and then using `.reduce` to manually nest
+    // them again.
+    //
+    // Example:
+    //
+    // INPUT  :: "1+2+3"
+    // PARSE  :: [1, ["+", 2], ["+", 3]]
+    // REDUCE :: ["+", ["+", 1, 2], 3]
+    return P.MonadicParser.seqMap(
+        nextParser,
+        P.MonadicParser.seq(opParser, nextParser).many(),
+        (first: any, rest: any) => {
+            return rest.reduce((acc: any, ch: any) => {
+                const [op, another] = ch;
+                return mapFn(op, acc, another);
+            }, first);
+        }
+    );
+}
+
+/**
+ * combine operators of decreasing binding strength
+ */
+export function combineOperators(opList: any[], rule: P.MonadicParser<any>) {
+    const x = opList.reduce(
+        (acc, level) => {
+            const map = level.isUnsupported ? makeError(`operator '${level.name}' not supported`) : level.map;
+            return level.type(level.rule, acc, map);
+        },
+        rule
+    );
+    return x;
+}
+
+export function infixOp(re: RegExp, group: number = 0) {
+    return P.MonadicParser.optWhitespace.then(P.MonadicParser.regexp(re, group).skip(P.MonadicParser.optWhitespace));
+}
+
+export function prefixOp(re: RegExp, group: number = 0) {
+    return P.MonadicParser.regexp(re, group).skip(P.MonadicParser.optWhitespace);
+}
+
+export function postfixOp(re: RegExp, group: number = 0) {
+    return P.MonadicParser.optWhitespace.then(P.MonadicParser.regexp(re, group));
+}
+
+export function ofOp(name: string, short?: string) {
+    const op = short ? `${name}|${escapeRegExp(short)}` : name;
+    const re = RegExp(`(${op})\\s+([-+]?[0-9]*\\.?[0-9]+)\\s+OF`, 'i');
+    return infixOp(re, 2).map(parseFloat);
+}
+
+export function makeError(msg: string) {
+    return function () {
+        throw new Error(msg);
+    };
+}
+
+export function andExpr(selections: any[]) {
+    if (selections.length === 1) {
+        return selections[0];
+    } else if (selections.length > 1) {
+        return B.core.logic.and(selections);
+    } else {
+        return undefined;
+    }
+}
+
+export function orExpr(selections: any[]) {
+    if (selections.length === 1) {
+        return selections[0];
+    } else if (selections.length > 1) {
+        return B.core.logic.or(selections);
+    } else {
+        return undefined;
+    }
+}
+
+export function testExpr(property: any, args: any) {
+    if (args && args.op !== undefined && args.val !== undefined) {
+        const opArgs = [property, args.val];
+        switch (args.op) {
+            case '=': return B.core.rel.eq(opArgs);
+            case '!=': return B.core.rel.neq(opArgs);
+            case '>': return B.core.rel.gr(opArgs);
+            case '<': return B.core.rel.lt(opArgs);
+            case '>=': return B.core.rel.gre(opArgs);
+            case '<=': return B.core.rel.lte(opArgs);
+            default: throw new Error(`operator '${args.op}' not supported`);
+        }
+    } else if (args && args.flags !== undefined) {
+        return B.core.flags.hasAny([property, args.flags]);
+    } else if (args && args.min !== undefined && args.max !== undefined) {
+        return B.core.rel.inRange([property, args.min, args.max]);
+    } else if (!Array.isArray(args)) {
+        return B.core.rel.eq([property, args]);
+    } else if (args.length > 1) {
+        return B.core.set.has([B.core.type.set(args), property]);
+    } else {
+        return B.core.rel.eq([property, args[0]]);
+    }
+}
+
+export function invertExpr(selection: Expression) {
+    return B.struct.generator.queryInSelection({
+        0: selection, query: B.struct.generator.all(), 'in-complement': true }
+    );
+}
+
+export function strLenSortFn(a: string, b: string) {
+    return a.length < b.length ? 1 : -1;
+}
+
+function getNamesRegex(name: string, abbr?: string[]) {
+    const names = (abbr ? [name].concat(abbr) : [name])
+        .sort(strLenSortFn).map(escapeRegExp).join('|');
+    return RegExp(`${names}`, 'i');
+}
+
+export function getPropertyRules(properties: PropertyDict) {
+    // in keyof typeof properties
+    const propertiesDict: { [name: string]: P.MonadicParser<any> } = {};
+
+    Object.keys(properties).sort(strLenSortFn).forEach(name => {
+        const ps = properties[name];
+        const errorFn = makeError(`property '${name}' not supported`);
+        const rule = P.MonadicParser.regexp(ps.regex).map((x: any) => {
+            if (ps.isUnsupported) errorFn();
+            return testExpr(ps.property, ps.map(x));
+        });
+
+        if (!ps.isNumeric) {
+            propertiesDict[name] = rule;
+        }
+    });
+
+    return propertiesDict;
+}
+
+export function getNamedPropertyRules(properties: PropertyDict) {
+    const namedPropertiesList: P.MonadicParser<any>[] = [];
+
+    Object.keys(properties).sort(strLenSortFn).forEach(name => {
+        const ps = properties[name];
+        const errorFn = makeError(`property '${name}' not supported`);
+        const rule = P.MonadicParser.regexp(ps.regex).map((x: any) => {
+            if (ps.isUnsupported) errorFn();
+            return testExpr(ps.property, ps.map(x));
+        });
+        const nameRule = P.MonadicParser.regexp(getNamesRegex(name, ps.abbr)).trim(P.MonadicParser.optWhitespace);
+        const groupMap = (x: any) => B.struct.generator.atomGroups({ [ps.level]: x });
+
+        if (ps.isNumeric) {
+            namedPropertiesList.push(
+                nameRule.then(P.MonadicParser.seq(
+                    P.MonadicParser.regexp(/>=|<=|=|!=|>|</).trim(P.MonadicParser.optWhitespace),
+                    P.MonadicParser.regexp(ps.regex).map(ps.map)
+                )).map((x: any) => {
+                    if (ps.isUnsupported) errorFn();
+                    return testExpr(ps.property, { op: x[0], val: x[1] });
+                }).map(groupMap)
+            );
+        } else {
+            namedPropertiesList.push(nameRule.then(rule).map(groupMap));
+        }
+    });
+
+    return namedPropertiesList;
+}
+
+export function getKeywordRules(keywords: KeywordDict) {
+    const keywordsList: P.MonadicParser<any>[] = [];
+
+    Object.keys(keywords).sort(strLenSortFn).forEach(name => {
+        const ks = keywords[name];
+        const mapFn = ks.map ? ks.map : makeError(`keyword '${name}' not supported`);
+        const rule = P.MonadicParser.regexp(getNamesRegex(name, ks.abbr)).map(mapFn);
+        keywordsList.push(rule);
+    });
+
+    return keywordsList;
+}
+
+export function getFunctionRules(functions: FunctionDict, argRule: P.MonadicParser<any>) {
+    const functionsList: P.MonadicParser<any>[] = [];
+    const begRule = P.MonadicParser.regexp(/\(\s*/);
+    const endRule = P.MonadicParser.regexp(/\s*\)/);
+
+    Object.keys(functions).sort(strLenSortFn).forEach(name => {
+        const fs = functions[name];
+        const mapFn = fs.map ? fs.map : makeError(`function '${name}' not supported`);
+        const rule = P.MonadicParser.regexp(new RegExp(name, 'i')).skip(begRule).then(argRule).skip(endRule).map(mapFn);
+        functionsList.push(rule);
+    });
+
+    return functionsList;
+}
+
+export function getPropertyNameRules(properties: PropertyDict, lookahead: RegExp) {
+    const list: P.MonadicParser<any>[] = [];
+    Object.keys(properties).sort(strLenSortFn).forEach(name => {
+        const ps = properties[name];
+        const errorFn = makeError(`property '${name}' not supported`);
+        const rule = (P.MonadicParser as any).regexp(getNamesRegex(name, ps.abbr)).lookahead(lookahead).map(() => {
+            if (ps.isUnsupported) errorFn();
+            return ps.property;
+        });
+        list.push(rule);
+    });
+
+    return list;
+}
+
+export function getReservedWords(properties: PropertyDict, keywords: KeywordDict, operators: OperatorList, functions?: FunctionDict) {
+    const w: string[] = [];
+    for (const name in properties) {
+        w.push(name);
+        if (properties[name].abbr) w.push(...properties[name].abbr!);
+    }
+    for (const name in keywords) {
+        w.push(name);
+        if (keywords[name].abbr) w.push(...keywords[name].abbr!);
+    }
+    operators.forEach(o => {
+        w.push(o.name);
+        if (o.abbr) w.push(...o.abbr);
+    });
+    return w;
+}
+
+export function atomNameSet(ids: string[]) {
+    return B.core.type.set(ids.map(B.atomName));
+}
+
+export function asAtoms(e: Expression) {
+    return B.struct.generator.queryInSelection({
+        0: e,
+        query: B.struct.generator.all()
+    });
+}
+
+export function wrapValue(property: any, value: any, sstrucDict?: any) {
+    switch (property.head.name) {
+        case 'structure-query.atom-property.macromolecular.label_atom_id':
+            return B.atomName(value);
+        case 'structure-query.atom-property.core.element-symbol':
+            return B.es(value);
+        case 'structure-query.atom-property.macromolecular.secondary-structure-flags':
+            if (sstrucDict) {
+                value = [sstrucDict[value.toUpperCase()] || 'none'];
+            }
+            return B.struct.type.secondaryStructureFlags([value]);
+        default:
+            return value;
+    }
+}
+
+const propPrefix = 'structure-query.atom-property.macromolecular.';
+const entityProps = ['entityKey', 'label_entity_id', 'entityType'];
+const chainProps = ['chainKey', 'label_asym_id', 'label_entity_id', 'auth_asym_id', 'entityType'];
+const residueProps = ['residueKey', 'label_comp_id', 'label_seq_id', 'auth_comp_id', 'auth_seq_id', 'pdbx_formal_charge', 'secondaryStructureKey', 'secondaryStructureFlags', 'isModified', 'modifiedParentName'];
+export function testLevel(property: any) {
+    if (property.head.name.startsWith(propPrefix)) {
+        const name = property.head.name.substr(propPrefix.length);
+        if (entityProps.includes(name)) return 'entity-test';
+        if (chainProps.includes(name)) return 'chain-test';
+        if (residueProps.includes(name)) return 'residue-test';
+    }
+    return 'atom-test';
+}
+
+const flagProps = [
+    'structure-query.atom-property.macromolecular.secondary-structure-flags'
+];
+export function valuesTest(property: any, values: any[]) {
+    if (flagProps.includes(property.head.name)) {
+        const name = values[0].head;
+        const flags: any[] = [];
+        values.forEach(v => flags.push(...v.args[0]));
+        return B.core.flags.hasAny([property, { head: name, args: flags }]);
+    } else {
+        if (values.length === 1) {
+            return B.core.rel.eq([property, values[0]]);
+        } else if (values.length > 1) {
+            return B.core.set.has([B.core.type.set(values), property]);
+        }
+    }
+}
+
+export function resnameExpr(resnameList: string[]) {
+    return B.struct.generator.atomGroups({
+        'residue-test': B.core.set.has([
+            B.core.type.set(resnameList),
+            B.ammp('label_comp_id')
+        ])
+    });
+}

src/mol-script/transpilers/jmol/examples.ts

@@ -0,0 +1,28 @@
+/**
+ * Copyright (c) 2017-2022 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>
+ *
+ * Adapted from MolQL project
+ */
+
+export const examples = [{
+    name: 'Residue 50 or 135',
+    value: '50 or 135'
+}, {
+    name: 'Atoms with no covalent bonds',
+    value: 'bondcount = 0'
+}, {
+    name: 'All 3-10 helices',
+    value: 'substructure = "helix310"'
+}, {
+    name: 'Metal atoms',
+    value: 'metal'
+}, {
+    name: 'Atoms invloved in aromatic bonds',
+    value: 'isAromatic'
+}, {
+    name: 'Pyrimidine residues',
+    value: 'pyrimidine'
+}];

