molstar 3.0.0-dev.6 → 3.0.0

package/lib/mol-model-formats/structure/property/bonds/index-pair.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
  */
@@ -10,6 +10,7 @@ import { FormatPropertyProvider } from '../../common/property';
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { ElementIndex } from '../../../../mol-model/structure';
 export declare type IndexPairsProps = {
+    readonly key: ArrayLike<number>;
     readonly order: ArrayLike<number>;
     readonly distance: ArrayLike<number>;
     readonly flag: ArrayLike<BondType.Flag>;
@@ -26,13 +27,29 @@ export declare namespace IndexPairBonds {
         pairs: {
             indexA: Column<number>;
             indexB: Column<number>;
+            key?: Column<number>;
             order?: Column<number>;
+            /**
+             * Useful for bonds in periodic cells. That is, only bonds within the given
+             * distance are added. This allows for bond between periodic image but
+             * avoids unwanted bonds with wrong distances. If negative, test using the
+             * `maxDistance` option from `Props`.
+             */
             distance?: Column<number>;
             flag?: Column<BondType.Flag>;
         };
         count: number;
     };
     const DefaultProps: {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
         maxDistance: number;
     };
     type Props = typeof DefaultProps;

package/lib/mol-model-formats/structure/property/bonds/index-pair.js

@@ -1,24 +1,25 @@
 /**
- * Copyright (c) 2019-2021 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>
  */
 import { __assign } from "tslib";
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';
 import { FormatPropertyProvider } from '../../common/property';
-import { DefaultBondMaxRadius } from '../../../../mol-model/structure/structure/unit/bonds/common';
 function getGraph(indexA, indexB, props, count) {
     var builder = new IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
+    var key = new Int32Array(builder.slotCount);
     var order = new Int8Array(builder.slotCount);
     var distance = new Array(builder.slotCount);
     var flag = new Array(builder.slotCount);
     for (var i = 0, _i = builder.edgeCount; i < _i; i++) {
         builder.addNextEdge();
+        builder.assignProperty(key, props.key ? props.key[i] : -1);
         builder.assignProperty(order, props.order ? props.order[i] : 1);
         builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
         builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* Covalent */);
     }
-    return builder.createGraph({ order: order, distance: distance, flag: flag });
+    return builder.createGraph({ key: key, order: order, distance: distance, flag: flag });
 }
 export var IndexPairBonds;
 (function (IndexPairBonds) {
@@ -26,18 +27,30 @@ export var IndexPairBonds;
         name: 'index_pair_bonds',
     };
     IndexPairBonds.Provider = FormatPropertyProvider.create(IndexPairBonds.Descriptor);
-    IndexPairBonds.DefaultProps = { maxDistance: DefaultBondMaxRadius };
+    IndexPairBonds.DefaultProps = {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
+        maxDistance: -1
+    };
     function fromData(data, props) {
         if (props === void 0) { props = {}; }
         var p = __assign(__assign({}, IndexPairBonds.DefaultProps), props);
         var pairs = data.pairs, count = data.count;
         var indexA = pairs.indexA.toArray();
         var indexB = pairs.indexB.toArray();
+        var key = pairs.key && pairs.key.toArray();
         var order = pairs.order && pairs.order.toArray();
         var distance = pairs.distance && pairs.distance.toArray();
         var flag = pairs.flag && pairs.flag.toArray();
         return {
-            bonds: getGraph(indexA, indexB, { order: order, distance: distance, flag: flag }, count),
+            bonds: getGraph(indexA, indexB, { key: key, order: order, distance: distance, flag: flag }, count),
             maxDistance: p.maxDistance
         };
     }

package/lib/mol-model-props/common/custom-property.d.ts

@@ -47,7 +47,7 @@ declare namespace CustomProperty {
             }>>;
         };
         setDefaultAutoAttach(name: string, value: boolean): void;
-        get(name: string): Provider<Data, any, any>;
+        get(name: string): Provider<Data, any, any> | undefined;
         register(provider: Provider<Data, any, any>, defaultAutoAttach: boolean): void;
         unregister(name: string): void;
     }

