molstar 3.0.0-dev.8 → 3.0.2

package/lib/mol-model-props/computed/representations/interactions-inter-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>
  */

package/lib/mol-model-props/computed/representations/interactions-inter-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>
  */
@@ -63,11 +63,12 @@ function createInterUnitInteractionCylinderMesh(ctx, structure, theme, props, me
                 if (!childUnitA)
                     return true;
                 var unitA = structure.unitMap.get(b.unitA);
-                var fA = unitsFeatures.get(b.unitA);
-                // TODO: check all members
-                var eA = unitA.elements[fA.members[fA.offsets[b.indexA]]];
-                if (!SortedArray.has(childUnitA.elements, eA))
-                    return true;
+                var _a = unitsFeatures.get(b.unitA), offsets = _a.offsets, members = _a.members;
+                for (var i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
+                    var eA = unitA.elements[members[i]];
+                    if (!SortedArray.has(childUnitA.elements, eA))
+                        return true;
+                }
             }
             return false;
         }
@@ -115,8 +116,9 @@ function getInteractionLoci(pickingId, structure, id) {
     }
     return EmptyLoci;
 }
+var __unitMap = new Map();
+var __contactIndicesSet = new Set();
 function eachInteraction(loci, structure, apply, isMarking) {
-    var _a;
     var changed = false;
     if (Interactions.isLoci(loci)) {
         if (!Structure.areEquivalent(loci.data.structure, structure))
@@ -125,8 +127,8 @@ function eachInteraction(loci, structure, apply, isMarking) {
         if (loci.data.interactions !== interactions)
             return false;
         var contacts = interactions.contacts;
-        for (var _i = 0, _b = loci.elements; _i < _b.length; _i++) {
-            var c = _b[_i];
+        for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
+            var c = _a[_i];
             var idx = contacts.getEdgeIndex(c.indexA, c.unitA.id, c.indexB, c.unitB.id);
             if (idx !== -1) {
                 if (apply(Interval.ofSingleton(idx)))
@@ -139,28 +141,52 @@ function eachInteraction(loci, structure, apply, isMarking) {
             return false;
         if (isMarking && loci.elements.length === 1)
             return false; // only a single unit
-        var contacts_1 = (_a = InteractionsProvider.get(structure).value) === null || _a === void 0 ? void 0 : _a.contacts;
-        if (!contacts_1)
+        var interactions = InteractionsProvider.get(structure).value;
+        if (!interactions)
             return false;
+        var contacts_1 = interactions.contacts, unitsFeatures_1 = interactions.unitsFeatures;
+        for (var _b = 0, _c = loci.elements; _b < _c.length; _b++) {
+            var e = _c[_b];
+            __unitMap.set(e.unit.id, e.indices);
+        }
         var _loop_1 = function (e) {
             var unit = e.unit;
             if (!Unit.isAtomic(unit))
                 return "continue";
-            if (isMarking && OrderedSet.size(e.indices) === 1)
-                return "continue";
             OrderedSet.forEach(e.indices, function (v) {
                 for (var _i = 0, _a = contacts_1.getContactIndicesForElement(v, unit); _i < _a.length; _i++) {
                     var idx = _a[_i];
-                    if (apply(Interval.ofSingleton(idx)))
-                        changed = true;
+                    __contactIndicesSet.add(idx);
                 }
             });
         };
-        // 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];
+        for (var _d = 0, _e = loci.elements; _d < _e.length; _d++) {
+            var e = _e[_d];
             _loop_1(e);
         }
+        __contactIndicesSet.forEach(function (i) {
+            if (isMarking) {
+                var _a = contacts_1.edges[i], indexA = _a.indexA, unitA = _a.unitA, indexB = _a.indexB, unitB = _a.unitB;
+                var indicesA = __unitMap.get(unitA);
+                var indicesB = __unitMap.get(unitB);
+                if (!indicesA || !indicesB)
+                    return;
+                var _b = unitsFeatures_1.get(unitA), offsetsA = _b.offsets, membersA = _b.members;
+                for (var j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
+                    if (!OrderedSet.has(indicesA, membersA[j]))
+                        return;
+                }
+                var _c = unitsFeatures_1.get(unitB), offsetsB = _c.offsets, membersB = _c.members;
+                for (var j = offsetsB[indexB], jl = offsetsB[indexB + 1]; j < jl; ++j) {
+                    if (!OrderedSet.has(indicesB, membersB[j]))
+                        return;
+                }
+            }
+            if (apply(Interval.ofSingleton(i)))
+                changed = true;
+        });
+        __unitMap.clear();
+        __contactIndicesSet.clear();
     }
     return changed;
 }