src/mol-script/transpilers/jmol/keywords.ts

@@ -0,0 +1,571 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
+ * Adapted from MolQL project
+ */
+
+
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import * as h from '../helper';
+import { KeywordDict } from '../types';
+
+const ResDict = {
+    acidic: ['ASP', 'GLU'],
+    aliphatic: ['ALA', 'GLY', 'ILE', 'LEU', 'VAL'],
+    amino: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ASX', 'GLX', 'UNK'],
+    aromatic: ['HIS', 'PHE', 'TRP', 'TYR'],
+    basic: ['ARG', 'HIS', 'LYS'],
+    buried: ['ALA', 'CYS', 'ILE', 'LEU', 'MET', 'PHE', 'TRP', 'VAL'],
+    cg: ['CYT', 'C', 'GUA', 'G'],
+    cyclic: ['HIS', 'PHE', 'PRO', 'TRP', 'TYR'],
+    hydrophobic: ['ALA', 'GLY', 'ILE', 'LEU', 'MET', 'PHE', 'PRO', 'TRP', 'TYR', 'VAL'],
+    large: ['ARG', 'GLU', 'GLN', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'TRP', 'TYR'],
+    medium: ['ASN', 'ASP', 'CYS', 'PRO', 'THR', 'VAL'],
+    small: ['ALA', 'GLY', 'SER'],
+
+    nucleic: ['G', 'C', 'A', 'T', 'U', 'I', 'DG', 'DC', 'DA', 'DT', 'DU', 'DI', '+G', '+C', '+A', '+T', '+U', '+I']
+};
+
+const Backbone = {
+    nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
+        "C2'", "C1'", "O4'", "O2'"],
+    protein: ['C', 'N', 'CA']
+};
+
+function nucleicExpr() {
+    return B.struct.combinator.merge([
+        B.struct.generator.atomGroups({
+            'residue-test': B.core.set.has([
+                B.set(...ResDict.nucleic),
+                B.ammp('label_comp_id')
+            ])
+        }),
+        B.struct.filter.pick({
+            0: B.struct.generator.atomGroups({
+                'group-by': B.ammp('residueKey')
+            }),
+            test: B.core.logic.and([
+                B.core.rel.eq([B.struct.atomSet.atomCount(), 1]),
+                B.core.rel.eq([B.ammp('label_atom_id'), B.atomName('P')]),
+            ])
+        }),
+        B.struct.filter.pick({
+            0: B.struct.generator.atomGroups({
+                'group-by': B.ammp('residueKey')
+            }),
+            test: B.core.logic.or([
+                B.core.set.isSubset([
+                    h.atomNameSet(["C1'", "C2'", "O3'", "C3'", "C4'", "C5'", "O5'"]),
+                    B.ammpSet('label_atom_id')
+                ]),
+                B.core.set.isSubset([
+                    h.atomNameSet(['C1*', 'C2*', 'O3*', 'C3*', 'C4*', 'C5*', 'O5*']),
+                    B.ammpSet('label_atom_id')
+                ])
+            ])
+        })
+    ]);
+}
+
+// TODO: improve, see keywords.protein['@desc'] below
+function proteinExpr() {
+    return B.struct.generator.atomGroups({
+        'residue-test': B.core.set.has([
+            B.set(...ResDict.amino),
+            B.ammp('label_comp_id')
+        ])
+    });
+}
+
+// TODO: improve, see keywords.backbone['@desc'] below
+function backboneExpr() {
+    return B.struct.combinator.merge([
+        B.struct.modifier.intersectBy({
+            0: B.struct.generator.atomGroups({
+                'residue-test': B.core.set.has([
+                    B.core.type.set(ResDict.amino),
+                    B.ammp('label_comp_id')
+                ])
+            }),
+            by: B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    B.core.type.set(Backbone.protein),
+                    B.ammp('label_atom_id')
+                ])
+            })
+        }),
+        B.struct.modifier.intersectBy({
+            0: B.struct.generator.atomGroups({
+                'residue-test': B.core.set.has([
+                    B.core.type.set(ResDict.nucleic),
+                    B.ammp('label_comp_id')
+                ])
+            }),
+            by: B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    B.core.type.set(Backbone.nucleic),
+                    B.ammp('label_atom_id')
+                ])
+            })
+        }),
+    ]);
+}
+
+export const keywords: KeywordDict = {
+    // general terms
+    all: {
+        '@desc': 'all atoms; same as *',
+        abbr: ['*'],
+        map: () => B.struct.generator.all()
+    },
+    bonded: {
+        '@desc': 'covalently bonded',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.gr([B.struct.atomProperty.core.bondCount({
+                flags: B.struct.type.bondFlags(['covalent', 'metallic', 'sulfide'])
+            }), 0])
+        })
+    },
+    clickable: {
+        '@desc': 'actually visible -- having some visible aspect such as wireframe, spacefill, or a label showing, or the alpha-carbon or phosphorus atom in a biomolecule that is rendered with only cartoon, rocket, or other biomolecule-specific shape.'
+    },
+    connected: {
+        '@desc': 'bonded in any way, including hydrogen bonds',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.gr([B.struct.atomProperty.core.bondCount({
+                flags: B.struct.type.bondFlags()
+            }), 0])
+        })
+    },
+    displayed: {
+        '@desc': 'displayed using the display or hide command; not necessarily visible'
+    },
+    hidden: {
+        '@desc': 'hidden using the display or hide command'
+    },
+    none: {
+        '@desc': 'no atoms',
+        map: () => B.struct.generator.empty()
+    },
+    selected: {
+        '@desc': 'atoms that have been selected; defaults to all when a file is first loaded'
+    },
+    thisModel: {
+        '@desc': 'atoms in the current frame set, as defined by frame, model, or animation commands. If more than one model is in this set, "thisModel" refers to all of them, regardless of atom displayed/hidden status.'
+    },
+    visible: {
+        '@desc': 'visible in any way, including PDB residue atoms for which a cartoon or other such rendering makes their group visible, even if they themselves are not visible.'
+    },
+    subset: {
+        '@desc': 'the currently defined subset. Note that if a subset is currently defined, then select/display all is the same as select/display subset, restrict none is the same as restrict not subset. In addition, select not subset selects nothing.'
+    },
+    specialPosition: {
+        '@desc': 'atoms in crystal structures that are at special positions - that is, for which there is more than one operator that leads to them.'
+    },
+    unitcell: {
+        '@desc': 'atoms within the current unitcell, which may be offset. This includes atoms on the faces and at the vertices of the unitcell.'
+    },
+    polyhedra: {
+        '@desc': 'all central atoms for which polyhedra have been created. See also polyhera(n), below. (Jmol 14.4)'
+    },
+    nonmetal: {
+        '@desc': '_H,_He,_B,_C,_N,_O,_F,_Ne,_Si,_P,_S,_Cl,_Ar,_As,_Se,_Br,_Kr,_Te,_I,_Xe,_At,_Rn',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.set.has([
+                B.set(...['H', 'He', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Si', 'P', 'S', 'Cl', 'Ar', 'As', 'Se', 'Br', 'Kr', 'Te', 'I', 'Xe', 'At', 'Rn'].map(B.es)),
+                B.acp('elementSymbol')
+            ])
+        })
+    },
+    metal: {
+        '@desc': '!nonmetal',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.logic.not([
+                B.core.set.has([
+                    B.set(...['H', 'He', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Si', 'P', 'S', 'Cl', 'Ar', 'As', 'Se', 'Br', 'Kr', 'Te', 'I', 'Xe', 'At', 'Rn'].map(B.es)),
+                    B.acp('elementSymbol')
+                ])
+            ])
+        })
+    },
+    alkaliMetal: {
+        '@desc': '_Li,_Na,_K,_Rb,_Cs,_Fr',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.set.has([
+                B.set(...['Li', 'Na', 'K', 'Rb', 'Cs', 'Fr'].map(B.es)),
+                B.acp('elementSymbol')
+            ])
+        })
+    },
+    alkalineEarth: {
+        '@desc': '_Be,_Mg,_Ca,_Sr,_Ba,_Ra',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.set.has([
+                B.set(...['Be', 'Mg', 'Ca', 'Sr', 'Ba', 'Ra'].map(B.es)),
+                B.acp('elementSymbol')
+            ])
+        })
+    },
+    nobleGas: {
+        '@desc': '_He,_Ne,_Ar,_Kr,_Xe,_Rn',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.set.has([
+                B.set(...['He', 'Ne', 'Ar', 'Kr', 'Xe', 'Rn'].map(B.es)),
+                B.acp('elementSymbol')
+            ])
+        })
+    },
+    metalloid: {
+        '@desc': '_B,_Si,_Ge,_As,_Sb,_Te',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.set.has([
+                B.set(...['B', 'Si', 'Ge', 'As', 'Sb', 'Te'].map(B.es)),
+                B.acp('elementSymbol')
+            ])
+        })
+    },
+    transitionMetal: {
+        '@desc': '(includes La and Ac) elemno>=21 and elemno<=30, elemno=57, elemno=89, elemno>=39 and elemno<=48, elemno>=72 and elemno<=80, elemno>=104 and elemno<=112',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.logic.or([
+                B.core.rel.inRange([B.acp('atomicNumber'), 21, 30]),
+                B.core.rel.inRange([B.acp('atomicNumber'), 39, 48]),
+                B.core.rel.inRange([B.acp('atomicNumber'), 72, 80]),
+                B.core.rel.inRange([B.acp('atomicNumber'), 104, 112]),
+                B.core.set.has([B.set(57, 89), B.acp('atomicNumber')])
+            ])
+        })
+    },
+    lanthanide: {
+        '@desc': '(does not include La) elemno>57 and elemno<=71',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.inRange([B.acp('atomicNumber'), 57, 71])
+        })
+    },
+    actinide: {
+        '@desc': '(does not include Ac) elemno>89 and elemno<=103',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.inRange([B.acp('atomicNumber'), 89, 103])
+        })
+    },
+    isaromatic: {
+        '@desc': 'atoms connected with the AROMATIC, AROMATICSINGLE, or AROMATICDOUBLE bond types',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.gr([
+                B.struct.atomProperty.core.bondCount({
+                    flags: B.struct.type.bondFlags(['aromatic'])
+                }),
+                0
+            ])
+        })
+    },
+
+    carbohydrate: {
+        '@desc': ''
+    },
+    ions: {
+        '@desc': '(specifically the PDB designations "PO4" and "SO4")'
+    },
+    ligand: {
+        '@desc': '(originally "hetero and not solvent"; changed to "!(protein,nucleic,water,UREA)" for Jmol 12.2)'
+    },
+    nucleic: {
+        '@desc': 'any group that (a) has one of the following group names: G, C, A, T, U, I, DG, DC, DA, DT, DU, DI, +G, +C, +A, +T, +U, +I; or (b) can be identified as a group that is only one atom, with name "P"; or (c) has all of the following atoms (prime, \', can replace * here): C1*, C2*, C3*, O3*, C4*, C5*, and O5*.',
+        map: () => nucleicExpr()
+    },
+    purine: {
+        '@desc': 'any nucleic group that (a) has one of the following group names: A, G, I, DA, DG, DI, +A, +G, or +I; or (b) also has atoms N7, C8, and N9.',
+        map: () => B.struct.modifier.intersectBy({
+            0: nucleicExpr(),
+            by: B.struct.combinator.merge([
+                B.struct.generator.atomGroups({
+                    'residue-test': B.core.set.has([
+                        B.set(...['A', 'G', 'I', 'DA', 'DG', 'DI', '+A', '+G', '+I']),
+                        B.ammp('label_comp_id')
+                    ])
+                }),
+                B.struct.filter.pick({
+                    0: B.struct.generator.atomGroups({
+                        'group-by': B.ammp('residueKey')
+                    }),
+                    test: B.core.set.isSubset([
+                        h.atomNameSet(['N7', 'C8', 'N9']),
+                        B.ammpSet('label_atom_id')
+                    ])
+                })
+            ])
+        })
+    },
+    pyrimidine: {
+        '@desc': 'any nucleic group that (a) has one of the following group names: C, T, U, DC, DT, DU, +C, +T, +U; or (b) also has atom O2.',
+        map: () => B.struct.modifier.intersectBy({
+            0: nucleicExpr(),
+            by: B.struct.combinator.merge([
+                B.struct.generator.atomGroups({
+                    'residue-test': B.core.set.has([
+                        B.set(...['C', 'T', 'U', 'DC', 'DT', 'DU', '+C', '+T', '+U']),
+                        B.ammp('label_comp_id')
+                    ])
+                }),
+                B.struct.filter.pick({
+                    0: B.struct.generator.atomGroups({
+                        'group-by': B.ammp('residueKey')
+                    }),
+                    test: B.core.logic.or([
+                        B.core.set.has([
+                            B.ammpSet('label_atom_id'),
+                            B.atomName('O2*')
+                        ]),
+                        B.core.set.has([
+                            B.ammpSet('label_atom_id'),
+                            B.atomName("O2'")
+                        ])
+                    ])
+                })
+            ])
+        })
+    },
+    dna: {
+        '@desc': 'any nucleic group that (a) has one of the following group names: DG, DC, DA, DT, DU, DI, T, +G, +C, +A, +T; or (b) has neither atom O2* or O2\'.',
+        map: () => B.struct.modifier.intersectBy({
+            0: nucleicExpr(),
+            by: B.struct.combinator.merge([
+                B.struct.generator.atomGroups({
+                    'residue-test': B.core.set.has([
+                        B.set(...['DG', 'DC', 'DA', 'DT', 'DU', 'DI', 'T', '+G', '+C', '+A', '+T']),
+                        B.ammp('label_comp_id')
+                    ])
+                }),
+                B.struct.filter.pick({
+                    0: B.struct.generator.atomGroups({
+                        'group-by': B.ammp('residueKey')
+                    }),
+                    test: B.core.logic.not([
+                        B.core.logic.or([
+                            B.core.set.has([
+                                B.ammpSet('label_atom_id'),
+                                B.atomName('O2*')
+                            ]),
+                            B.core.set.has([
+                                B.ammpSet('label_atom_id'),
+                                B.atomName("O2'")
+                            ])
+                        ])
+                    ])
+                })
+            ])
+        })
+    },
+    rna: {
+        '@desc': 'any nucleic group that (a) has one of the following group names: G, C, A, U, I, +U, +I; or (b) has atom O2* or O2\'.',
+        map: () => B.struct.modifier.intersectBy({
+            0: nucleicExpr(),
+            by: B.struct.combinator.merge([
+                B.struct.generator.atomGroups({
+                    'residue-test': B.core.set.has([
+                        B.set(...['G', 'C', 'A', 'U', 'I', '+U', '+I']),
+                        B.ammp('label_comp_id')
+                    ])
+                }),
+                B.struct.filter.pick({
+                    0: B.struct.generator.atomGroups({
+                        'group-by': B.ammp('residueKey')
+                    }),
+                    test: B.core.logic.or([
+                        B.core.set.has([
+                            B.ammpSet('label_atom_id'),
+                            B.atomName('O2*')
+                        ]),
+                        B.core.set.has([
+                            B.ammpSet('label_atom_id'),
+                            B.atomName("O2'")
+                        ])
+                    ])
+                })
+            ])
+        })
+    },
+    protein: {
+        '@desc': 'defined as a group that (a) has one of the following group names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, or UNK; or (b) contains PDB atom designations [C, O, CA, and N] bonded correctly; or (c) does not contain "O" but contains [C, CA, and N] bonded correctly; or (d) has only one atom, which has name CA and does not have the group name CA (indicating a calcium atom).',
+        map: () => proteinExpr()
+    },
+    acidic: {
+        '@desc': 'ASP GLU',
+        map: () => h.resnameExpr(ResDict.acidic)
+    },
+    acyclic: {
+        '@desc': 'amino and not cyclic',
+        map: () => B.struct.modifier.intersectBy({
+            0: h.resnameExpr(ResDict.amino),
+            by: h.invertExpr(h.resnameExpr(ResDict.cyclic))
+        })
+    },
+    aliphatic: {
+        '@desc': 'ALA GLY ILE LEU VAL',
+        map: () => h.resnameExpr(ResDict.aliphatic)
+    },
+    amino: {
+        '@desc': 'all twenty standard amino acids, plus ASX, GLX, UNK',
+        map: () => h.resnameExpr(ResDict.amino)
+    },
+    aromatic: {
+        '@desc': 'HIS PHE TRP TYR (see also "isaromatic" for aromatic bonds)',
+        map: () => h.resnameExpr(ResDict.aromatic)
+    },
+    basic: {
+        '@desc': 'ARG HIS LYS',
+        map: () => h.resnameExpr(ResDict.basic)
+    },
+    buried: {
+        '@desc': 'ALA CYS ILE LEU MET PHE TRP VAL',
+        map: () => h.resnameExpr(ResDict.buried)
+    },
+    charged: {
+        '@desc': 'same as acidic or basic -- ASP GLU, ARG HIS LYS',
+        map: () => h.resnameExpr(ResDict.acidic.concat(ResDict.basic))
+    },
+    cyclic: {
+        '@desc': 'HIS PHE PRO TRP TYR',
+        map: () => h.resnameExpr(ResDict.cyclic)
+    },
+    helix: {
+        '@desc': 'secondary structure-related.',
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.flags.hasAny([
+                B.struct.type.secondaryStructureFlags(['helix']),
+                B.ammp('secondaryStructureFlags')
+            ])
+        })
+    },
+    helixalpha: {
+        '@desc': 'secondary structure-related.',
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.flags.hasAny([
+                B.struct.type.secondaryStructureFlags(['alpha']),
+                B.ammp('secondaryStructureFlags')
+            ])
+        })
+    },
+    helix310: {
+        '@desc': 'secondary structure-related.',
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.flags.hasAny([
+                B.struct.type.secondaryStructureFlags(['3-10']),
+                B.ammp('secondaryStructureFlags')
+            ])
+        })
+    },
+    helixpi: {
+        '@desc': 'secondary structure-related.',
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.flags.hasAny([
+                B.struct.type.secondaryStructureFlags(['pi']),
+                B.ammp('secondaryStructureFlags')
+            ])
+        })
+    },
+    hetero: {
+        '@desc': 'PDB atoms designated as HETATM',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.ammp('isHet')
+        })
+    },
+    hydrophobic: {
+        '@desc': 'ALA GLY ILE LEU MET PHE PRO TRP TYR VAL',
+        map: () => h.resnameExpr(ResDict.hydrophobic)
+    },
+    large: {
+        '@desc': 'ARG GLU GLN HIS ILE LEU LYS MET PHE TRP TYR',
+        map: () => h.resnameExpr(ResDict.large)
+    },
+    medium: {
+        '@desc': 'ASN ASP CYS PRO THR VAL',
+        map: () => h.resnameExpr(ResDict.medium)
+    },
+    negative: {
+        '@desc': 'same as acidic -- ASP GLU',
+        map: () => h.resnameExpr(ResDict.acidic)
+    },
+    neutral: {
+        '@desc': 'amino and not (acidic or basic)',
+        map: () => B.struct.modifier.intersectBy({
+            0: h.resnameExpr(ResDict.amino),
+            by: h.invertExpr(h.resnameExpr(ResDict.acidic.concat(ResDict.basic)))
+        })
+    },
+    polar: {
+        '@desc': 'amino and not hydrophobic',
+        map: () => B.struct.modifier.intersectBy({
+            0: h.resnameExpr(ResDict.amino),
+            by: h.invertExpr(h.resnameExpr(ResDict.hydrophobic))
+        })
+    },
+    positive: {
+        '@desc': 'same as basic -- ARG HIS LYS',
+        map: () => h.resnameExpr(ResDict.basic)
+    },
+    sheet: {
+        '@desc': 'secondary structure-related',
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.flags.hasAny([
+                B.struct.type.secondaryStructureFlags(['sheet']),
+                B.ammp('secondaryStructureFlags')
+            ])
+        })
+    },
+    small: {
+        '@desc': 'ALA GLY SER',
+        map: () => h.resnameExpr(ResDict.small)
+    },
+    surface: {
+        '@desc': 'amino and not buried',
+        map: () => B.struct.modifier.intersectBy({
+            0: h.resnameExpr(ResDict.amino),
+            by: h.invertExpr(h.resnameExpr(ResDict.buried))
+        })
+    },
+    turn: {
+        '@desc': 'secondary structure-related',
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.flags.hasAny([
+                B.struct.type.secondaryStructureFlags(['turn']),
+                B.ammp('secondaryStructureFlags')
+            ])
+        })
+    },
+    alpha: {
+        '@desc': '(*.CA)',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.eq([
+                B.atomName('CA'),
+                B.ammp('label_atom_id')
+            ])
+        })
+    },
+    base: {
+        '@desc': '(nucleic bases)'
+    },
+    backbone: {
+        '@desc': '(*.C, *.CA, *.N, and all nucleic other than the bases themselves)',
+        abbr: ['mainchain'],
+        map: () => backboneExpr()
+    },
+    sidechain: {
+        '@desc': '((protein or nucleic) and not backbone)'
+    },
+    spine: {
+        '@desc': '(*.CA, *.N, *.C for proteins; *.P, *.O3\', *.O5\', *.C3\', *.C4\', *.C5 for nucleic acids)'
+    },
+    leadatom: {
+        '@desc': '(*.CA, *.P, and terminal *.O5\')'
+    },
+    solvent: {
+        '@desc': 'PDB "HOH", water, also the connected set of H-O-H in any model'
+    },
+};
+
+

src/mol-script/transpilers/jmol/markdown-docs.ts

@@ -0,0 +1,64 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+
+
+const _docs: string[] = [
+    'Jmol',
+    '============',
+    '--------------------------------',
+    ''
+];
+
+_docs.push(`## Properties\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in properties) {
+    if (properties[name].isUnsupported) continue;
+
+    const names = [name];
+    if (properties[name].abbr) names.push(...properties[name].abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (properties[name]['@desc']) {
+        _docs.push(`*${properties[name]['@desc']}*\n`);
+    }
+}
+
+_docs.push(`## Operators\n\n`);
+_docs.push('--------------------------------\n');
+operators.forEach(o => {
+    if (o.isUnsupported) return;
+
+    const names = [o.name];
+    if (o.abbr) names.push(...o.abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (o['@desc']) {
+        _docs.push(`*${o['@desc']}*\n`);
+    }
+});
+
+_docs.push(`## Keywords\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in keywords) {
+    if (!keywords[name].map) continue;
+
+    const names = [name];
+    if (keywords[name].abbr) names.push(...keywords[name].abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (keywords[name]['@desc']) {
+        _docs.push(`*${keywords[name]['@desc']}*\n`);
+    }
+}
+
+export const docs = _docs.join('\n');