package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts

@@ -34,6 +34,16 @@ export declare const InteractionsInterUnitParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsInterUnitParams = typeof InteractionsInterUnitParams;
 export declare function InteractionsInterUnitVisual(materialId: number): ComplexVisual<InteractionsInterUnitParams>;

package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
  */
@@ -34,6 +34,16 @@ export declare const InteractionsIntraUnitParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams;
 export declare function InteractionsIntraUnitVisual(materialId: number): UnitsVisual<InteractionsIntraUnitParams>;

package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
  */
@@ -98,6 +98,7 @@ function getInteractionLoci(pickingId, structureGroup, id) {
     }
     return EmptyLoci;
 }
+var __contactIndicesSet = new Set();
 function eachInteraction(loci, structureGroup, apply, isMarking) {
     var changed = false;
     if (Interactions.isLoci(loci)) {
@@ -132,28 +133,42 @@ function eachInteraction(loci, structureGroup, apply, isMarking) {
         if (!interactions)
             return false;
         var unit = group.units[0];
-        var contacts = interactions.unitsContacts.get(unit.id);
+        var contacts_1 = interactions.unitsContacts.get(unit.id);
         var features = interactions.unitsFeatures.get(unit.id);
-        var groupCount_1 = contacts.edgeCount * 2;
-        var offset_1 = contacts.offset;
+        var groupCount_1 = contacts_1.edgeCount * 2;
+        var offset_1 = contacts_1.offset;
         var _b = features.elementsIndex, fOffsets_1 = _b.offsets, fIndices_1 = _b.indices;
+        var members_1 = features.members, offsets_1 = features.offsets;
         var _loop_1 = function (e) {
             var unitIdx = group.unitIndexMap.get(e.unit.id);
-            if (unitIdx !== undefined)
-                return "continue";
-            if (isMarking && OrderedSet.size(e.indices) === 1)
+            if (unitIdx === undefined)
                 return "continue";
+            __contactIndicesSet.clear();
             OrderedSet.forEach(e.indices, function (v) {
                 for (var i = fOffsets_1[v], il = fOffsets_1[v + 1]; i < il; ++i) {
                     var fI = fIndices_1[i];
                     for (var j = offset_1[fI], jl = offset_1[fI + 1]; j < jl; ++j) {
-                        if (apply(Interval.ofSingleton(unitIdx * groupCount_1 + j)))
-                            changed = true;
+                        __contactIndicesSet.add(j);
+                    }
+                }
+            });
+            __contactIndicesSet.forEach(function (i) {
+                if (isMarking) {
+                    var fA = contacts_1.a[i];
+                    for (var j = offsets_1[fA], jl = offsets_1[fA + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members_1[j]))
+                            return;
+                    }
+                    var fB = contacts_1.b[i];
+                    for (var j = offsets_1[fB], jl = offsets_1[fB + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members_1[j]))
+                            return;
                     }
                 }
+                if (apply(Interval.ofSingleton(unitIdx * groupCount_1 + i)))
+                    changed = true;
             });
         };
-        // TODO: when isMarking, all elements of contact features need to be in the loci
         for (var _c = 0, _d = loci.elements; _c < _d.length; _c++) {
             var e = _d[_c];
             _loop_1(e);

package/lib/mol-model-props/computed/representations/interactions.d.ts

@@ -38,6 +38,16 @@ export declare const InteractionsParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsParams = typeof InteractionsParams;
 export declare function getInteractionParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -70,6 +80,16 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionRepresentation = StructureRepresentation<InteractionsParams>;
 export declare function InteractionRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InteractionsParams>): InteractionRepresentation;
@@ -103,4 +123,14 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "interactions">;

package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -39,6 +39,16 @@ export declare const CrossLinkRestraintCylinderParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintCylinderParams = typeof CrossLinkRestraintCylinderParams;
 export declare function CrossLinkRestraintVisual(materialId: number): ComplexVisual<CrossLinkRestraintCylinderParams>;
@@ -71,6 +81,16 @@ export declare const CrossLinkRestraintParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintParams = typeof CrossLinkRestraintParams;
 export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -102,6 +122,16 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintRepresentation = StructureRepresentation<CrossLinkRestraintParams>;
 export declare function CrossLinkRestraintRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CrossLinkRestraintParams>): CrossLinkRestraintRepresentation;
@@ -134,4 +164,14 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, CrossLinkRestraint.Tag>;