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>
  */

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>
  */
@@ -49,9 +49,19 @@ function createIntraUnitInteractionsCylinderMesh(ctx, unit, structure, theme, pr
                     var sizeB = theme.size.size(location);
                     return Math.min(sizeA, sizeB) * sizeFactor;
                 },
-                ignore: function (edgeIndex) { return (flag[edgeIndex] === 1 /* Filtered */ ||
-                    // TODO: check all members
-                    (!!childUnit && !SortedArray.has(childUnit.elements, unit.elements[members[offsets[a[edgeIndex]]]]))); }
+                ignore: function (edgeIndex) {
+                    if (flag[edgeIndex] === 1 /* Filtered */)
+                        return true;
+                    if (childUnit) {
+                        var f = a[edgeIndex];
+                        for (var i = offsets[f], jl = offsets[f + 1]; i < jl; ++i) {
+                            var e = unit.elements[members[offsets[i]]];
+                            if (!SortedArray.has(childUnit.elements, e))
+                                return true;
+                        }
+                    }
+                    return false;
+                }
             };
             m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
             sphere = Sphere3D.expand(Sphere3D(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
@@ -98,6 +108,7 @@ 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 +143,42 @@ 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";
             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;
             });
+            __contactIndicesSet.clear();
         };
-        // 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/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.d.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -213,11 +213,16 @@ export var DefaultLociLabelProvider = PluginBehavior.create({
             this.f = {
                 label: function (loci) {
                     var label = [];
-                    if (StructureElement.Loci.is(loci) && loci.elements.length === 1) {
-                        var u = loci.elements[0].unit;
-                        var l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
-                        var name_1 = StructureProperties.entity.pdbx_description(l).join(', ');
-                        label.push(name_1);
+                    if (StructureElement.Loci.is(loci)) {
+                        var entityNames = new Set();
+                        for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
+                            var u = _a[_i].unit;
+                            var l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
+                            var name_1 = StructureProperties.entity.pdbx_description(l).join(', ');
+                            entityNames.add(name_1);
+                        }
+                        if (entityNames.size === 1)
+                            entityNames.forEach(function (name) { return label.push(name); });
                     }
                     label.push(lociLabel(loci));
                     return label.filter(function (l) { return !!l; }).join('</br>');

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

@@ -82,7 +82,7 @@ export function UpdateRepresentationVisibility(ctx) {
     });
 }
 function updateVisibility(cell, r) {
-    if (r.state.visible === cell.state.isHidden) {
+    if (r.state.visible === !!cell.state.isHidden) {
         r.setState({ visible: !cell.state.isHidden });
         return true;
     }

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

@@ -278,8 +278,12 @@ export declare const PluginCommands: {
                     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;

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

@@ -47,7 +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/spec.d.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-plugin/spec.js

@@ -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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -16,6 +16,7 @@ import { StateTransforms } from '../mol-plugin-state/transforms';
 import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { AnimateStateInterpolation } from '../mol-plugin-state/animation/built-in/state-interpolation';
 import { AnimateStructureSpin } from '../mol-plugin-state/animation/built-in/spin-structure';
+import { AnimateCameraRock } from '../mol-plugin-state/animation/built-in/camera-rock';
 export { PluginSpec };
 var PluginSpec;
 (function (PluginSpec) {
@@ -95,6 +96,7 @@ export var DefaultPluginSpec = function () { return ({
     animations: [
         AnimateModelIndex,
         AnimateCameraSpin,
+        AnimateCameraRock,
         AnimateStateSnapshots,
         AnimateAssemblyUnwind,
         AnimateStructureSpin,