src/mol-script/transpilers/jmol/operators.ts

@@ -0,0 +1,42 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../../mol-util/monadic-parser';
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { OperatorList } from '../types';
+
+export const operators: OperatorList = [
+    {
+        '@desc': 'Selects atoms that are not included in s1.',
+        '@examples': ['not ARG'],
+        name: 'not',
+        type: h.prefix,
+        rule: P.MonadicParser.alt(P.MonadicParser.regex(/NOT/i).skip(P.MonadicParser.whitespace), P.MonadicParser.string('!').skip(P.MonadicParser.optWhitespace)),
+        map: (op, selection) => h.invertExpr(selection),
+    },
+    {
+        '@desc': 'Selects atoms included in both s1 and s2.',
+        '@examples': ['ASP and .CA'],
+        name: 'and',
+        type: h.binaryLeft,
+        rule: h.infixOp(/AND|&/i),
+        map: (op, selection, by) => B.struct.modifier.intersectBy({ 0: selection, by })
+    },
+    {
+        '@desc': 'Selects atoms included in either s1 or s2.',
+        '@examples': ['ASP or GLU'],
+        name: 'or',
+        type: h.binaryLeft,
+        rule: h.infixOp(/OR|\||,/i),
+        map: (op, s1, s2) => B.struct.combinator.merge([s1, s2])
+    }
+];
+

src/mol-script/transpilers/jmol/parser.ts

@@ -0,0 +1,267 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Koya Sakuma < koya.sakuma.work@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../../mol-util/monadic-parser';
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { properties, structureMap } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+import { AtomGroupArgs } from '../types';
+import { Transpiler } from '../transpiler';
+import { OperatorList } from '../types';
+import { Expression } from '../../language/expression';
+
+// <, <=, =, >=, >, !=, and LIKE
+const valueOperators: OperatorList = [
+    {
+        '@desc': 'value comparisons',
+        '@examples': [],
+        name: '=',
+        abbr: ['=='],
+        type: h.binaryLeft,
+        rule: P.MonadicParser.regexp(/\s*(LIKE|>=|<=|=|!=|>|<)\s*/i, 1),
+        map: (op, e1, e2) => {
+            let expr;
+            if (e1 === 'structure') {
+                expr = B.core.flags.hasAny([B.ammp('secondaryStructureFlags'), structureMap(e2)]);
+            } else if (e2 === 'structure') {
+                expr = B.core.flags.hasAny([B.ammp('secondaryStructureFlags'), structureMap(e1)]);
+            } else if (e1.head !== undefined) {
+                if (e1.head.name === 'core.type.regex') {
+                    expr = B.core.str.match([e1, B.core.type.str([e2])]);
+                }
+            } else if (e2.head !== undefined) {
+                if (e2.head.name === 'core.type.regex') {
+                    expr = B.core.str.match([e2, B.core.type.str([e1])]);
+                }
+            } else if (op.toUpperCase() === 'LIKE') {
+                if (e1.head) {
+                    expr = B.core.str.match([
+                        B.core.type.regex([`^${e2}$`, 'i']),
+                        B.core.type.str([e1])
+                    ]);
+                } else {
+                    expr = B.core.str.match([
+                        B.core.type.regex([`^${e1}$`, 'i']),
+                        B.core.type.str([e2])
+                    ]);
+                }
+            }
+            if (!expr) {
+                if (e1.head) e2 = h.wrapValue(e1, e2);
+                if (e2.head) e1 = h.wrapValue(e2, e1);
+                switch (op) {
+                    case '=':
+                        expr = B.core.rel.eq([e1, e2]);
+                        break;
+                    case '!=':
+                        expr = B.core.rel.neq([e1, e2]);
+                        break;
+                    case '>':
+                        expr = B.core.rel.gr([e1, e2]);
+                        break;
+                    case '<':
+                        expr = B.core.rel.lt([e1, e2]);
+                        break;
+                    case '>=':
+                        expr = B.core.rel.gre([e1, e2]);
+                        break;
+                    case '<=':
+                        expr = B.core.rel.lte([e1, e2]);
+                        break;
+                    default: throw new Error(`value operator '${op}' not supported`);
+                }
+            }
+            return B.struct.generator.atomGroups({ 'atom-test': expr });
+        }
+    }
+];
+
+function atomExpressionQuery(x: any[]) {
+    const [resname, resnoRange, resno, inscode, chainname, atomname, altloc] = x[1];
+    const tests: AtomGroupArgs = {};
+
+    if (chainname) {
+        // TODO: should be configurable, there is an option in Jmol to use auth or label
+        tests['chain-test'] = B.core.rel.eq([B.ammp('auth_asym_id'), chainname]);
+    }
+
+    const resProps = [];
+    if (resname) resProps.push(B.core.rel.eq([B.ammp('label_comp_id'), resname]));
+    if (resnoRange) resProps.push(B.core.logic.and([
+        B.core.rel.gre([B.ammp('auth_seq_id'), resnoRange[0]]),
+        B.core.rel.lte([B.ammp('auth_seq_id'), resnoRange[1]])
+    ]));
+    if (resno) resProps.push(B.core.rel.eq([B.ammp('auth_seq_id'), resno]));
+    if (inscode) resProps.push(B.core.rel.eq([B.ammp('pdbx_PDB_ins_code'), inscode]));
+    if (resProps.length) tests['residue-test'] = h.andExpr(resProps);
+
+    const atomProps = [];
+    if (atomname) atomProps.push(B.core.rel.eq([B.ammp('auth_atom_id'), atomname]));
+    if (altloc) atomProps.push(B.core.rel.eq([B.ammp('label_alt_id'), altloc]));
+    if (atomProps.length) tests['atom-test'] = h.andExpr(atomProps);
+
+    return B.struct.generator.atomGroups(tests);
+}
+
+const lang = P.MonadicParser.createLanguage({
+    Integer: () => P.MonadicParser.regexp(/-?[0-9]+/).map(Number).desc('integer'),
+
+    Parens: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Parens,
+            r.Operator,
+            r.Expression
+        ).wrap(P.MonadicParser.regexp(/\(\s*/), P.MonadicParser.regexp(/\s*\)/));
+    },
+
+    Expression: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Keywords,
+
+            r.AtomExpression.map(atomExpressionQuery),
+
+            r.Within.map((x: [number, Expression]) => B.struct.modifier.includeSurroundings({ 0: x[1], radius: x[0] })),
+            r.ValueQuery,
+
+            r.Element.map((x: string) => B.struct.generator.atomGroups({
+                'atom-test': B.core.rel.eq([B.acp('elementSymbol'), B.struct.type.elementSymbol(x)])
+            })),
+            r.Resname.map((x: string) => B.struct.generator.atomGroups({
+                'residue-test': B.core.rel.eq([B.ammp('label_comp_id'), x])
+            })),
+        );
+    },
+
+    Operator: function (r: any) {
+        return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression));
+    },
+
+    AtomExpression: function (r: any) {
+        return P.MonadicParser.seq(
+            P.MonadicParser.lookahead(r.AtomPrefix),
+            P.MonadicParser.seq(
+                r.BracketedResname.or(P.MonadicParser.of(null)),
+                r.ResnoRange.or(P.MonadicParser.of(null)),
+                r.Resno.or(P.MonadicParser.of(null)),
+                r.Inscode.or(P.MonadicParser.of(null)),
+                r.Chainname.or(P.MonadicParser.of(null)),
+                r.Atomname.or(P.MonadicParser.of(null)),
+                r.Altloc.or(P.MonadicParser.of(null)),
+                r.Model.or(P.MonadicParser.of(null))
+            )
+        ).desc('expression');
+    },
+
+    AtomPrefix: () => P.MonadicParser.regexp(/[\[0-9:^%/.-]/).desc('atom-prefix'),
+
+    Chainname: () => P.MonadicParser.regexp(/:([A-Za-z]{1,3})/, 1).desc('chainname'),
+    Model: () => P.MonadicParser.regexp(/\/([0-9]+)/, 1).map(Number).desc('model'),
+    Element: () => P.MonadicParser.regexp(/_([A-Za-z]{1,3})/, 1).desc('element'),
+    Atomname: () => P.MonadicParser.regexp(/\.([a-zA-Z0-9]{1,4})/, 1).map(B.atomName).desc('atomname'),
+    Resname: () => P.MonadicParser.regexp(/[a-zA-Z0-9]{1,4}/).desc('resname'),
+    Resno: (r: any) => r.Integer.desc('resno'),
+    Altloc: () => P.MonadicParser.regexp(/%([a-zA-Z0-9])/, 1).desc('altloc'),
+    Inscode: () => P.MonadicParser.regexp(/\^([a-zA-Z0-9])/, 1).desc('inscode'),
+
+    BracketedResname: () => P.MonadicParser.regexp(/\[([a-zA-Z0-9]{1,4})\]/, 1).desc('bracketed-resname'),
+    ResnoRange: (r: any) => {
+        return P.MonadicParser.seq(
+            r.Integer.skip(P.MonadicParser.seq(
+                P.MonadicParser.optWhitespace,
+                P.MonadicParser.string('-'),
+                P.MonadicParser.optWhitespace
+            )),
+            r.Integer
+        ).desc('resno-range');
+    },
+    Within: (r: any) => {
+        return P.MonadicParser.regexp(/within/i)
+            .skip(P.MonadicParser.regexp(/\s*\(\s*/))
+            .then(P.MonadicParser.seq(
+                r.Integer.skip(P.MonadicParser.regexp(/\s*,\s*/)),
+                r.Query
+            ))
+            .skip(P.MonadicParser.regexp(/\)/));
+    },
+
+    Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)).desc('keyword'),
+
+    Query: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Operator,
+            r.Parens,
+            r.Expression
+        ).trim(P.MonadicParser.optWhitespace);
+    },
+
+    Number: function () {
+        return P.MonadicParser.regexp(/-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/)
+            .map(Number)
+            .desc('number');
+    },
+
+    String: function () {
+        const w = h.getReservedWords(properties, keywords, operators)
+            .sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
+        return P.MonadicParser.alt(
+            P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i')),
+            P.MonadicParser.regexp(/'((?:[^"\\]|\\.)*)'/, 1),
+            P.MonadicParser.regexp(/"((?:[^"\\]|\\.)*)"/, 1).map(x => B.core.type.regex([`^${x}$`, 'i']))
+        ).desc('string');
+    },
+
+    Value: function (r: any) {
+        return P.MonadicParser.alt(r.Number, r.String);
+    },
+
+    ValueParens: function (r: any) {
+        return P.MonadicParser.alt(
+            r.ValueParens,
+            r.ValueOperator,
+            r.ValueExpressions
+        ).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
+    },
+
+    ValuePropertyNames: function () {
+        return P.MonadicParser.alt(...h.getPropertyNameRules(properties, /LIKE|>=|<=|=|!=|>|<|\)|\s/i));
+    },
+
+    ValueOperator: function (r: any) {
+        return h.combineOperators(valueOperators, P.MonadicParser.alt(r.ValueParens, r.ValueExpressions));
+    },
+
+    ValueExpressions: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Value,
+            r.ValuePropertyNames
+        );
+    },
+
+    ValueQuery: function (r: any) {
+        return P.MonadicParser.alt(
+            r.ValueOperator.map((x: any) => {
+                if (x.head) {
+                    if (x.head.name.startsWith('structure-query.generator')) return x;
+                } else {
+                    if (typeof x === 'string' && x.length <= 4) {
+                        return B.struct.generator.atomGroups({
+                            'residue-test': B.core.rel.eq([B.ammp('label_comp_id'), x])
+                        });
+                    }
+                }
+                throw new Error(`values must be part of an comparison, value '${x}'`);
+            })
+        );
+    }
+});
+
+export const transpiler: Transpiler = str => lang.Query.tryParse(str);

src/mol-script/transpilers/jmol/symbols.ts

@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+
+export const Properties: string[] = [];
+for (const name in properties) {
+    if (properties[name].isUnsupported) continue;
+    Properties.push(name);
+    if (properties[name].abbr) Properties.push(...properties[name].abbr!);
+}
+
+export const Operators: string[] = [];
+operators.forEach(o => {
+    if (o.isUnsupported) return;
+    Operators.push(o.name);
+    if (o.abbr) Operators.push(...o.abbr);
+});
+
+export const Keywords: string[] = [];
+for (const name in keywords) {
+    if (!keywords[name].map) continue;
+    Keywords.push(name);
+    if (keywords[name].abbr) Keywords.push(...keywords[name].abbr!);
+}
+
+export const _all = { Properties, Operators, Keywords };

src/mol-script/transpilers/pymol/examples.ts

@@ -0,0 +1,56 @@
+/**
+ * Copyright (c) 2017-2022 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 Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+export const examples = [{
+    name: 'ALA residues',
+    value: 'resn ALA'
+}, {
+    name: 'Atoms named "C", "O", "N", or "CA"',
+    value: 'name c+o+n+ca'
+}, {
+    name: 'Residues with helix or sheet secondary structure',
+    value: 'ss h+s'
+}, {
+    name: 'C-alpha atoms of residues 100 to 180 in chain A',
+    value: 'A/100-180/CA'
+}, {
+    name: 'Residues 100 to 180',
+    value: 'resi 100-180'
+}, {
+    name: 'Atoms that are 1 ang + vdw radius away from polymer',
+    value: 'polymer gap 1'
+}, {
+    name: 'Residues within 4 ang of HEM',
+    value: 'byres resn HEM around 4'
+}, {
+    name: 'HEM and residues within 4 ang',
+    value: 'byres resn HEM expand 4'
+}, {
+    name: 'Solvent close (2.5 ang) to polymer',
+    value: 'solvent NEAR_TO 2.5 OF polymer'
+}, {
+    name: 'Cystein residues within 3 ang of HEM',
+    value: 'byres resn CYS WITHIN 3 OF resn HEM'
+}, {
+    name: 'Solvent atoms 4 ang away from oxygen',
+    value: 'solvent beyond 4 of (name O and not solvent)'
+}, {
+    name: 'All rings in PHE',
+    value: 'byring resn PHE'
+}, {
+    name: 'CYS and all bound residues',
+    value: 'byres BOUND_TO resn CYS'
+}, {
+    name: 'HEM and atoms up to 7 bonds away',
+    value: 'resn HEM extend 7'
+}, {
+    name: 'Atoms with alternate location A or none',
+    value: 'alt A+""'
+}];