package/lib/mol-model-props/sequence/best-database-mapping.js

@@ -19,7 +19,7 @@ var BestDatabaseSequenceMapping;
         type: 'static',
         defaultParams: {},
         getParams: function () { return ({}); },
-        isApplicable: function (data) { var _a, _b; return MmcifFormat.is(data.sourceData) && ((_b = (_a = data.sourceData.data.frame.categories) === null || _a === void 0 ? void 0 : _a.atom_site) === null || _b === void 0 ? void 0 : _b.fieldNames.indexOf('db_name')) >= 0; },
+        isApplicable: function (data) { var _a, _b; return MmcifFormat.is(data.sourceData) && ((_b = (_a = data.sourceData.data.frame.categories) === null || _a === void 0 ? void 0 : _a.atom_site) === null || _b === void 0 ? void 0 : _b.fieldNames.indexOf('pdbx_sifts_xref_db_name')) >= 0; },
         obtain: function (ctx, data) { return __awaiter(_this, void 0, void 0, function () {
             return __generator(this, function (_a) {
                 return [2 /*return*/, { value: fromCif(data) }];
@@ -32,7 +32,7 @@ var BestDatabaseSequenceMapping;
         if (!data)
             return '';
         var eI = loc.unit.elements[loc.element];
-        var rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        var rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         return data.accession[rI];
     }
     BestDatabaseSequenceMapping.getKey = getKey;
@@ -42,7 +42,7 @@ var BestDatabaseSequenceMapping;
         if (!data)
             return;
         var eI = loc.unit.elements[loc.element];
-        var rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        var rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         var dbName = data.dbName[rI];
         if (!dbName)
             return;
@@ -53,10 +53,10 @@ var BestDatabaseSequenceMapping;
         if (!MmcifFormat.is(model.sourceData))
             return;
         var atom_site = model.sourceData.data.frame.categories.atom_site;
-        var db_name = atom_site.getField('db_name');
-        var db_acc = atom_site.getField('db_acc');
-        var db_num = atom_site.getField('db_num');
-        var db_res = atom_site.getField('db_res');
+        var db_name = atom_site.getField('pdbx_sifts_xref_db_name');
+        var db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
+        var db_num = atom_site.getField('pdbx_sifts_xref_db_num');
+        var db_res = atom_site.getField('pdbx_sifts_xref_db_res');
         if (!db_name || !db_acc || !db_num || !db_res)
             return;
         var atomSourceIndex = model.atomicHierarchy.atomSourceIndex;
@@ -68,16 +68,16 @@ var BestDatabaseSequenceMapping;
         for (var i = 0; i < count; i++) {
             var row = atomSourceIndex.value(residueOffsets[i]);
             if (db_name.valueKind(row) !== 0 /* Present */) {
-                dbName[row] = '';
-                accession[row] = '';
-                num[row] = 0;
-                residue[row] = '';
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = 0;
+                residue[i] = '';
                 continue;
             }
-            dbName[row] = db_name.str(row);
-            accession[row] = db_acc.str(row);
-            num[row] = db_num.int(row);
-            residue[row] = db_res.str(row);
+            dbName[i] = db_name.str(row);
+            accession[i] = db_acc.str(row);
+            num[i] = db_num.int(row);
+            residue[i] = db_res.str(row);
         }
         return { dbName: dbName, accession: accession, num: num, residue: residue };
     }

package/lib/mol-plugin/animation-loop.d.ts

@@ -4,6 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { PluginContext } from './context';
+import { PluginAnimationManager } from '../mol-plugin-state/manager/animation';
 export declare class PluginAnimationLoop {
     private plugin;
     private currentFrame;
@@ -12,6 +13,7 @@ export declare class PluginAnimationLoop {
     tick(t: number, options?: {
         isSynchronous?: boolean;
         manualDraw?: boolean;
+        animation?: PluginAnimationManager.AnimationInfo;
     }): Promise<void>;
     private frame;
     resetTime(t?: number): void;

