Merge branch 'master' into molql_integration_PR

CHANGELOG.md

@@ -10,6 +10,10 @@ Note that since we don't clearly distinguish between a public and private interf
 - 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
 
 ## [v3.16.0] - 2022-08-25
 

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],

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);
@@ -91,7 +91,7 @@ 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/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/filters.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 { SetUtils } from '../../../../mol-util/set';
@@ -246,7 +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;
 
@@ -271,6 +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;
             }
 
@@ -293,6 +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;
                 }
             }

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-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/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>
@@ -377,6 +377,7 @@ const symbols = [
     // ============= 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),