src/mol-script/transpilers/pymol/keywords.ts

@@ -0,0 +1,275 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import * as h from '../helper';
+import { KeywordDict } from '../types';
+
+const ResDict = {
+    nucleic: ['A', 'C', 'T', 'G', 'U', 'DA', 'DC', 'DT', 'DG', 'DU'],
+    protein: ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'CYX', 'GLN', 'GLU', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'ILE', 'LEU', 'LYS', 'MET', 'MSE', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL'],
+    solvent: ['HOH', 'WAT', 'H20', 'TIP', 'SOL']
+};
+
+const Backbone = {
+    nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*',
+        "C2'", "C1'", "O4'", "O2'"],
+    protein: ['C', 'N', 'CA', 'O']
+};
+
+function backboneExpr() {
+    return B.struct.combinator.merge([
+        B.struct.modifier.intersectBy({
+            0: B.struct.generator.atomGroups({
+                'residue-test': B.core.set.has([
+                    B.core.type.set(ResDict.protein),
+                    B.ammp('label_comp_id')
+                ])
+            }),
+            by: B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    B.core.type.set(Backbone.protein),
+                    B.ammp('label_atom_id')
+                ])
+            })
+        }),
+        B.struct.modifier.intersectBy({
+            0: B.struct.generator.atomGroups({
+                'residue-test': B.core.set.has([
+                    B.core.type.set(ResDict.nucleic),
+                    B.ammp('label_comp_id')
+                ])
+            }),
+            by: B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    B.core.type.set(Backbone.nucleic),
+                    B.ammp('label_atom_id')
+                ])
+            })
+        }),
+    ]);
+}
+
+export const keywords: KeywordDict = {
+    all: {
+        '@desc': 'All atoms currently loaded into PyMOL',
+        abbr: ['*'],
+        map: () => B.struct.generator.all()
+    },
+    none: {
+        '@desc': 'No atoms (empty selection)',
+        map: () => B.struct.generator.empty()
+    },
+    hydrogens: {
+        '@desc': 'All hydrogen atoms currently loaded into PyMOL',
+        abbr: ['hydro', 'h.'],
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.eq([
+                B.acp('elementSymbol'),
+                B.es('H')
+            ])
+        })
+    },
+    hetatm: {
+        '@desc': 'All atoms loaded from Protein Data Bank HETATM records',
+        abbr: ['het'],
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.eq([B.ammp('isHet'), true])
+        })
+    },
+    visible: {
+        '@desc': 'All atoms in enabled objects with at least one visible representation',
+        abbr: ['v.']
+    },
+    polymer: {
+        '@desc': 'All atoms on the polymer (not het). Finds atoms with residue identifiers matching a known polymer, such a peptide and DNA.',
+        abbr: ['pol.'],
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.set.has([
+                B.core.type.set(ResDict.nucleic.concat(ResDict.protein)),
+                B.ammp('label_comp_id')
+            ])
+        })
+    },
+    sidechain: {
+        '@desc': 'Polymer non-backbone atoms (new in PyMOL 1.6.1)',
+        abbr: ['sc.'],
+        map: () => {
+            return B.struct.modifier.exceptBy({
+                '0': B.struct.generator.atomGroups({
+                    'residue-test': B.core.set.has([
+                        B.core.type.set(ResDict.nucleic.concat(ResDict.protein)),
+                        B.ammp('label_comp_id')
+                    ])
+                }),
+                by: backboneExpr()
+            });
+        },
+    },
+    present: {
+        '@desc': 'All atoms with defined coordinates in the current state (used in creating movies)',
+        abbr: ['pr.']
+    },
+    center: {
+        '@desc': 'Pseudo-atom at the center of the scene'
+    },
+    origin: {
+        '@desc': 'Pseudo-atom at the origin of rotation',
+    },
+    enabled: {
+        '@desc': 'All enabled objects or selections from the object list.',
+    },
+    masked: {
+        '@desc': 'All masked atoms.',
+        abbr: ['msk.']
+    },
+    protected: {
+        '@desc': 'All protected atoms.',
+        abbr: ['pr.']
+    },
+    bonded: {
+        '@desc': 'All bonded atoms',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.rel.gr([B.struct.atomProperty.core.bondCount({
+                flags: B.struct.type.bondFlags(['covalent', 'metallic', 'sulfide'])
+            }), 0])
+        })
+    },
+    donors: {
+        '@desc': 'All hydrogen bond donor atoms.',
+        abbr: ['don.']
+    },
+    acceptors: {
+        '@desc': 'All hydrogen bond acceptor atoms.',
+        abbr: ['acc.']
+    },
+    fixed: {
+        '@desc': 'All fixed atoms.',
+        abbr: ['fxd.']
+    },
+    restrained: {
+        '@desc': 'All restrained atoms.',
+        abbr: ['rst.']
+    },
+    organic: {
+        '@desc': 'All atoms in non-polymer organic compounds (e.g. ligands, buffers). Finds carbon-containing molecules that do not match known polymers.',
+        abbr: ['org.'],
+        map: () => h.asAtoms(B.struct.modifier.expandProperty({
+            '0': B.struct.modifier.union([
+                B.struct.generator.queryInSelection({
+                    '0': B.struct.generator.atomGroups({
+                        'residue-test': B.core.logic.not([
+                            B.core.set.has([
+                                B.core.type.set(ResDict.nucleic.concat(ResDict.protein)),
+                                B.ammp('label_comp_id')
+                            ])
+                        ])
+                    }),
+                    query: B.struct.generator.atomGroups({
+                        'atom-test': B.core.rel.eq([
+                            B.es('C'),
+                            B.acp('elementSymbol')
+                        ])
+                    })
+                })
+            ]),
+            property: B.ammp('residueKey')
+        }))
+    },
+    inorganic: {
+        '@desc': 'All non-polymer inorganic atoms/ions. Finds atoms in molecules that do not contain carbon and do not match any known solvent residues.',
+        abbr: ['ino.'],
+        map: () => h.asAtoms(B.struct.modifier.expandProperty({
+            '0': B.struct.modifier.union([
+                B.struct.filter.pick({
+                    '0': B.struct.generator.atomGroups({
+                        'residue-test': B.core.logic.not([
+                            B.core.set.has([
+                                B.core.type.set(ResDict.nucleic.concat(ResDict.protein).concat(ResDict.solvent)),
+                                B.ammp('label_comp_id')
+                            ])
+                        ]),
+                        'group-by': B.ammp('residueKey')
+                    }),
+                    test: B.core.logic.not([
+                        B.core.set.has([
+                            B.struct.atomSet.propertySet([B.acp('elementSymbol')]),
+                            B.es('C')
+                        ])
+                    ])
+                })
+            ]),
+            property: B.ammp('residueKey')
+        }))
+    },
+    solvent: {
+        '@desc': 'All water molecules. The hardcoded solvent residue identifiers are currently: HOH, WAT, H20, TIP, SOL.',
+        abbr: ['sol.'],
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.set.has([
+                B.core.type.set(ResDict.solvent),
+                B.ammp('label_comp_id')
+            ])
+        })
+    },
+    guide: {
+        '@desc': 'All protein CA and nucleic acid C4*/C4',
+        map: () => B.struct.combinator.merge([
+            B.struct.generator.atomGroups({
+                'atom-test': B.core.rel.eq([
+                    B.atomName('CA'),
+                    B.ammp('label_atom_id')
+                ]),
+                'residue-test': B.core.set.has([
+                    B.core.type.set(ResDict.protein),
+                    B.ammp('label_comp_id')
+                ])
+            }),
+            B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    h.atomNameSet(['C4*', 'C4\'']),
+                    B.ammp('label_atom_id')
+                ]),
+                'residue-test': B.core.set.has([
+                    B.core.type.set(ResDict.nucleic),
+                    B.ammp('label_comp_id')
+                ])
+            })
+        ]),
+    },
+    metals: {
+        '@desc': 'All metal atoms (new in PyMOL 1.6.1)'
+    },
+    backbone: {
+        '@desc': 'Polymer backbone atoms (new in PyMOL 1.6.1)',
+        abbr: ['bb.'],
+        map: () => backboneExpr()
+    },
+    'polymer.protein': {
+        '@desc': 'Protein (New in PyMOL 2.1)',
+        abbr: ['polymer.protein'],
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.set.has([
+                B.core.type.set(ResDict.protein),
+                B.ammp('label_comp_id')
+            ])
+        })
+    },
+    'polymer.nucleic': {
+        '@desc': 'Nucleic Acid (New in PyMOL 2.1)',
+        abbr: ['polymer.nucleic'],
+        map: () => B.struct.generator.atomGroups({
+            'residue-test': B.core.set.has([
+                B.core.type.set(ResDict.nucleic),
+                B.ammp('label_comp_id')
+            ])
+        })
+    }
+};

src/mol-script/transpilers/pymol/markdown-docs.ts

@@ -0,0 +1,63 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+
+const _docs: string[] = [
+    'PyMol',
+    '============',
+    '--------------------------------',
+    ''
+];
+
+_docs.push(`## Properties\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in properties) {
+    if (properties[name].isUnsupported) continue;
+
+    const names = [name];
+    if (properties[name].abbr) names.push(...properties[name].abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (properties[name]['@desc']) {
+        _docs.push(`*${properties[name]['@desc']}*\n`);
+    }
+}
+
+_docs.push(`## Operators\n\n`);
+_docs.push('--------------------------------\n');
+operators.forEach(o => {
+    if (o.isUnsupported) return;
+
+    const names = [o.name];
+    if (o.abbr) names.push(...o.abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (o['@desc']) {
+        _docs.push(`*${o['@desc']}*\n`);
+    }
+});
+
+_docs.push(`## Keywords\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in keywords) {
+    if (!keywords[name].map) continue;
+
+    const names = [name];
+    if (keywords[name].abbr) names.push(...keywords[name].abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (keywords[name]['@desc']) {
+        _docs.push(`*${keywords[name]['@desc']}*\n`);
+    }
+}
+
+export const docs = _docs.join('\n');

src/mol-script/transpilers/pymol/operators.ts

@@ -0,0 +1,371 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../../mol-util/monadic-parser';
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { OperatorList } from '../types';
+import { Expression } from '../../language/expression';
+
+export const operators: OperatorList = [
+    {
+        '@desc': 'Selects atoms that are not included in s1.',
+        '@examples': [
+            'NOT resn ALA',
+            'not (resi 42 or chain A)',
+            '!resi 42 or chain A',
+        ],
+        name: 'not',
+        type: h.prefix,
+        rule: P.MonadicParser.alt(
+            P.MonadicParser.regexp(/NOT/i).skip(P.MonadicParser.whitespace),
+            P.MonadicParser.string('!').skip(P.MonadicParser.optWhitespace)
+        ),
+        map: (op, selection) => h.invertExpr(selection),
+    },
+    {
+        '@desc': 'Selects atoms included in both s1 and s2.',
+        '@examples': ['chain A AND name CA'],
+        name: 'and',
+        type: h.binaryLeft,
+        rule: h.infixOp(/AND|&/i),
+        map: (op, selection, by) =>
+            B.struct.modifier.intersectBy({ 0: selection, by }),
+    },
+    {
+        '@desc': 'Selects atoms included in either s1 or s2.',
+        '@examples': ['chain A OR chain B'],
+        name: 'or',
+        type: h.binaryLeft,
+        rule: h.infixOp(/OR|\|/i),
+        map: (op: string, s1: Expression, s2: Expression) => B.struct.combinator.merge([s1, s2]),
+    },
+    {
+        '@desc':
+            'Selects atoms in s1 whose identifiers name, resi, resn, chain and segi all match atoms in s2.',
+        '@examples': ['chain A IN chain B'],
+        name: 'in',
+        type: h.binaryLeft,
+        rule: h.infixOp(/IN/i),
+        map: (op: string, selection: Expression, source: Expression) => {
+            return B.struct.filter.withSameAtomProperties({
+                0: selection,
+                source,
+                property: B.core.type.compositeKey([
+                    B.ammp('label_atom_id'),
+                    B.ammp('label_seq_id'),
+                    B.ammp('label_comp_id'),
+                    B.ammp('auth_asym_id'),
+                    B.ammp('label_asym_id'),
+                ]),
+            });
+        },
+    },
+    {
+        '@desc':
+            'Selects atoms in s1 whose identifiers name and resi match atoms in s2.',
+        '@examples': ['chain A LIKE chain B'],
+        name: 'like',
+        type: h.binaryLeft,
+        rule: h.infixOp(/LIKE|l\./i),
+        map: (op: string, selection: Expression, source: Expression) => {
+            return B.struct.filter.withSameAtomProperties({
+                0: selection,
+                source,
+                property: B.core.type.compositeKey([
+                    B.ammp('label_atom_id'),
+                    B.ammp('label_seq_id'),
+                ]),
+            });
+        },
+    },
+    {
+        '@desc':
+            'Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms.',
+        '@examples': ['solvent GAP 2'],
+        name: 'gap',
+        type: h.postfix,
+        rule: h
+            .postfixOp(/GAP\s+([-+]?[0-9]*\.?[0-9]+)/i, 1)
+            .map((x: any) => parseFloat(x)),
+        map: (distance: number, target: Expression) => {
+            return B.struct.filter.within({
+                '0': B.struct.generator.all(),
+                target,
+                'atom-radius': B.acp('vdw'),
+                'max-radius': distance,
+                invert: true,
+            });
+        },
+    },
+    {
+        '@desc':
+            'Selects atoms with centers within X Angstroms of the center of any atom in s1.',
+        '@examples': ['resname LIG AROUND 1'],
+        name: 'around',
+        abbr: ['a.'],
+        type: h.postfix,
+        rule: h
+            .postfixOp(/(AROUND|a\.)\s+([-+]?[0-9]*\.?[0-9]+)/i, 2)
+            .map((x: any) => parseFloat(x)),
+        map: (radius: number, target: Expression) => {
+            return B.struct.modifier.exceptBy({
+                '0': B.struct.filter.within({
+                    '0': B.struct.generator.all(),
+                    target,
+                    'max-radius': radius,
+                }),
+                by: target,
+            });
+        },
+    },
+    {
+        '@desc':
+            'Expands s1 by all atoms within X Angstroms of the center of any atom in s1.',
+        '@examples': ['chain A EXPAND 3'],
+        name: 'expand',
+        abbr: ['x.'],
+        type: h.postfix,
+        rule: h
+            .postfixOp(/(EXPAND|x\.)\s+([-+]?[0-9]*\.?[0-9]+)/i, 2)
+            .map((x: any) => parseFloat(x)),
+        map: (radius: number, selection: Expression) => {
+            return B.struct.modifier.includeSurroundings({ 0: selection, radius });
+        },
+    },
+    {
+        '@desc':
+            'Selects atoms in s1 that are within X Angstroms of any atom in s2.',
+        '@examples': ['chain A WITHIN 3 OF chain B'],
+        name: 'within',
+        abbr: ['w.'],
+        type: h.binaryLeft,
+        rule: h.ofOp('WITHIN', 'w.'),
+        map: (radius: number, selection: Expression, target: Expression) => {
+            return B.struct.filter.within({
+                0: selection,
+                target,
+                'max-radius': radius,
+            });
+        },
+    },
+    {
+        '@desc':
+            'Same as within, but excludes s2 from the selection (and thus is identical to s1 and s2 around X).',
+        '@examples': ['chain A NEAR_TO 3 OF chain B'],
+        name: 'near_to',
+        abbr: ['nto.'],
+        type: h.binaryLeft,
+        rule: h.ofOp('NEAR_TO', 'nto.'),
+        map: (radius: number, selection: Expression, target: Expression) => {
+            return B.struct.modifier.exceptBy({
+                '0': B.struct.filter.within({
+                    '0': selection,
+                    target,
+                    'max-radius': radius,
+                }),
+                by: target,
+            });
+        },
+    },
+    {
+        '@desc': 'Selects atoms in s1 that are at least X Anstroms away from s2.',
+        '@examples': ['solvent BEYOND 2 OF chain A'],
+        name: 'beyond',
+        abbr: ['be.'],
+        type: h.binaryLeft,
+        rule: h.ofOp('BEYOND', 'be.'),
+        map: (radius: number, selection: Expression, target: Expression) => {
+            return B.struct.modifier.exceptBy({
+                '0': B.struct.filter.within({
+                    '0': selection,
+                    target,
+                    'max-radius': radius,
+                    invert: true,
+                }),
+                by: target,
+            });
+        },
+    },
+    {
+        '@desc': 'Expands selection to complete residues.',
+        '@examples': ['BYRESIDUE name N'],
+        name: 'byresidue',
+        abbr: ['byresi', 'byres', 'br.'],
+        type: h.prefix,
+        rule: h.prefixOp(/BYRESIDUE|byresi|byres|br\./i),
+        map: (op: string, selection: Expression) => {
+            return h.asAtoms(
+                B.struct.modifier.expandProperty({
+                    '0': B.struct.modifier.union({ 0: selection }),
+                    property: B.ammp('residueKey'),
+                })
+            );
+        },
+    },
+    {
+        '@desc':
+            'Completely selects all alpha carbons in all residues covered by a selection.',
+        '@examples': ['BYCALPHA chain A'],
+        name: 'bycalpha',
+        abbr: ['bca.'],
+        type: h.prefix,
+        rule: h.prefixOp(/BYCALPHA|bca\./i),
+        map: (op: string, selection: Expression) => {
+            return B.struct.generator.queryInSelection({
+                '0': B.struct.modifier.expandProperty({
+                    '0': B.struct.modifier.union({ 0: selection }),
+                    property: B.ammp('residueKey'),
+                }),
+                query: B.struct.generator.atomGroups({
+                    'atom-test': B.core.rel.eq([
+                        B.atomName('CA'),
+                        B.ammp('label_atom_id'),
+                    ]),
+                }),
+            });
+        },
+    },
+    {
+        '@desc': 'Expands selection to complete molecules.',
+        '@examples': ['BYMOLECULE resi 20-30'],
+        name: 'bymolecule',
+        isUnsupported: true, // structure-query.atom-property.topology.connected-component-key' is not implemented
+        abbr: ['bymol', 'bm.'],
+        type: h.prefix,
+        rule: h.prefixOp(/BYMOLECULE|bymol|bm\./i),
+        map: (op: string, selection: Expression) => {
+            return h.asAtoms(
+                B.struct.modifier.expandProperty({
+                    '0': B.struct.modifier.union({ 0: selection }),
+                    property: B.atp('connectedComponentKey'),
+                })
+            );
+        },
+    },
+    {
+        '@desc': 'Expands selection to complete fragments.',
+        '@examples': ['BYFRAGMENT resi 10'],
+        name: 'byfragment',
+        abbr: ['byfrag', 'bf.'],
+        isUnsupported: true,
+        type: h.prefix,
+        rule: h.prefixOp(/BYFRAGMENT|byfrag|bf\./i),
+        map: (op: string, selection: Expression) => [op, selection],
+    },
+    {
+        '@desc': 'Expands selection to complete segments.',
+        '@examples': ['BYSEGMENT resn CYS'],
+        name: 'bysegment',
+        abbr: ['bysegi', 'byseg', 'bs.'],
+        type: h.prefix,
+        rule: h.prefixOp(/BYSEGMENT|bysegi|byseg|bs\./i),
+        map: (op: string, selection: Expression) => {
+            return h.asAtoms(
+                B.struct.modifier.expandProperty({
+                    '0': B.struct.modifier.union({ 0: selection }),
+                    property: B.ammp('chainKey'),
+                })
+            );
+        },
+    },
+    {
+        '@desc': 'Expands selection to complete objects.',
+        '@examples': ['BYOBJECT chain A'],
+        name: 'byobject',
+        abbr: ['byobj', 'bo.'],
+        isUnsupported: true,
+        type: h.prefix,
+        rule: h.prefixOp(/BYOBJECT|byobj|bo\./i),
+        map: (op: string, selection: Expression) => [op, selection],
+    },
+    {
+        '@desc': 'Expands selection to unit cell.',
+        '@examples': ['BYCELL chain A'],
+        name: 'bycell',
+        isUnsupported: true,
+        type: h.prefix,
+        rule: h.prefixOp(/BYCELL/i),
+        map: (op: string, selection: Expression) => [op, selection],
+    },
+    {
+        '@desc': 'All rings of size ≤ 7 which have at least one atom in s1.',
+        '@examples': ['BYRING resn HEM'],
+        name: 'byring',
+        // isUnsupported: true, // structure-query.atom-set.atom-count' is not implemented.
+        type: h.prefix,
+        rule: h.prefixOp(/BYRING/i),
+        map: (op: string, selection: Expression) => {
+            return h.asAtoms(
+                B.struct.modifier.intersectBy({
+                    '0': B.struct.filter.pick({
+                        '0': B.struct.generator.rings(),
+                        test: B.core.logic.and([
+                            B.core.rel.lte([B.struct.atomSet.atomCount(), 7]),
+                            B.core.rel.gr([B.struct.atomSet.countQuery([selection]), 1]),
+                        ]),
+                    }),
+                    by: selection,
+                })
+            );
+        },
+    },
+    {
+        '@desc': 'Selects atoms directly bonded to s1, excludes s1.',
+        '@examples': ['NEIGHBOR resn CYS'],
+        name: 'neighbor',
+        type: h.prefix,
+        abbr: ['nbr.'],
+        rule: h.prefixOp(/NEIGHBOR|nbr\./i),
+        map: (op: string, selection: Expression) => {
+            return B.struct.modifier.exceptBy({
+                '0': h.asAtoms(
+                    B.struct.modifier.includeConnected({
+                        '0': B.struct.modifier.union({ 0: selection }),
+                        'bond-test': true,
+                    })
+                ),
+                by: selection,
+            });
+        },
+    },
+    {
+        '@desc': 'Selects atoms directly bonded to s1, may include s1.',
+        '@examples': ['BOUND_TO name CA'],
+        name: 'bound_to',
+        abbr: ['bto.'],
+        type: h.prefix,
+        rule: h.prefixOp(/BOUND_TO|bto\./i),
+        map: (op: string, selection: Expression) => {
+            return h.asAtoms(
+                B.struct.modifier.includeConnected({
+                    '0': B.struct.modifier.union({ 0: selection }),
+                })
+            );
+        },
+    },
+    {
+        '@desc': 'Extends s1 by X bonds connected to atoms in s1.',
+        '@examples': ['resname LIG EXTEND 3'],
+        name: 'extend',
+        abbr: ['xt.'],
+        type: h.postfix,
+        rule: h.postfixOp(/(EXTEND|xt\.)\s+([0-9]+)/i, 2).map((x: any) => parseInt(x)),
+        map: (count: number, selection: Expression) => {
+            return h.asAtoms(
+                B.struct.modifier.includeConnected({
+                    '0': B.struct.modifier.union({ 0: selection }),
+                    'bond-test': true,
+                    'layer-count': count,
+                })
+            );
+        },
+    },
+];