package/lib/mol-plugin/animation-loop.js

@@ -30,7 +30,7 @@ var PluginAnimationLoop = /** @class */ (function () {
         return __awaiter(this, void 0, void 0, function () {
             return __generator(this, function (_b) {
                 switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.plugin.managers.animation.tick(t, options === null || options === void 0 ? void 0 : options.isSynchronous)];
+                    case 0: return [4 /*yield*/, this.plugin.managers.animation.tick(t, options === null || options === void 0 ? void 0 : options.isSynchronous, options === null || options === void 0 ? void 0 : options.animation)];
                     case 1:
                         _b.sent();
                         (_a = this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.tick(t, options);

package/lib/mol-plugin/behavior/dynamic/representation.js

@@ -53,12 +53,11 @@ export var HighlightLoci = PluginBehavior.create({
         class_1.prototype.register = function () {
             var _this = this;
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, function (_a) {
-                var _b;
                 var current = _a.current, buttons = _a.buttons, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0) {
+                if (_this.params.ignore.includes(loci.kind)) {
                     _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EmptyLoci });
                     return;
                 }
@@ -156,16 +155,15 @@ export var SelectLoci = PluginBehavior.create({
                 return l - k;
             });
             this.subscribeObservable(this.ctx.behaviors.interaction.click, function (_a) {
-                var _b;
                 var current = _a.current, button = _a.button, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy || !_this.ctx.selectionMode)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0)
+                if (_this.params.ignore.includes(loci.kind))
                     return;
                 // only trigger the 1st action that matches
                 for (var _i = 0, actions_1 = actions; _i < actions_1.length; _i++) {
-                    var _c = actions_1[_i], binding = _c[0], action = _c[1], condition = _c[2];
+                    var _b = actions_1[_i], binding = _b[0], action = _b[1], condition = _b[2];
                     if (Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
                         action({ repr: current.repr, loci: loci });
                         break;
@@ -189,7 +187,7 @@ export var SelectLoci = PluginBehavior.create({
                         Structure.areEquivalent(structure, oldStructure) &&
                         Structure.areHierarchiesEqual(structure, oldStructure))
                         return;
-                    var reprs = _this.ctx.state.data.select(StateSelection.Generators.ofType(SO.Molecule.Structure.Representation3D, ref));
+                    var reprs = _this.ctx.state.data.select(StateSelection.children(ref).ofType(SO.Molecule.Structure.Representation3D));
                     for (var _i = 0, reprs_1 = reprs; _i < reprs_1.length; _i++) {
                         var repr = reprs_1[_i];
                         _this.applySelectMark(repr.transform.ref, true);

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -7,6 +7,7 @@
 import { PluginBehavior } from '../../../behavior';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginContext } from '../../../context';
+import { Clip } from '../../../../mol-util/clip';
 declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     expandRadius: PD.Numeric;
     targetParams: PD.Group<PD.Normalize<{
@@ -26,6 +27,16 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 declare type StructureFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof StructureFocusRepresentationParams>>;
 export declare enum StructureFocusRepresentationTags {

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js

@@ -17,6 +17,7 @@ import { SizeTheme } from '../../../../mol-theme/size';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginCommands } from '../../../commands';
 import { Material } from '../../../../mol-util/material';
+import { Clip } from '../../../../mol-util/clip';
 var StructureFocusRepresentationParams = function (plugin) {
     var reprParams = StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
     return {
@@ -41,6 +42,7 @@ var StructureFocusRepresentationParams = function (plugin) {
         excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: PD.Boolean(false),
         material: Material.getParam(),
+        clip: PD.Group(Clip.Params),
     };
 };
 var FocusComponents = ['target', 'surroundings', 'interactions'];
@@ -68,7 +70,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
     StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
         return __assign(__assign({}, this.params.targetParams), { type: {
                 name: reprParams.type.name,
-                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material })
+                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip })
             } });
     };
     StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {