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.0.0-dev.8';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1640979636220);
+export var PLUGIN_VERSION = '3.0.2';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1643574187710);

package/lib/mol-plugin-state/actions/file.d.ts

@@ -4,15 +4,16 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { StateAction } from '../../mol-state';
+import { Asset } from '../../mol-util/assets';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject } from '../objects';
 export declare const OpenFiles: StateAction<PluginStateObject.Root, void, PD.Normalize<{
-    files: import("../../mol-util/assets").Asset.File[] | null;
+    files: Asset.File[] | null;
     format: PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<string, "specific">;
     visuals: boolean;
 }>>;
 export declare const DownloadFile: StateAction<PluginStateObject.Root, void, PD.Normalize<{
-    url: string | import("../../mol-util/assets").Asset.Url;
+    url: string | Asset.Url;
     format: string;
     isBinary: boolean;
     visuals: boolean;

package/lib/mol-plugin-state/actions/file.js

@@ -6,8 +6,10 @@
 import { __awaiter, __generator } from "tslib";
 import { StateAction } from '../../mol-state';
 import { Task } from '../../mol-task';
+import { Asset } from '../../mol-util/assets';
 import { getFileInfo } from '../../mol-util/file-info';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { unzip } from '../../mol-util/zip/zip';
 import { PluginStateObject } from '../objects';
 export var OpenFiles = StateAction.build({
     display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
@@ -31,53 +33,87 @@ export var OpenFiles = StateAction.build({
                 case 0:
                     plugin.behaviors.layout.leftPanelTabName.next('data');
                     return [4 /*yield*/, state.transaction(function () { return __awaiter(void 0, void 0, void 0, function () {
-                            var _i, _a, file, info, isBinary, data, provider, parsed, e_1;
-                            var _b, _c;
-                            return __generator(this, function (_d) {
-                                switch (_d.label) {
+                            var processFile, _i, _a, file, zippedFiles, _b, _c, _d, _e, _f, fn, filedata, asset, e_1;
+                            return __generator(this, function (_g) {
+                                switch (_g.label) {
                                     case 0:
                                         if (params.files === null) {
                                             plugin.log.error('No file(s) selected');
                                             return [2 /*return*/];
                                         }
+                                        processFile = function (file) { return __awaiter(void 0, void 0, void 0, function () {
+                                            var info, isBinary, data, provider, parsed;
+                                            var _a, _b;
+                                            return __generator(this, function (_c) {
+                                                switch (_c.label) {
+                                                    case 0:
+                                                        info = getFileInfo(file.file);
+                                                        isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
+                                                        return [4 /*yield*/, plugin.builders.data.readFile({ file: file, isBinary: isBinary })];
+                                                    case 1:
+                                                        data = (_c.sent()).data;
+                                                        provider = params.format.name === 'auto'
+                                                            ? plugin.dataFormats.auto(info, (_a = data.cell) === null || _a === void 0 ? void 0 : _a.obj)
+                                                            : plugin.dataFormats.get(params.format.params);
+                                                        if (!provider) {
+                                                            plugin.log.warn("OpenFiles: could not find data provider for '".concat(info.name, ".").concat(info.ext, "'"));
+                                                            return [2 /*return*/];
+                                                        }
+                                                        return [4 /*yield*/, provider.parse(plugin, data)];
+                                                    case 2:
+                                                        parsed = _c.sent();
+                                                        if (!params.visuals) return [3 /*break*/, 4];
+                                                        return [4 /*yield*/, ((_b = provider.visuals) === null || _b === void 0 ? void 0 : _b.call(provider, plugin, parsed))];
+                                                    case 3:
+                                                        _c.sent();
+                                                        _c.label = 4;
+                                                    case 4: return [2 /*return*/];
+                                                }
+                                            });
+                                        }); };