src/mol-script/transpilers/pymol/parser.ts

@@ -0,0 +1,173 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+// https://pymol.org/dokuwiki/doku.php?id=selection:alpha
+// https://pymolwiki.org/index.php/Selection_Algebra
+// https://github.com/evonove/pymol/blob/master/pymol/layer3/Selector.cpp
+
+import * as P from '../../../mol-util/monadic-parser';
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+import { AtomGroupArgs } from '../types';
+import { Transpiler } from '../transpiler';
+
+const propertiesDict = h.getPropertyRules(properties);
+
+const slash = P.MonadicParser.string('/');
+
+function orNull(rule: P.MonadicParser<any>) {
+    return rule.or(P.MonadicParser.of(null));
+}
+
+function atomSelectionQuery(x: any) {
+    const tests: AtomGroupArgs = {};
+    const props: { [k: string]: any[] } = {};
+
+    for (const k in x) {
+        const ps = properties[k];
+        if (!ps) {
+            throw new Error(`property '${k}' not supported, value '${x[k]}'`);
+        }
+        if (x[k] === null) continue;
+        if (!props[ps.level]) props[ps.level] = [];
+        props[ps.level].push(x[k]);
+    }
+
+    for (const p in props) {
+        tests[p] = h.andExpr(props[p]);
+    }
+
+    return B.struct.generator.atomGroups(tests);
+}
+
+const lang = P.MonadicParser.createLanguage({
+    Parens: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Parens,
+            r.Operator,
+            r.Expression
+        ).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
+    },
+
+    Expression: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Keywords,
+            r.AtomSelectionMacro.map(atomSelectionQuery),
+            r.NamedAtomProperties,
+            r.Pepseq,
+            r.Rep,
+            r.Object
+        );
+    },
+
+    AtomSelectionMacro: function (r: any) {
+        return P.MonadicParser.alt(
+            slash.then(P.MonadicParser.alt(
+                P.MonadicParser.seq(
+                    orNull(r.ObjectProperty).skip(slash),
+                    orNull(propertiesDict.segi).skip(slash),
+                    orNull(propertiesDict.chain).skip(slash),
+                    orNull(propertiesDict.resi).skip(slash),
+                    orNull(propertiesDict.name)
+                ).map(x => { return { object: x[0], segi: x[1], chain: x[2], resi: x[3], name: x[4] }; }),
+                P.MonadicParser.seq(
+                    orNull(r.ObjectProperty).skip(slash),
+                    orNull(propertiesDict.segi).skip(slash),
+                    orNull(propertiesDict.chain).skip(slash),
+                    orNull(propertiesDict.resi)
+                ).map(x => { return { object: x[0], segi: x[1], chain: x[2], resi: x[3] }; }),
+                P.MonadicParser.seq(
+                    orNull(r.ObjectProperty).skip(slash),
+                    orNull(propertiesDict.segi).skip(slash),
+                    orNull(propertiesDict.chain)
+                ).map(x => { return { object: x[0], segi: x[1], chain: x[2] }; }),
+                P.MonadicParser.seq(
+                    orNull(r.ObjectProperty).skip(slash),
+                    orNull(propertiesDict.segi)
+                ).map(x => { return { object: x[0], segi: x[1] }; }),
+                P.MonadicParser.seq(
+                    orNull(r.ObjectProperty)
+                ).map(x => { return { object: x[0] }; }),
+            )),
+            P.MonadicParser.alt(
+                P.MonadicParser.seq(
+                    orNull(r.ObjectProperty).skip(slash),
+                    orNull(propertiesDict.segi).skip(slash),
+                    orNull(propertiesDict.chain).skip(slash),
+                    orNull(propertiesDict.resi).skip(slash),
+                    orNull(propertiesDict.name)
+                ).map(x => { return { object: x[0], segi: x[1], chain: x[2], resi: x[3], name: x[4] }; }),
+                P.MonadicParser.seq(
+                    orNull(propertiesDict.segi).skip(slash),
+                    orNull(propertiesDict.chain).skip(slash),
+                    orNull(propertiesDict.resi).skip(slash),
+                    orNull(propertiesDict.name)
+                ).map(x => { return { segi: x[0], chain: x[1], resi: x[2], name: x[3] }; }),
+                P.MonadicParser.seq(
+                    orNull(propertiesDict.chain).skip(slash),
+                    orNull(propertiesDict.resi).skip(slash),
+                    orNull(propertiesDict.name)
+                ).map(x => { return { chain: x[0], resi: x[1], name: x[2] }; }),
+                P.MonadicParser.seq(
+                    orNull(propertiesDict.resi).skip(slash),
+                    orNull(propertiesDict.name)
+                ).map(x => { return { resi: x[0], name: x[1] }; }),
+            )
+        );
+    },
+
+    NamedAtomProperties: function () {
+        return P.MonadicParser.alt(...h.getNamedPropertyRules(properties));
+    },
+
+    Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
+
+    ObjectProperty: () => {
+        const w = h.getReservedWords(properties, keywords, operators)
+            .sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
+        return P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i'));
+    },
+    Object: (r: any) => {
+        return r.ObjectProperty.notFollowedBy(slash)
+            .map((x: any) => { throw new Error(`property 'object' not supported, value '${x}'`); });
+    },
+
+    // Selects peptide sequence matching upper-case one-letter
+    // sequence SEQ (see also FindSeq).
+    // PEPSEQ seq
+    Pepseq: () => {
+        return P.MonadicParser.regexp(/(PEPSEQ|ps\.)\s+([a-z]+)/i, 2)
+            .map(h.makeError(`operator 'pepseq' not supported`));
+    },
+
+    // Selects atoms which show representation rep.
+    // REP rep
+    Rep: () => {
+        return P.MonadicParser.regexp(/REP\s+(lines|spheres|mesh|ribbon|cartoon|sticks|dots|surface|labels|extent|nonbonded|nb_spheres|slice|extent|slice|dashes|angles|dihedrals|cgo|cell|callback|everything)/i, 1)
+            .map(h.makeError(`operator 'rep' not supported`));
+    },
+
+    Operator: function (r: any) {
+        return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression, r.Operator));
+    },
+
+    Query: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Operator,
+            r.Parens,
+            r.Expression
+        ).trim(P.MonadicParser.optWhitespace);
+    }
+});
+
+export const transpiler: Transpiler = str => lang.Query.tryParse(str);

src/mol-script/transpilers/pymol/properties.ts

@@ -0,0 +1,215 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { PropertyDict } from '../types';
+
+const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
+
+function atomNameListMap(x: string) { return x.split('+').map(B.atomName); }
+function listMap(x: string) { return x.split('+').map(x => x.replace(/^["']|["']$/g, '')); }
+
+function listOrRangeMap(x: string) {
+    // cases
+    if (x.includes('-') && x.includes('+')) {
+        const pSplit = x.split('+').map(x => x.replace(/^["']|["']$/g, ''));
+        const res: number[] = [];
+        pSplit.forEach(x => {
+            if (x.includes('-') && !x.startsWith('-')) {
+                const [min, max] = x.split('-').map(x => parseInt(x));
+                for (let i = min; i <= max; i++) {
+                    res.push(i);
+                }
+            } else if (x.includes('-') && x.startsWith('-') && x.match(/[0-9]+-[-0-9]+/)) {
+                const min = -parseInt(x.split('-')[1]);
+                let max;
+                if (x.includes('--')) {
+                    max = -parseInt(x.split('-')[3]);
+                } else {
+                    max = parseInt(x.split('-')[2]);
+                }
+                for (let i = min; i <= max; i++) {
+                    res.push(i);
+                }
+            } else if (x.includes('-') && x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
+                res.push(parseInt(x));
+            } else {
+                res.push(parseInt(x));
+            }
+        });
+        return res;
+    } else if (x.includes('-') && !x.includes('+')) {
+        const res: number[] = [];
+        if (!x.startsWith('-')) {
+            const [min, max] = x.split('-').map(x => parseInt(x));
+            for (let i = min; i <= max; i++) {
+                res.push(i);
+            }
+        } else if (x.startsWith('-') && x.match(/[0-9]+-[-0-9]+/)) {
+            const min = -parseInt(x.split('-')[1]);
+            let max;
+            if (x.includes('--')) {
+                max = -parseInt(x.split('-')[3]);
+            } else {
+                max = parseInt(x.split('-')[2]);
+            }
+            for (let i = min; i <= max; i++) {
+                res.push(i);
+            }
+        } else if (x.startsWith('-') && !x.match(/[0-9]+-[-0-9]+/)) {
+            res.push(parseInt(x));
+        } else {
+            res.push(parseInt(x));
+        }
+        return res;
+    } else if (!x.includes('-') && x.includes('+')) {
+        return listMap(x).map(x => parseInt(x));
+    } else {
+        return [parseInt(x)];
+    }
+}
+
+function elementListMap(x: string) {
+    return x.split('+').map(B.struct.type.elementSymbol);
+}
+
+const sstrucDict: { [k: string]: string } = {
+    H: 'helix',
+    S: 'beta',
+    L: 'none'
+};
+function sstrucListMap(x: string) {
+    return {
+        flags: B.struct.type.secondaryStructureFlags(
+            x.toUpperCase().split('+').map(ss => sstrucDict[ss] || 'none')
+        )
+    };
+}
+
+export const properties: PropertyDict = {
+    symbol: {
+        '@desc': 'chemical-symbol-list: list of 1- or 2-letter chemical symbols from the periodic table',
+        '@examples': ['symbol O+N'],
+        abbr: ['e.'], regex: /[a-zA-Z'"+]+/, map: elementListMap,
+        level: 'atom-test', property: B.acp('elementSymbol')
+    },
+    name: {
+        '@desc': 'atom-name-list: list of up to 4-letter codes for atoms in proteins or nucleic acids',
+        '@examples': ['name CA+CB+CG+CD'],
+        abbr: ['n.'], regex: /[a-zA-Z0-9'"+]+/, map: atomNameListMap,
+        level: 'atom-test', property: B.ammp('label_atom_id')
+    },
+    resn: {
+        '@desc': 'residue-name-list: list of 3-letter codes for amino acids or list of up to 2-letter codes for nucleic acids',
+        '@examples': ['resn ASP+GLU+ASN+GLN', 'resn A+G'],
+        abbr: ['resname', 'r.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        level: 'residue-test', property: B.ammp('label_comp_id')
+    },
+    resi: {
+        '@desc': 'residue-identifier-list list of up to 4-digit residue numbers or residue-identifier-range',
+        '@examples': ['resi 1+10+100+1000', 'resi 1-10'],
+        abbr: ['resident', 'residue', 'resid', 'i.'], regex: /[0-9+-]+/, map: listOrRangeMap,
+        level: 'residue-test', property: B.ammp('auth_seq_id')
+    },
+    alt: {
+        '@desc': 'alternate-conformation-identifier-list list of single letters',
+        '@examples': ['alt A+B', 'alt ""', 'alt ""+A'],
+        abbr: [], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        level: 'atom-test', property: B.ammp('label_alt_id')
+    },
+    chain: {
+        '@desc': 'chain-identifier-list list of single letters or sometimes numbers',
+        '@examples': ['chain A'],
+        abbr: ['c.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        level: 'chain-test', property: B.ammp('auth_asym_id')
+    },
+    segi: {
+        '@desc': 'segment-identifier-list list of up to 4 letter identifiers',
+        '@examples': ['segi lig'],
+        abbr: ['segid', 's.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        level: 'chain-test', property: B.ammp('label_asym_id')
+    },
+    flag: {
+        '@desc': 'flag-number a single integer from 0 to 31',
+        '@examples': ['flag 0'],
+        isUnsupported: true,
+        abbr: ['f.'], regex: /[0-9]+/, map: x => parseInt(x),
+        level: 'atom-test'
+    },
+    numeric_type: {
+        '@desc': 'type-number a single integer',
+        '@examples': ['nt. 5'],
+        isUnsupported: true,
+        abbr: ['nt.'], regex: /[0-9]+/, map: x => parseInt(x),
+        level: 'atom-test'
+    },
+    text_type: {
+        '@desc': 'type-string a list of up to 4 letter codes',
+        '@examples': ['text_type HA+HC'],
+        isUnsupported: true,
+        abbr: ['tt.'], regex: /[a-zA-Z0-9'"+]+/, map: listMap,
+        level: 'atom-test'
+    },
+    id: {
+        '@desc': 'external-index-number a single integer',
+        '@examples': ['id 23'],
+        regex: /[0-9+-]+/, map: listOrRangeMap,
+        level: 'atom-test', property: B.ammp('id')
+    },
+    index: {
+        '@desc': 'internal-index-number a single integer',
+        '@examples': ['index 11'],
+        regex: /[0-9+-]+/, map: listOrRangeMap,
+        level: 'atom-test', property: B.ammp('id')
+    },
+    ss: {
+        '@desc': 'secondary-structure-type list of single letters. Helical regions should be assigned H and sheet regions S. Loop regions can either be assigned L or be blank.',
+        '@examples': ['ss H+S+L', 'ss S+""'],
+        abbr: [], regex: /[a-zA-Z'"+]+/, map: sstrucListMap,
+        level: 'residue-test', property: B.ammp('secondaryStructureFlags')
+    },
+
+    b: {
+        '@desc': 'comparison-operator b-factor-value a real number',
+        '@examples': ['b > 10'],
+        isNumeric: true,
+        abbr: [], regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.ammp('B_iso_or_equiv')
+    },
+    q: {
+        '@desc': 'comparison-operator occupancy-value a real number',
+        '@examples': ['q <0.50'],
+        isNumeric: true,
+        abbr: [], regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.ammp('occupancy')
+    },
+    formal_charge: {
+        '@desc': 'comparison-operator formal charge-value an integer',
+        '@examples': ['fc. = -1'],
+        isNumeric: true,
+        abbr: ['fc.'], regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.ammp('pdbx_formal_charge')
+    },
+    partial_charge: {
+        '@desc': 'comparison-operator partial charge-value a real number',
+        '@examples': ['pc. > 1'],
+        isUnsupported: true,
+        isNumeric: true,
+        abbr: ['pc.'], regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test'
+    },
+    elem: {
+        '@desc': 'str  atomic element symbol string ("X" if undefined)',
+        '@examples': ['elem N'],
+        regex: /[a-zA-Z0-9]{1,3}/, map: x => B.es(x),
+        level: 'atom-test', property: B.acp('elementSymbol')
+    }
+};

src/mol-script/transpilers/pymol/symbols.ts

@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+
+export const Properties: string[] = [];
+for (const name in properties) {
+    if (properties[name].isUnsupported) continue;
+    Properties.push(name);
+    if (properties[name].abbr) Properties.push(...properties[name].abbr!);
+}
+
+export const Operators: string[] = [];
+operators.forEach(o => {
+    if (o.isUnsupported) return;
+    Operators.push(o.name);
+    if (o.abbr) Operators.push(...o.abbr);
+});
+
+export const Keywords: string[] = [];
+for (const name in keywords) {
+    if (!keywords[name].map) continue;
+    Keywords.push(name);
+    if (keywords[name].abbr) Keywords.push(...keywords[name].abbr!);
+}
+
+export const all = { Properties, Operators: [...Operators, 'of'], Keywords };