package/lib/mol-plugin/commands.d.ts

@@ -272,18 +272,18 @@ export declare const PluginCommands: {
                     }>[];
                     ambientColor: import("../mol-util/color").Color;
                     ambientIntensity: number;
-                    clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        variant: any;
-                        objects: any;
-                    }>;
                 }>>;
                 trackball: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                     noScroll: boolean;
                     rotateSpeed: number;
                     zoomSpeed: number;
                     panSpeed: number;
-                    spin: boolean;
-                    spinSpeed: number;
+                    animate: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                        speed: any;
+                    }>, "spin"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                        speed: any;
+                        angle: any;
+                    }>, "rock">;
                     staticMoving: boolean;
                     dynamicDampingFactor: number;
                     minDistance: number;
@@ -334,6 +334,7 @@ export declare const PluginCommands: {
                         bumpAmplitude: any;
                         quality: any;
                         material: any;
+                        clip: any;
                     }>, "on">;
                 }>>;
             }>> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void);

package/lib/mol-plugin/config.d.ts

@@ -16,7 +16,6 @@ export declare class PluginConfigItem<T = any> {
     constructor(key: string, defaultValue?: T | undefined);
 }
 declare function item<T>(key: string, defaultValue?: T): PluginConfigItem<T>;
-export declare function preferWebGl1(): boolean;
 export declare const PluginConfig: {
     item: typeof item;
     General: {
@@ -48,7 +47,7 @@ export declare const PluginConfig: {
         ShowAnimation: PluginConfigItem<boolean>;
     };
     Download: {
-        DefaultPdbProvider: PluginConfigItem<"rcsb" | "pdbe">;
+        DefaultPdbProvider: PluginConfigItem<"rcsb" | "pdbe" | "pdbj">;
         DefaultEmdbProvider: PluginConfigItem<EmdbDownloadProvider>;
     };
     Structure: {

package/lib/mol-plugin/config.js

@@ -5,6 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Structure, Model } from '../mol-model/structure';
+import { PluginFeatureDetection } from './features';
 var PluginConfigItem = /** @class */ (function () {
     function PluginConfigItem(key, defaultValue) {
         this.key = key;
@@ -16,27 +17,6 @@ var PluginConfigItem = /** @class */ (function () {
 }());
 export { PluginConfigItem };
 function item(key, defaultValue) { return new PluginConfigItem(key, defaultValue); }
-export function preferWebGl1() {
-    if (typeof navigator === 'undefined' || typeof window === 'undefined')
-        return false;
-    // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1, 15.2. It is working in Safari 15.4 tech preview, so disabling all versions before that.
-    // prefer webgl 1 based on the userAgent substring
-    var unpportedSafariVersions = [
-        'Version/15.1 Safari',
-        'Version/15.2 Safari',
-        'Version/15.3 Safari'
-    ];
-    if (unpportedSafariVersions.some(function (v) { return navigator.userAgent.indexOf(v) > 0; })) {
-        return true;
-    }
-    // Check for iOS device which enabled WebGL2 recently but it doesn't seem
-    // to be full up to speed yet.
-    // adapted from https://stackoverflow.com/questions/9038625/detect-if-device-is-ios
-    var isIOS = /iPad|iPhone|iPod/.test(navigator.userAgent);
-    var isAppleDevice = navigator.userAgent.includes('Macintosh');
-    var isTouchScreen = navigator.maxTouchPoints >= 4; // true for iOS 13 (and hopefully beyond)
-    return !window.MSStream && (isIOS || (isAppleDevice && isTouchScreen));
-}
 export var PluginConfig = {
     item: item,
     General: {
@@ -46,10 +26,10 @@ export var PluginConfig = {
         PixelScale: item('plugin-config.pixel-scale', 1),
         PickScale: item('plugin-config.pick-scale', 0.25),
         PickPadding: item('plugin-config.pick-padding', 3),
-        EnableWboit: item('plugin-config.enable-wboit', true),
+        EnableWboit: item('plugin-config.enable-wboit', PluginFeatureDetection.wboit),
         // 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', preferWebGl1()),
+        PreferWebGl1: item('plugin-config.prefer-webgl1', PluginFeatureDetection.preferWebGl1),
     },
     State: {
         DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),

package/lib/mol-plugin/features.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+export declare const PluginFeatureDetection: {
+    readonly preferWebGl1: boolean;
+    readonly wboit: boolean;
+};