                                         _i = 0, _a = params.files;
-                                        _d.label = 1;
+                                        _g.label = 1;
                                     case 1:
-                                        if (!(_i < _a.length)) return [3 /*break*/, 9];
+                                        if (!(_i < _a.length)) return [3 /*break*/, 14];
                                         file = _a[_i];
-                                        _d.label = 2;
+                                        _g.label = 2;
                                     case 2:
-                                        _d.trys.push([2, 7, , 8]);
-                                        info = getFileInfo(file.file);
-                                        isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
-                                        return [4 /*yield*/, plugin.builders.data.readFile({ file: file, isBinary: isBinary })];
-                                    case 3:
-                                        data = (_d.sent()).data;
-                                        provider = params.format.name === 'auto'
-                                            ? plugin.dataFormats.auto(info, (_b = data.cell) === null || _b === void 0 ? void 0 : _b.obj)
-                                            : plugin.dataFormats.get(params.format.params);
-                                        if (!provider) {
-                                            plugin.log.warn("OpenFiles: could not find data provider for '".concat(info.name, ".").concat(info.ext, "'"));
-                                            return [3 /*break*/, 8];
-                                        }
-                                        return [4 /*yield*/, provider.parse(plugin, data)];
+                                        _g.trys.push([2, 12, , 13]);
+                                        if (!(file.file && file.name.toLowerCase().endsWith('.zip'))) return [3 /*break*/, 9];
+                                        _b = unzip;
+                                        _c = [taskCtx];
+                                        return [4 /*yield*/, file.file.arrayBuffer()];
+                                    case 3: return [4 /*yield*/, _b.apply(void 0, _c.concat([_g.sent()]))];
                                     case 4:
-                                        parsed = _d.sent();
-                                        if (!params.visuals) return [3 /*break*/, 6];
-                                        return [4 /*yield*/, ((_c = provider.visuals) === null || _c === void 0 ? void 0 : _c.call(provider, plugin, parsed))];
+                                        zippedFiles = _g.sent();
+                                        _d = 0, _e = Object.entries(zippedFiles);
+                                        _g.label = 5;
                                     case 5:
-                                        _d.sent();
-                                        _d.label = 6;
-                                    case 6: return [3 /*break*/, 8];
+                                        if (!(_d < _e.length)) return [3 /*break*/, 8];
+                                        _f = _e[_d], fn = _f[0], filedata = _f[1];
+                                        asset = Asset.File(new File([filedata], fn));
+                                        return [4 /*yield*/, processFile(asset)];
+                                    case 6:
+                                        _g.sent();
+                                        _g.label = 7;
                                     case 7:
-                                        e_1 = _d.sent();
+                                        _d++;
+                                        return [3 /*break*/, 5];
+                                    case 8: return [3 /*break*/, 11];
+                                    case 9: return [4 /*yield*/, processFile(file)];
+                                    case 10:
+                                        _g.sent();
+                                        _g.label = 11;
+                                    case 11: return [3 /*break*/, 13];
+                                    case 12:
+                                        e_1 = _g.sent();
                                         console.error(e_1);
                                         plugin.log.error("Error opening file '".concat(file.name, "'"));
-                                        return [3 /*break*/, 8];
-                                    case 8:
+                                        return [3 /*break*/, 13];
+                                    case 13:
                                         _i++;
                                         return [3 /*break*/, 1];
-                                    case 9: return [2 /*return*/];
+                                    case 14: return [2 /*return*/];
                                 }
                             });
                         }); }).runInContext(taskCtx)];

package/lib/mol-plugin-state/actions/structure.d.ts

@@ -14,6 +14,7 @@ export declare const PdbDownloadProvider: {
     pdbe: PD.Group<PD.Normalize<{
         variant: "updated" | "updated-bcif" | "updtaed-bcif" | "archival";
     }>>;
+    pdbj: PD.Group<PD.Normalize<unknown>>;
 };
 export declare type PdbDownloadProvider = keyof typeof PdbDownloadProvider;
 export { DownloadStructure };