src/mol-script/transpilers/transpiler.ts

@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { Expression } from '../language/expression';
+
+export type Transpiler = (source: string) => Expression
+
+export const Transpiler = (source: string) => Expression;

src/mol-script/transpilers/types.ts

@@ -0,0 +1,63 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../mol-util/monadic-parser';
+import { Expression } from '../language/expression';
+
+export interface AtomGroupArgs {
+    [index: string]: any
+    'entity-test'?: Expression
+    'chain-test'?: Expression
+    'residue-test'?: Expression
+    'atom-test'?: Expression
+    'groupBy'?: Expression
+}
+
+export interface Keyword {
+    '@desc': string
+    abbr?: string[]
+    map?: () => Expression /* not given means the keyword is unsupported */
+}
+
+export type KeywordDict = { [name: string]: Keyword }
+
+export interface Property {
+    '@desc': string
+    '@examples': string[]
+    isUnsupported?: boolean
+    isNumeric?: boolean
+    abbr?: string[]
+    regex: RegExp
+    map: (s: string) => any
+    level: 'atom-test' | 'residue-test' | 'chain-test' | 'entity-test'
+    property?: Expression
+}
+
+export type PropertyDict = { [name: string]: Property }
+
+export interface Operator {
+    '@desc': string
+    '@examples': string[]
+    name: string
+    abbr?: string[]
+    isUnsupported?: boolean
+    type: (p1: P.MonadicParser<any>, p2: P.MonadicParser<any>, fn: any) => P.MonadicParser<any>
+    rule: P.MonadicParser<any>
+    map: (x: any, y: any, z?: any) => Expression | Expression[]
+}
+
+export type OperatorList = Operator[]
+
+export interface Function {
+    '@desc': string
+    '@examples': string[]
+    map?: (x: any) => Expression /* not given means the keyword is unsupported */
+}
+
+export type FunctionDict = { [name: string]: Function }

src/mol-script/transpilers/vmd/examples.ts

@@ -0,0 +1,79 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+export const examples = [{
+    name: 'All water residues',
+    value: 'water'
+}, {
+    name: 'All C-alpha atoms',
+    value: 'name CA'
+}, {
+    name: 'Residue 35',
+    value: 'resid 35'
+}, {
+    name: 'C-alpha atoms of ALA',
+    value: 'name CA and resname ALA'
+}, {
+    name: 'Backbone atoms',
+    value: 'backbone'
+}, {
+    name: 'Non-protein atoms',
+    value: 'not protein'
+}, {
+    name: 'Protein backbone or hydrogen atoms',
+    value: 'protein (backbone or name H)'
+}, {
+    name: 'Atoms heavier than 20',
+    value: 'mass > 20'
+}, {
+    name: 'Atoms with two bonds',
+    value: 'numbonds = 2'
+}, {
+    name: 'Atoms with an absolute charge greater 1',
+    value: 'abs(charge) > 1'
+}, {
+    name: 'Atoms with an x coordinate between -25 and -20',
+    value: 'x < -20 and x > -25'
+}, {
+    name: 'Helices',
+    value: 'structure H'
+}, {
+    name: 'Atoms with name "A 1"',
+    value: "name 'A 1'"
+}, {
+    name: 'Atoms with name "A *"',
+    value: "name 'A *'"
+}, {
+    name: 'Atoms with names starting with C',
+    value: 'name "C.*"'
+}, {
+    name: 'Atoms within 10 ang of [25, 15, 10]',
+    value: 'sqr(x+25)+sqr(y+15)+sqr(z+10) <= sqr(10)'
+}, {
+    name: 'Atoms within 5 ang of iron atoms',
+    value: 'within 5 of name FE'
+}, {
+    name: 'Atoms around 10 ang of HEM residue',
+    value: 'exwithin 10 of resname HEM'
+}, {
+    name: 'ALA residues within 15 ang of HEM',
+    value: 'resname ALA within 15 of resname HEM'
+}, {
+    name: 'All groups that include an iron atom',
+    value: 'same resid as name FE'
+}, {
+    name: 'Atoms with mass between 12 and 17.5',
+    value: 'mass 12 to 17.5'
+}, {
+    name: 'Residues 60, 80, 90 and 142',
+    value: 'resid 60 80 90 142'
+}/* , {
+    name: 'Residues ala, arg, asn, asp, cys, and tyr',
+    value: 'resname ALA to CYS TYR'
+}*/];

src/mol-script/transpilers/vmd/functions.ts

@@ -0,0 +1,100 @@
+/**
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { FunctionDict } from '../types';
+
+export const functions: FunctionDict = {
+    'sqr': {
+        '@desc': 'square of x',
+        '@examples': ['sqr(2)'],
+        map: x => B.core.math.pow([x, 2]),
+    },
+    'sqrt': {
+        '@desc': 'square root of x',
+        '@examples': ['sqrt(2)'],
+        map: x => B.core.math.sqrt([x]),
+    },
+    'abs': {
+        '@desc': 'absolute value of x',
+        '@examples': ['abs(2)'],
+        map: x => B.core.math.abs([x]),
+    },
+    'floor': {
+        '@desc': 'largest integer not greater than x',
+        '@examples': ['floor(2)'],
+        map: x => B.core.math.floor([x]),
+    },
+    'ceil': {
+        '@desc': 'smallest integer not less than x',
+        '@examples': ['ceil(2)'],
+        map: x => B.core.math.ceil([x]),
+    },
+    'sin': {
+        '@desc': 'sine of x',
+        '@examples': ['sin(2)'],
+        map: x => B.core.math.sin([x]),
+    },
+    'cos': {
+        '@desc': 'cosine of x',
+        '@examples': ['cos(2)'],
+        map: x => B.core.math.cos([x]),
+    },
+    'tan': {
+        '@desc': 'tangent of x',
+        '@examples': ['tan(2)'],
+        map: x => B.core.math.tan([x]),
+    },
+    'atan': {
+        '@desc': 'arctangent of x',
+        '@examples': ['atan(2)'],
+        map: x => B.core.math.atan([x]),
+    },
+    'asin': {
+        '@desc': 'arcsin of x',
+        '@examples': ['asin(2)'],
+        map: x => B.core.math.asin([x]),
+    },
+    'acos': {
+        '@desc': 'arccos of x',
+        '@examples': ['acos(2)'],
+        map: x => B.core.math.acos([x]),
+    },
+    'sinh': {
+        '@desc': 'hyperbolic sine of x',
+        '@examples': ['sinh(2)'],
+        map: x => B.core.math.sinh([x]),
+    },
+    'cosh': {
+        '@desc': 'hyperbolic cosine of x',
+        '@examples': ['cosh(2)'],
+        map: x => B.core.math.cosh([x]),
+    },
+    'tanh': {
+        '@desc': 'hyperbolic tangent of x',
+        '@examples': ['tanh(2)'],
+        map: x => B.core.math.tanh([x]),
+    },
+    'exp': {
+        '@desc': 'e to the power x',
+        '@examples': ['exp(2)'],
+        map: x => B.core.math.exp([x]),
+    },
+    'log': {
+        '@desc': 'natural log of x',
+        '@examples': ['log(2)'],
+        map: x => B.core.math.log([x]),
+    },
+    'log10': {
+        '@desc': 'log base 10 of x',
+        '@examples': ['log10(2)'],
+        map: x => B.core.math.log10([x]),
+    }
+};

src/mol-script/transpilers/vmd/keywords.ts

@@ -0,0 +1,303 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { KeywordDict } from '../types';
+
+function proteinExpr() {
+    return B.struct.filter.pick({
+        0: B.struct.generator.atomGroups({
+            'group-by': B.ammp('residueKey')
+        }),
+        test: B.core.set.isSubset([
+            h.atomNameSet(['C', 'N', 'CA', 'O']),
+            B.ammpSet('label_atom_id')
+        ])
+    });
+}
+
+function nucleicExpr() {
+    return B.struct.filter.pick({
+        0: B.struct.generator.atomGroups({
+            'group-by': B.ammp('residueKey')
+        }),
+        test: B.core.logic.and([
+            B.core.set.isSubset([
+                h.atomNameSet(['P']),
+                B.ammpSet('label_atom_id')
+            ]),
+            B.core.logic.or([
+                B.core.set.isSubset([
+                    h.atomNameSet(["O3'", "C3'", "C4'", "C5'", "O5'"]),
+                    B.ammpSet('label_atom_id')
+                ]),
+                B.core.set.isSubset([
+                    h.atomNameSet(['O3*', 'C3*', 'C4*', 'C5*', 'O5*']),
+                    B.ammpSet('label_atom_id')
+                ])
+            ])
+        ])
+    });
+}
+
+function backboneExpr() {
+    return B.struct.combinator.merge([
+        B.struct.generator.queryInSelection({
+            0: proteinExpr(),
+            query: B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    h.atomNameSet(Backbone.protein),
+                    B.ammp('label_atom_id')
+                ])
+            })
+        }),
+        B.struct.generator.queryInSelection({
+            0: nucleicExpr(),
+            query: B.struct.generator.atomGroups({
+                'atom-test': B.core.set.has([
+                    h.atomNameSet(Backbone.nucleic),
+                    B.ammp('label_atom_id')
+                ])
+            })
+        })
+    ]);
+}
+
+function secStrucExpr(flags: string[]) {
+    return B.struct.generator.atomGroups({
+        'residue-test': B.core.flags.hasAll([
+            B.ammp('secondaryStructureFlags'),
+            B.struct.type.secondaryStructureFlags(flags)
+        ])
+    });
+}
+
+const Backbone = {
+    nucleic: ['P', "O3'", "O5'", "C5'", "C4'", "C3'", 'OP1', 'OP2', 'O3*', 'O5*', 'C5*', 'C4*', 'C3*'],
+    protein: ['C', 'N', 'CA', 'O']
+};
+
+const ResDict = {
+    acidic: ['ASP', 'GLU'],
+    aliphatic: ['ALA', 'GLY', 'ILE', 'LEU', 'VAL'],
+    aromatic: ['HIS', 'PHE', 'TRP', 'TYR'],
+    at: ['ADA', 'A', 'THY', 'T'],
+    basic: ['ARG', 'HIS', 'LYS'],
+    buried: ['ALA', 'LEU', 'VAL', 'ILE', 'PHE', 'CYS', 'MET', 'TRP'],
+    cg: ['CYT', 'C', 'GUA', 'G'],
+    cyclic: ['HIS', 'PHE', 'PRO', 'TRP', 'TYR'],
+    hydrophobic: ['ALA', 'LEU', 'VAL', 'ILE', 'PRO', 'PHE', 'MET', 'TRP'],
+    medium: ['VAL', 'THR', 'ASP', 'ASN', 'PRO', 'CYS', 'ASX', 'PCA', 'HYP'],
+    neutral: ['VAL', 'PHE', 'GLN', 'TYR', 'HIS', 'CYS', 'MET', 'TRP', 'ASX', 'GLX', 'PCA', 'HYP'],
+    purine: ['ADE', 'A', 'GUA', 'G'],
+    pyrimidine: ['CYT', 'C', 'THY', 'T', 'URI', 'U'],
+    small: ['ALA', 'GLY', 'SER'],
+    water: ['H2O', 'HH0', 'OHH', 'HOH', 'OH2', 'SOL', 'WAT', 'TIP', 'TIP2', 'TIP3', 'TIP4']
+};
+
+export const keywords: KeywordDict = {
+    all: {
+        '@desc': 'everything',
+        map: () => B.struct.generator.all()
+    },
+    none: {
+        '@desc': 'nothing',
+        map: () => B.struct.generator.empty()
+    },
+    protein: {
+        '@desc': 'a residue with atoms named C, N, CA, and O',
+        map: () => proteinExpr()
+    },
+    nucleic: {
+        '@desc': "a residue with atoms named P, O1P, O2P and either O3', C3', C4', C5', O5' or O3*, C3*, C4*, C5*, O5*. This definition assumes that the base is phosphorylated, an assumption which will be corrected in the future.",
+        map: () => nucleicExpr()
+    },
+    backbone: {
+        '@desc': 'the C, N, CA, and O atoms of a protein and the equivalent atoms in a nucleic acid.',
+        map: () => backboneExpr()
+    },
+    sidechain: {
+        '@desc': 'non-backbone atoms and bonds', // TODO: what does 'bonds' mean here?
+        map: () => h.invertExpr(backboneExpr())
+    },
+    water: {
+        '@desc': 'all atoms with the resname H2O, HH0, OHH, HOH, OH2, SOL, WAT, TIP, TIP2, TIP3 or TIP4',
+        abbr: ['waters'],
+        map: () => h.resnameExpr(ResDict.water)
+    },
+    at: {
+        '@desc': 'residues named ADA A THY T',
+        map: () => h.resnameExpr(ResDict.at)
+    },
+    acidic: {
+        '@desc': 'residues named ASP GLU',
+        map: () => h.resnameExpr(ResDict.acidic)
+    },
+    acyclic: {
+        '@desc': '"protein and not cyclic"',
+        map: () => B.struct.modifier.intersectBy({
+            0: proteinExpr(),
+            by: h.invertExpr(h.resnameExpr(ResDict.cyclic))
+        })
+    },
+    aliphatic: {
+        '@desc': 'residues named ALA GLY ILE LEU VAL',
+        map: () => h.resnameExpr(ResDict.aliphatic)
+    },
+    alpha: {
+        '@desc': "atom's residue is an alpha helix",
+        map: () => secStrucExpr(['alpha'])
+    },
+    amino: {
+        '@desc': 'a residue with atoms named C, N, CA, and O',
+        map: () => proteinExpr()
+    },
+    aromatic: {
+        '@desc': 'residues named HIS PHE TRP TYR',
+        map: () => h.resnameExpr(ResDict.aromatic)
+    },
+    basic: {
+        '@desc': 'residues named ARG HIS LYS',
+        map: () => h.resnameExpr(ResDict.basic)
+    },
+    bonded: {
+        '@desc': 'atoms for which numbonds > 0',
+        map: () => h.asAtoms(B.struct.filter.pick({
+            '0': B.struct.modifier.includeConnected({
+                '0': B.struct.generator.all(),
+                'bond-test': B.core.flags.hasAny([
+                    B.struct.bondProperty.flags(),
+                    B.struct.type.bondFlags(['covalent', 'metallic', 'sulfide'])
+                ])
+            }),
+            test: B.core.rel.gr([
+                B.struct.atomSet.atomCount(), 1
+            ])
+        }))
+    },
+    buried: {
+        '@desc': 'residues named ALA LEU VAL ILE PHE CYS MET TRP',
+        map: () => h.resnameExpr(ResDict.buried)
+    },
+    cg: {
+        '@desc': 'residues named CYT C GUA G',
+        map: () => h.resnameExpr(ResDict.cg)
+    },
+    charged: {
+        '@desc': '"basic or acidic"',
+        map: () => h.resnameExpr(ResDict.basic.concat(ResDict.acidic))
+    },
+    cyclic: {
+        '@desc': 'residues named HIS PHE PRO TRP TYR',
+        map: () => h.resnameExpr(ResDict.cyclic)
+    },
+    hetero: {
+        '@desc': '"not (protein or nucleic)"',
+        map: () => h.invertExpr(
+            B.struct.combinator.merge([proteinExpr(), nucleicExpr()])
+        )
+    },
+    hydrogen: {
+        '@desc': 'name "[0-9]?H.*"',
+        map: () => B.struct.generator.atomGroups({
+            'atom-test': B.core.str.match([
+                B.core.type.regex(['^[0-9]?[H].*$', 'i']),
+                B.core.type.str([B.ammp('label_atom_id')])
+            ])
+        })
+    },
+    large: {
+        '@desc': '"protein and not (small or medium)"',
+        map: () => B.struct.modifier.intersectBy({
+            0: proteinExpr(),
+            by: h.invertExpr(
+                h.resnameExpr(ResDict.small.concat(ResDict.medium))
+            )
+        })
+    },
+    medium: {
+        '@desc': 'residues named VAL THR ASP ASN PRO CYS ASX PCA HYP',
+        map: () => h.resnameExpr(ResDict.medium)
+    },
+    neutral: {
+        '@desc': 'residues named VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP',
+        map: () => h.resnameExpr(ResDict.neutral)
+    },
+    hydrophobic: {
+        '@desc': 'hydrophobic resname ALA LEU VAL ILE PRO PHE MET TRP',
+        map: () => h.resnameExpr(ResDict.hydrophobic)
+    },
+    polar: {
+        '@desc': '"protein and not hydrophobic"',
+        map: () => B.struct.modifier.intersectBy({
+            0: proteinExpr(),
+            by: h.invertExpr(h.resnameExpr(ResDict.hydrophobic))
+        })
+    },
+    purine: {
+        '@desc': 'residues named ADE A GUA G',
+        map: () => h.resnameExpr(ResDict.purine)
+    },
+    pyrimidine: {
+        '@desc': 'residues named CYT C THY T URI U',
+        map: () => h.resnameExpr(ResDict.pyrimidine)
+    },
+    small: {
+        '@desc': 'residues named ALA GLY SER',
+        map: () => h.resnameExpr(ResDict.small)
+    },
+    surface: {
+        '@desc': '"protein and not buried"',
+        map: () => B.struct.modifier.intersectBy({
+            0: proteinExpr(),
+            by: h.invertExpr(h.resnameExpr(ResDict.buried))
+        })
+    },
+    alpha_helix: {
+        '@desc': "atom's residue is in an alpha helix",
+        map: () => secStrucExpr(['alpha'])
+    },
+    pi_helix: {
+        '@desc': "atom's residue is in a pi helix",
+        map: () => secStrucExpr(['pi'])
+    },
+    helix_3_10: {
+        '@desc': "atom's residue is in a 3-10 helix",
+        map: () => secStrucExpr(['3-10'])
+    },
+    helix: {
+        '@desc': "atom's residue is in an alpha or pi or 3-10 helix",
+        map: () => secStrucExpr(['helix'])
+    },
+    extended_beta: {
+        '@desc': "atom's residue is a beta sheet",
+        map: () => secStrucExpr(['sheet'])
+    },
+    bridge_beta: {
+        '@desc': "atom's residue is a beta sheet",
+        map: () => secStrucExpr(['strand'])
+    },
+    sheet: {
+        '@desc': "atom's residue is a beta sheet",
+        map: () => secStrucExpr(['beta'])
+    },
+    turn: {
+        '@desc': "atom's residue is in a turn conformation",
+        map: () => secStrucExpr(['turn'])
+    },
+    coil: {
+        '@desc': "atom's residue is in a coil conformation",
+        map: () => B.struct.modifier.intersectBy({
+            0: proteinExpr(),
+            by: secStrucExpr(['none'])
+        })
+    }
+};

src/mol-script/transpilers/vmd/markdown-docs.ts

@@ -0,0 +1,77 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+import { functions } from './functions';
+
+const _docs: string[] = [
+    'VMD',
+    '============',
+    '--------------------------------',
+    ''
+];
+
+_docs.push(`## Properties\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in properties) {
+    if (properties[name].isUnsupported) continue;
+
+    const names = [name];
+    if (properties[name].abbr) names.push(...properties[name].abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (properties[name]['@desc']) {
+        _docs.push(`*${properties[name]['@desc']}*\n`);
+    }
+}
+
+_docs.push(`## Operators\n\n`);
+_docs.push('--------------------------------\n');
+operators.forEach(o => {
+    if (o.isUnsupported) return;
+
+    const names = [o.name];
+    if (o.abbr) names.push(...o.abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (o['@desc']) {
+        _docs.push(`*${o['@desc']}*\n`);
+    }
+});
+
+_docs.push(`## Keywords\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in keywords) {
+    if (!keywords[name].map) continue;
+
+    const names = [name];
+    if (keywords[name].abbr) names.push(...keywords[name].abbr!);
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (keywords[name]['@desc']) {
+        _docs.push(`*${keywords[name]['@desc']}*\n`);
+    }
+}
+
+_docs.push(`## Functions\n\n`);
+_docs.push('--------------------------------\n');
+for (const name in functions) {
+    if (!functions[name].map) continue;
+
+    const names = [name];
+    _docs.push(`\`\`\`\n${names.join(', ')}\n\`\`\`\n`);
+
+    if (functions[name]['@desc']) {
+        _docs.push(`*${functions[name]['@desc']}*\n`);
+    }
+}
+
+export const docs = _docs.join('\n');

src/mol-script/transpilers/vmd/operators.ts

@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../../mol-util/monadic-parser';
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { properties } from './properties';
+import { Expression } from '../../language/expression';
+import { OperatorList } from '../types';
+
+const propNames = Object.keys(properties).sort(h.strLenSortFn)
+    .filter(name => !properties[name].isUnsupported).join('|');
+
+export const operators: OperatorList = [
+    {
+        '@desc': 'Selects atoms that are not included in s1.',
+        '@examples': ['not protein'],
+        name: 'not',
+        type: h.prefix,
+        rule: P.MonadicParser.regexp(/NOT/i).skip(P.MonadicParser.whitespace),
+        map: (op, selection) => h.invertExpr(selection),
+    },
+    {
+        '@desc': 'Selects atoms within a specified distance of a selection',
+        '@examples': ['within 5 of name FE'],
+        name: 'within',
+        type: h.prefix,
+        rule: h.prefixOp(/WITHIN\s+([-+]?[0-9]*\.?[0-9]+)\s+OF/i, 1).map((x: any) => parseFloat(x)),
+        map: (radius: number, selection: Expression) => {
+            return B.struct.modifier.includeSurroundings({ 0: selection, radius });
+        }
+    },
+    {
+        '@desc': 'Exclusive within, equivalent to (within 3 of X) and not X',
+        '@examples': ['exwithin 10 of resname HEM'],
+        name: 'exwithin',
+        type: h.prefix,
+        rule: h.prefixOp(/EXWITHIN\s+([-+]?[0-9]*\.?[0-9]+)\s+OF/i, 1).map((x: any) => parseFloat(x)),
+        map: (radius: number, target: Expression) => {
+            return B.struct.modifier.exceptBy({
+                '0': B.struct.modifier.includeSurroundings({ 0: target, radius }),
+                by: target
+            });
+        }
+    },
+    {
+        '@desc': 'Selects atoms which have the same keyword as the atoms in a given selection',
+        '@examples': ['same resid as name FE'],
+        name: 'same',
+        type: h.prefix,
+        rule: h.prefixOp(new RegExp(`SAME\\s+(${propNames})\\s+AS`, 'i'), 1).map((x: any) => properties[x].property),
+        map: (property: Expression, source: Expression) => {
+            return B.struct.filter.withSameAtomProperties({
+                '0': B.struct.generator.all(),
+                source,
+                property
+            });
+        }
+    },
+    {
+        '@desc': 'Selects atoms included in both s1 and s2.',
+        '@examples': ['backbone and protein'],
+        name: 'and',
+        type: h.binaryLeft,
+        rule: P.MonadicParser.alt(h.infixOp(/AND/i), P.MonadicParser.whitespace),
+        map: (op, selection, by) => B.struct.modifier.intersectBy({ 0: selection, by })
+    },
+    {
+        '@desc': 'Selects atoms included in either s1 or s2.',
+        '@examples': ['water or protein'],
+        name: 'or',
+        type: h.binaryLeft,
+        rule: h.infixOp(/OR/i),
+        map: (op, s1, s2) => B.struct.combinator.merge([s1, s2])
+    }
+];

src/mol-script/transpilers/vmd/parser.ts

@@ -0,0 +1,262 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import * as P from '../../../mol-util/monadic-parser';
+import * as h from '../helper';
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { sstrucMap, sstrucDict, properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+import { functions } from './functions';
+import { OperatorList } from '../types';
+import { Transpiler } from '../transpiler';
+
+// <, <=, = or ==, >=, >, and !=
+// lt, le, eq, ge, gt, and ne, =~
+const valueOperators: OperatorList = [
+    {
+        '@desc': 'multiplication, division',
+        '@examples': [],
+        name: 'mul-div',
+        type: h.binaryLeft,
+        rule: P.MonadicParser.regexp(/\s*(\*|\/)\s*/, 1),
+        map: (op, e1, e2) => {
+            switch (op) {
+                case '*': return B.core.math.mult([e1, e2]);
+                case '/': return B.core.math.div([e1, e2]);
+                default: throw new Error(`value operator '${op}' not supported`);
+            }
+        }
+    },
+    {
+        '@desc': 'addition, substraction',
+        '@examples': [],
+        name: 'add-sub',
+        type: h.binaryLeft,
+        rule: P.MonadicParser.regexp(/\s*(-|\+)\s*/, 1),
+        map: (op, e1, e2) => {
+            switch (op) {
+                case '-': return B.core.math.sub([e1, e2]);
+                case '+': return B.core.math.add([e1, e2]);
+                default: throw new Error(`value operator '${op}' not supported`);
+            }
+        }
+    },
+    {
+        '@desc': 'value comparisons',
+        '@examples': [],
+        name: 'comparison',
+        type: h.binaryLeft,
+        rule: P.MonadicParser.alt(P.MonadicParser.regexp(/\s*(=~|==|>=|<=|=|!=|>|<)\s*/, 1), P.MonadicParser.whitespace.result('=')),
+        map: (op, e1, e2) => {
+            let expr;
+            if (e1.head !== undefined) {
+                if (e1.head.name === 'structure-query.atom-property.macromolecular.secondary-structure-flags') {
+                    expr = B.core.flags.hasAny([e1, sstrucMap(e2)]);
+                }
+                if (e1.head.name === 'core.type.regex') {
+                    expr = B.core.str.match([e1, B.core.type.str([e2])]);
+                }
+            } else if (e2.head !== undefined) {
+                if (e2.head.name === 'structure-query.atom-property.macromolecular.secondary-structure-flags') {
+                    expr = B.core.flags.hasAny([e2, sstrucMap(e1)]);
+                }
+                if (e2.head.name === 'core.type.regex') {
+                    expr = B.core.str.match([e2, B.core.type.str([e1])]);
+                }
+            } else if (op === '=~') {
+                if (e1.head) {
+                    expr = B.core.str.match([
+                        B.core.type.regex([`^${e2}$`, 'i']),
+                        B.core.type.str([e1])
+                    ]);
+                } else {
+                    expr = B.core.str.match([
+                        B.core.type.regex([`^${e1}$`, 'i']),
+                        B.core.type.str([e2])
+                    ]);
+                }
+            }
+            if (!expr) {
+                if (e1.head) e2 = h.wrapValue(e1, e2);
+                if (e2.head) e1 = h.wrapValue(e2, e1);
+                switch (op) {
+                    case '=':
+                    case '==':
+                        expr = B.core.rel.eq([e1, e2]);
+                        break;
+                    case '!=':
+                        expr = B.core.rel.neq([e1, e2]);
+                        break;
+                    case '>':
+                        expr = B.core.rel.gr([e1, e2]);
+                        break;
+                    case '<':
+                        expr = B.core.rel.lt([e1, e2]);
+                        break;
+                    case '>=':
+                        expr = B.core.rel.gre([e1, e2]);
+                        break;
+                    case '<=':
+                        expr = B.core.rel.lte([e1, e2]);
+                        break;
+                    default: throw new Error(`value operator '${op}' not supported`);
+                }
+            }
+            return B.struct.generator.atomGroups({ 'atom-test': expr });
+        }
+    }
+];
+
+const lang = P.MonadicParser.createLanguage({
+    Parens: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Parens,
+            r.Operator,
+            r.Expression
+        ).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
+    },
+
+    Expression: function (r: any) {
+        return P.MonadicParser.alt(
+            r.RangeListProperty,
+            //	    r.NamedAtomProperties,
+            r.ValueQuery,
+            r.Keywords,
+        );
+    },
+
+    NamedAtomProperties: function () {
+        return P.MonadicParser.alt(...h.getNamedPropertyRules(properties));
+    },
+
+    Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
+
+    ValueRange: function (r: any) {
+        return P.MonadicParser.seq(
+            r.Value
+                .skip(P.MonadicParser.regexp(/\s+TO\s+/i)),
+            r.Value
+        ).map(x => ({ range: x }));
+    },
+
+    RangeListProperty: function (r: any) {
+        return P.MonadicParser.seq(
+            P.MonadicParser.alt(...h.getPropertyNameRules(properties, /\s/))
+                .skip(P.MonadicParser.whitespace),
+            P.MonadicParser.alt(
+                r.ValueRange,
+                r.Value
+            ).sepBy1(P.MonadicParser.whitespace)
+        ).map(x => {
+            const [property, values] = x;
+            const listValues: (string | number)[] = [];
+            const rangeValues: any[] = [];
+
+            values.forEach((v: any) => {
+                if (v.range) {
+                    rangeValues.push(
+                        B.core.rel.inRange([property, v.range[0], v.range[1]])
+                    );
+                } else {
+                    listValues.push(h.wrapValue(property, v, sstrucDict));
+                }
+            });
+
+            const rangeTest = h.orExpr(rangeValues);
+            const listTest = h.valuesTest(property, listValues);
+
+            let test;
+            if (rangeTest && listTest) {
+                test = B.core.logic.or([rangeTest, listTest]);
+            } else {
+                test = rangeTest ? rangeTest : listTest;
+            }
+
+            return B.struct.generator.atomGroups({ [h.testLevel(property)]: test });
+        });
+    },
+
+    Operator: function (r: any) {
+        return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression, r.ValueQuery));
+    },
+
+    Query: function (r: any) {
+        return P.MonadicParser.alt(
+            r.Operator,
+            r.Parens,
+            r.Expression
+        ).trim(P.MonadicParser.optWhitespace);
+    },
+
+    Number: function () {
+        return P.MonadicParser.regexp(/-?(0|[1-9][0-9]*)([.][0-9]+)?([eE][+-]?[0-9]+)?/)
+            .map(Number)
+            .desc('number');
+    },
+
+    String: function () {
+        const w = h.getReservedWords(properties, keywords, operators)
+            .sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
+        return P.MonadicParser.alt(
+            P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i')),
+            P.MonadicParser.regexp(/'((?:[^"\\]|\\.)*)'/, 1),
+            P.MonadicParser.regexp(/"((?:[^"\\]|\\.)*)"/, 1).map((x: any) => B.core.type.regex([`^${x}$`, 'i']))
+        ).desc('string');
+    },
+
+    Value: function (r: any) {
+        return P.MonadicParser.alt(r.Number, r.String);
+    },
+
+    ValueParens: function (r: any) {
+        return P.MonadicParser.alt(
+            r.ValueParens,
+            r.ValueOperator,
+            r.ValueExpressions
+        ).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
+    },
+
+    ValuePropertyNames: function () {
+        return P.MonadicParser.alt(...h.getPropertyNameRules(properties, /=~|==|>=|<=|=|!=|>|<|\)|\s|\+|-|\*|\//i));
+    },
+
+    ValueOperator: function (r: any) {
+        return h.combineOperators(valueOperators, P.MonadicParser.alt(r.ValueParens, r.ValueExpressions));
+    },
+
+    ValueExpressions: function (r: any) {
+        return P.MonadicParser.alt(
+            r.ValueFunctions,
+            r.Value,
+            r.ValuePropertyNames
+        );
+    },
+
+    ValueFunctions: function (r: any) {
+        return P.MonadicParser.alt(...h.getFunctionRules(functions, r.ValueOperator));
+    },
+
+    ValueQuery: function (r: any) {
+        return P.MonadicParser.alt(
+            r.ValueOperator.map((x: any) => {
+                // if (!x.head || x.head.startsWith('core.math') || x.head.startsWith('structure-query.atom-property')) {
+                if (!x.head.name || !x.head.name.startsWith('structure-query.generator')) {
+                    throw new Error(`values must be part of an comparison, value '${x}'`);
+                } else {
+                    return x as any;
+                }
+            })
+        );
+    }
+});
+
+export const transpiler: Transpiler = str => lang.Query.tryParse(str);

src/mol-script/transpilers/vmd/properties.ts

@@ -0,0 +1,269 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { MolScriptBuilder } from '../../../mol-script/language/builder';
+const B = MolScriptBuilder;
+import { PropertyDict } from '../types';
+
+const reFloat = /[-+]?[0-9]*\.?[0-9]+/;
+const rePosInt = /[+]?[0-9]+/;
+const reInt = /[-+]?[0-9]+/;
+
+function str(x: string) { return x; }
+
+export const sstrucDict: { [key: string]: string } = {
+    T: 'turn', // Turn
+    E: 'sheet', // Extended conformation ($\beta$ sheets)
+    B: 'strand', // Isolated bridge
+    H: 'alpha', // Alpha helix
+    G: '3-10', // 3-10 helix
+    I: 'pi', // Pi helix
+    C: 'none', // Coil
+};
+export function sstrucMap(x: string) {
+    return B.struct.type.secondaryStructureFlags(
+        [sstrucDict[x.toUpperCase()] || 'none']
+    );
+}
+
+export const properties: PropertyDict = {
+    name: {
+        '@desc': 'str    atom name',
+        '@examples': ['name CA'],
+        regex: /[a-zA-Z0-9]+/, map: B.atomName,
+        level: 'atom-test', property: B.ammp('label_atom_id')
+    },
+    type: {
+        '@desc': 'str    atom type',
+        '@examples': ['type C3'],
+        isUnsupported: true,
+        regex: /[a-zA-Z0-9]+/, map: str,
+        level: 'atom-test'
+    },
+    index: {
+        '@desc': 'num    the atom number, starting at 0',
+        '@examples': ['index 10'],
+        isNumeric: true,
+        regex: rePosInt, map: x => (parseInt(x) - 1),
+        level: 'atom-test', property: B.ammp('id')
+    },
+    serial: {
+        '@desc': 'num    the atom number, starting at 1',
+        '@examples': ['serial 11'],
+        isNumeric: true,
+        regex: rePosInt, map: x => parseInt(x),
+        level: 'atom-test', property: B.ammp('id')
+    },
+    atomicnumber: {
+        '@desc': 'num    atomic number (0 if undefined)',
+        '@examples': ['atomicnumber 13'],
+        isNumeric: true,
+        regex: rePosInt, map: x => parseInt(x),
+        level: 'atom-test', property: B.acp('atomicNumber')
+    },
+    element: {
+        '@desc': 'str  atomic element symbol string ("X" if undefined)',
+        '@examples': ['element N'],
+        regex: /[a-zA-Z0-9]{1,3}/, map: x => B.es(x),
+        level: 'atom-test', property: B.acp('elementSymbol')
+    },
+    altloc: {
+        '@desc': 'str  alternate location/conformation identifier',
+        '@examples': ['altloc C'],
+        regex: /[a-zA-Z0-9]+/, map: str,
+        level: 'atom-test', property: B.ammp('label_alt_id')
+    },
+    chain: {
+        '@desc': 'str  the one-character chain identifier',
+        '@examples': ['chain A'],
+        regex: /[a-zA-Z0-9]+/, map: str,
+        level: 'residue-test', property: B.ammp('auth_asym_id')
+    },
+    residue: {
+        '@desc': 'num  a set of connected atoms with the same residue number',
+        '@examples': ['residue < 11', 'residue 11'],
+        isNumeric: true,
+        regex: reInt, map: x => parseInt(x),
+        level: 'residue-test', property: B.ammp('auth_seq_id')
+    },
+    fragment: {
+        '@desc': 'num  a set of connected residues',
+        '@examples': ['fragment 42'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reInt, map: x => parseInt(x),
+        level: 'residue-test'
+    },
+    pfrag: {
+        '@desc': 'num  a set of connected protein residues',
+        '@examples': ['pfrag 42'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reInt, map: x => parseInt(x),
+        level: 'residue-test'
+    },
+    nfrag: {
+        '@desc': 'num  a set of connected nucleic residues',
+        '@examples': ['nfrag 42'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reInt, map: x => parseInt(x),
+        level: 'residue-test'
+    },
+    sequence: {
+        '@desc': 'str  a sequence given by one letter names',
+        '@examples': ['sequence PGATTACA'],
+        isUnsupported: true,
+        regex: /[a-zA-Z0-9]+/, map: str,
+        level: 'residue-test'
+    },
+    numbonds: {
+        '@desc': 'num  number of bonds',
+        '@examples': ['numbonds = 2', 'numbonds >= 3'],
+        isNumeric: true,
+        regex: rePosInt, map: x => parseInt(x),
+        level: 'atom-test', property: B.acp('bondCount')
+    },
+    resname: {
+        '@desc': 'str  residue name',
+        '@examples': ['resname ALA'],
+        regex: /[a-zA-Z0-9]+/, map: str,
+        level: 'residue-test', property: B.ammp('auth_comp_id')
+    },
+    resid: {
+        '@desc': 'num  residue id',
+        '@examples': ['resid 42'],
+        isNumeric: true,
+        regex: reInt, map: x => parseInt(x),
+        level: 'residue-test', property: B.ammp('auth_seq_id')
+    },
+    segname: {
+        '@desc': 'str  segment name',
+        '@examples': ['segname B'],
+        regex: /[a-zA-Z0-9]+/, map: str,
+        level: 'residue-test', property: B.ammp('label_asym_id')
+    },
+    x: {
+        '@desc': 'float  x coordinate',
+        '@examples': ['x 42'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.acp('x')
+    },
+    y: {
+        '@desc': 'float  y coordinate',
+        '@examples': ['y > 1.7'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.acp('y')
+    },
+    z: {
+        '@desc': 'float  z coordinate',
+        '@examples': ['z < 11', 'z > -21'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.acp('z')
+    },
+    radius: {
+        '@desc': 'float  atomic radius',
+        '@examples': ['radius > 1.3'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.acp('vdw')
+    },
+    mass: {
+        '@desc': 'float  atomic mass',
+        '@examples': ['mass > 2'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.acp('mass')
+    },
+    charge: {
+        '@desc': 'float  atomic charge',
+        '@examples': ['charge > 0', 'charge 1'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.ammp('pdbx_formal_charge')
+    },
+    beta: {
+        '@desc': 'float  temperature factor',
+        '@examples': ['beta < 20', 'beta > 35'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.ammp('B_iso_or_equiv')
+    },
+    occupancy: {
+        '@desc': 'float  occupancy',
+        '@examples': ['occupancy 1', 'occupancy < 1'],
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test', property: B.ammp('occupancy')
+    },
+    user: {
+        '@desc': 'float  time-varying user-specified value',
+        '@examples': ['user < 0.1'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'atom-test'
+    },
+    rasmol: {
+        '@desc': 'str  translates Rasmol selection string to VMD',
+        '@examples': ["rasmol 'all'"],
+        isUnsupported: true,
+        regex: /[^']*/, map: str,
+        level: 'atom-test'
+    },
+    structure: {
+        '@desc': 'str  single letter name for the secondary structure',
+        '@examples': ['structure H', 'structure H E'],
+        regex: /T|E|B|H|G|I|C/i, map: sstrucMap,
+        level: 'atom-test', property: B.ammp('secondaryStructureFlags')
+    },
+    phi: {
+        '@desc': 'float  phi backbone conformational angles',
+        '@examples': ['phi < 160'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'residue-test'
+    },
+    psi: {
+        '@desc': 'float  psi backbone conformational angles',
+        '@examples': ['psi < 160'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reFloat, map: x => parseFloat(x),
+        level: 'residue-test'
+    },
+    ufx: {
+        '@desc': 'num  force to apply in the x coordinate',
+        '@examples': ['ufx 1'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reFloat, map: x => parseInt(x),
+        level: 'atom-test'
+    },
+    ufy: {
+        '@desc': 'num  force to apply in the y coordinate',
+        '@examples': ['ufy 1'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reFloat, map: x => parseInt(x),
+        level: 'atom-test'
+    },
+    ufz: {
+        '@desc': 'num  force to apply in the z coordinate',
+        '@examples': ['ufz 1'],
+        isUnsupported: true,
+        isNumeric: true,
+        regex: reFloat, map: x => parseInt(x),
+        level: 'atom-test'
+    },
+};

src/mol-script/transpilers/vmd/symbols.ts

@@ -0,0 +1,42 @@
+/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ *
+ * Adapted from MolQL project
+ */
+
+import { properties } from './properties';
+import { operators } from './operators';
+import { keywords } from './keywords';
+import { functions } from './functions';
+
+export const Properties: string[] = [];
+for (const name in properties) {
+    if (properties[name].isUnsupported) continue;
+    Properties.push(name);
+    if (properties[name].abbr) Properties.push(...properties[name].abbr!);
+}
+
+export const Operators: string[] = [];
+operators.forEach(o => {
+    if (o.isUnsupported) return;
+    Operators.push(o.name);
+    if (o.abbr) Operators.push(...o.abbr);
+});
+
+export const Keywords: string[] = [];
+for (const name in keywords) {
+    if (!keywords[name].map) continue;
+    Keywords.push(name);
+    if (keywords[name].abbr) Keywords.push(...keywords[name].abbr!);
+}
+
+export const Functions: string[] = [];
+for (const name in functions) {
+    if (!functions[name].map) continue;
+    Functions.push(name);
+}
+
+export const all = { Properties, Operators: [...Operators, ...Functions], Keywords };

src/mol-state/action.ts

@@ -84,7 +84,7 @@ namespace StateAction {
     }
 
     export namespace Builder {
-        export interface Type<A extends StateObject.Ctor, P extends { }> {
+        export interface Type<A extends StateObject.Ctor, P extends {}> {
             from?: A | A[],
             params?: PD.For<P> | ((a: StateObject.From<A>, globalCtx: any) => PD.For<P>),
             display?: string | { name: string, description?: string },
@@ -95,7 +95,7 @@ namespace StateAction {
             <A extends StateObject.Ctor, P extends { }>(info: Type<A, P>): Define<StateObject.From<A>, PD.Normalize<P>>
         }
 
-        export interface Define<A extends StateObject, P> {
+        export interface Define<A extends StateObject, P extends {}> {
             <T>(def: DefinitionBase<A, T, P> | DefinitionBase<A, T, P>['run']): StateAction<A, T, P>,
         }
 

src/mol-state/transformer.ts

@@ -196,7 +196,7 @@ namespace Transformer {
     }
 
     export namespace Builder {
-        export interface Type<A extends StateObject.Ctor, B extends StateObject.Ctor, P extends { }> {
+        export interface Type<A extends StateObject.Ctor, B extends StateObject.Ctor, P extends {}> {
             name: string,
             from: A | A[],
             to: B | B[],
@@ -210,7 +210,7 @@ namespace Transformer {
             <A extends StateObject.Ctor, B extends StateObject.Ctor, P extends { }>(info: Type<A, B, P>): Define<StateObject.From<A>, StateObject.From<B>, PD.Normalize<P>>
         }
 
-        export interface Define<A extends StateObject, B extends StateObject, P> {
+        export interface Define<A extends StateObject, B extends StateObject, P extends {}> {
             (def: DefinitionBase<A, B, P>): Transformer<A, B, P>
         }
 

src/mol-util/index.ts

@@ -117,7 +117,7 @@ export function defaults<T>(value: T | undefined, defaultValue: T): T {
     return value !== undefined ? value : defaultValue;
 }
 
-export function extend<S, T, U>(object: S, source: T, guard?: U): S & T & U {
+export function extend<S extends {}, T extends {}, U extends {}>(object: S, source: T, guard?: U): S & T & U {
     let v: any;
 
     const s = <any>source;
@@ -139,7 +139,7 @@ export function extend<S, T, U>(object: S, source: T, guard?: U): S & T & U {
     return <any>object;
 }
 
-export function shallowClone<T>(o: T): T {
+export function shallowClone<T extends {}>(o: T): T {
     return extend({}, o) as T;
 }
 
@@ -158,7 +158,7 @@ function _assign<T>(target: T): T {
 export declare function _assignType<T>(o: T, ...from: any[]): T;
 export const assign: (<T>(o: T, ...from: any[]) => T) = (Object as any).assign || _assign;
 
-function _shallowMerge1<T>(source: T, update: T) {
+function _shallowMerge1<T extends {}>(source: T, update: T) {
     let changed = false;
     for (const k of Object.keys(update)) {
         if (!hasOwnProperty.call(update, k)) continue;

src/mol-util/input/input-observer.ts

@@ -304,6 +304,7 @@ namespace InputObserver {
         let buttons = ButtonsType.create(ButtonsType.Flag.None);
         let button = ButtonsType.Flag.None;
         let isInside = false;
+        let hasMoved = false;
 
         const events = createEvents();
         const { drag, interactionEnd, wheel, pinch, gesture, click, move, leave, enter, resize, modifiers, key } = events;
@@ -577,12 +578,13 @@ namespace InputObserver {
             if (!mask(ev.clientX, ev.clientY)) return;
 
             eventOffset(pointerEnd, ev);
-            if (Vec2.distance(pointerEnd, pointerDown) < 4) {
+            if (!hasMoved && Vec2.distance(pointerEnd, pointerDown) < 4) {
                 const { pageX, pageY } = ev;
                 const [x, y] = pointerEnd;
 
                 click.next({ x, y, pageX, pageY, buttons, button, modifiers: getModifierKeys() });
             }
+            hasMoved = false;
         }
 
         function onPointerMove(ev: PointerEvent) {
@@ -604,6 +606,10 @@ namespace InputObserver {
             const isStart = dragging === DraggingState.Started;
             if (isStart && !mask(ev.clientX, ev.clientY)) return;
 
+            if (Vec2.distance(pointerEnd, pointerDown) >= 4) {
+                hasMoved = true;
+            }
+
             const [dx, dy] = pointerDelta;
             drag.next({ x, y, dx, dy, pageX, pageY, buttons, button, modifiers: getModifierKeys(), isStart });
 

src/mol-util/monadic-parser.ts

@@ -2,12 +2,11 @@
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-/**
+ * @author Koya Sakuma <koya.sakuma.work@gmail.com>
+ **
  * Adapted from Parsimmon (https://github.com/jneen/parsimmon)
  * Copyright (c) 2011-present J. Adkisson (http://jneen.net).
- */
+ **/
 
 export class MonadicParser<A> {
     constructor(public _: MonadicParser.Action<A>) { }
@@ -234,15 +233,27 @@ export namespace MonadicParser {
 
     export type Result<T> = Success<T> | Failure
 
-    // export function createLanguage(parsers: any) {
-    //     const language: any = {};
-    //     for (const key of Object.keys(parsers)) {
-    //         (function (key) {
-    //             language[key] = lazy(() => parsers[key](language));
-    //         })(key);
-    //     }
-    //     return language;
-    // }
+    export function seqMap<A, B>(a: MonadicParser<A>, b: MonadicParser<B>, c: any) {
+        const args = [].slice.call(arguments);
+        if (args.length === 0) {
+            throw new Error('seqMap needs at least one argument');
+        }
+        const mapper = args.pop();
+        assertFunction(mapper);
+        return seq.apply(null, args).map(function (results: any) {
+            return mapper.apply(null, results);
+        });
+    }
+
+    export function createLanguage(parsers: any) {
+        const language: any = {};
+        for (const key of Object.keys(parsers)) {
+            (function (key) {
+                language[key] = lazy(() => parsers[key](language));
+            })(key);
+        }
+        return language;
+    }
 
     export function seq<A>(a: MonadicParser<A>): MonadicParser<[A]>
     export function seq<A, B>(a: MonadicParser<A>, b: MonadicParser<B>): MonadicParser<[A, B]>
@@ -326,7 +337,7 @@ export namespace MonadicParser {
     export function regexp(re: RegExp, group = 0) {
         const anchored = anchoredRegexp(re);
         const expected = '' + re;
-        return new MonadicParser(function (input, i) {
+        return new MonadicParser((input, i) => {
             const match = anchored.exec(input.slice(i));
             if (match) {
                 if (0 <= group && group <= match.length) {
@@ -455,6 +466,15 @@ export namespace MonadicParser {
     export const crlf = string('\r\n');
     export const newline = alt(crlf, lf, cr).desc('newline');
     export const end = alt(newline, eof);
+
+    export function of<A>(value: A) {
+        return succeed(value);
+    }
+
+    export function regex(re: RegExp) {
+        return regexp(re);
+    }
+
 }
 
 function seqPick(idx: number, ...parsers: MonadicParser<any>[]): MonadicParser<any> {
@@ -550,4 +570,10 @@ function unsafeUnion(xs: string[], ys: string[]) {
 
 function isParser(obj: any): obj is MonadicParser<any> {
     return obj instanceof MonadicParser;
-}
+}
+
+function assertFunction(x: any) {
+    if (typeof x !== 'function') {
+        throw new Error('not a function: ' + x);
+    }
+}

src/mol-util/object.ts

@@ -8,7 +8,7 @@
 const hasOwnProperty = Object.prototype.hasOwnProperty;
 
 /** Assign to the object if a given property in update is undefined */
-export function assignIfUndefined<T>(to: Partial<T>, full: T): T {
+export function assignIfUndefined<T extends {}>(to: Partial<T>, full: T): T {
     for (const k of Object.keys(full)) {
         if (!hasOwnProperty.call(full, k)) continue;
 
@@ -20,7 +20,7 @@ export function assignIfUndefined<T>(to: Partial<T>, full: T): T {
 }
 
 /** Create new object if any property in "update" changes in "source". */
-export function shallowMerge2<T>(source: T, update: Partial<T>): T {
+export function shallowMerge2<T extends {}>(source: T, update: Partial<T>): T {
     // Adapted from LiteMol (https://github.com/dsehnal/LiteMol)
     let changed = false;
     for (const k of Object.keys(update)) {
@@ -36,7 +36,7 @@ export function shallowMerge2<T>(source: T, update: Partial<T>): T {
     return Object.assign({}, source, update);
 }
 
-export function shallowEqual<T>(a: T, b: T) {
+export function shallowEqual<T extends {}>(a: T, b: T) {
     if (!a) {
         if (!b) return true;
         return false;
@@ -52,11 +52,11 @@ export function shallowEqual<T>(a: T, b: T) {
     return true;
 }
 
-export function shallowMerge<T>(source: T, ...rest: (Partial<T> | undefined)[]): T {
+export function shallowMerge<T extends {}>(source: T, ...rest: (Partial<T> | undefined)[]): T {
     return shallowMergeArray(source, rest);
 }
 
-export function shallowMergeArray<T>(source: T, rest: (Partial<T> | undefined)[]): T {
+export function shallowMergeArray<T extends {}>(source: T, rest: (Partial<T> | undefined)[]): T {
     // Adapted from LiteMol (https://github.com/dsehnal/LiteMol)
     let ret: any = source;
 

src/mol-util/param-definition.ts

@@ -324,7 +324,7 @@ export namespace ParamDefinition {
         conditionForValue(v: T): keyof C
         conditionedValue(v: T, condition: keyof C): T,
     }
-    export function Conditioned<T, P extends Base<T>, C = { [k: string]: P }>(defaultValue: T, conditionParams: C, conditionForValue: (v: T) => keyof C, conditionedValue: (v: T, condition: keyof C) => T, info?: Info): Conditioned<T, P, C> {
+    export function Conditioned<T, P extends Base<T>, C extends {} = { [k: string]: P }>(defaultValue: T, conditionParams: C, conditionForValue: (v: T) => keyof C, conditionedValue: (v: T, condition: keyof C) => T, info?: Info): Conditioned<T, P, C> {
         const options = Object.keys(conditionParams).map(k => [k, k]) as [string, string][];
         return setInfo({ type: 'conditioned', select: Select<string>(conditionForValue(defaultValue) as string, options, info), defaultValue, conditionParams, conditionForValue, conditionedValue }, info);
     }