molstar 3.0.0-dev.9 → 3.1.0

package/lib/apps/docking-viewer/viewport.d.ts

@@ -9,6 +9,7 @@ import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
 export declare const StructurePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;
@@ -31,6 +32,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/apps/viewer/app.d.ts

@@ -21,7 +21,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -202,6 +202,7 @@ export interface LoadTrajectoryParams {
 }
 export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/apps/viewer/app.js

@@ -13,9 +13,11 @@ import { GeometryExport } from '../../extensions/geo-export';
 import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { Volume } from '../../mol-model/volume';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
@@ -44,6 +46,7 @@ var Extensions = {
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
     'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
     'g3d': PluginSpec.Behavior(G3DFormat),
+    'model-export': PluginSpec.Behavior(ModelExport),
     'mp4-export': PluginSpec.Behavior(Mp4Export),
     'geo-export': PluginSpec.Behavior(GeometryExport),
     'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
@@ -85,11 +88,19 @@ var Viewer = /** @class */ (function () {
         var _a;
         if (options === void 0) { options = {}; }
         return __awaiter(this, void 0, void 0, function () {
-            var o, defaultSpec, spec, element, plugin;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
+            var definedOptions, _i, _b, p, o, defaultSpec, spec, element, plugin;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
                     case 0:
-                        o = __assign(__assign({}, DefaultViewerOptions), options);
+                        definedOptions = {};
+                        // filter for defined properies only so the default values
+                        // are property applied
+                        for (_i = 0, _b = Object.keys(options); _i < _b.length; _i++) {
+                            p = _b[_i];
+                            if (options[p] !== void 0)
+                                definedOptions[p] = options[p];
+                        }
+                        o = __assign(__assign({}, DefaultViewerOptions), definedOptions);
                         defaultSpec = DefaultPluginUISpec();
                         spec = {
                             actions: defaultSpec.actions,
@@ -145,7 +156,7 @@ var Viewer = /** @class */ (function () {
                                 }
                             })];
                     case 1:
-                        plugin = _b.sent();
+                        plugin = _c.sent();
                         return [2 /*return*/, new Viewer(plugin)];
                 }
             });
@@ -351,7 +362,7 @@ var Viewer = /** @class */ (function () {
                     return [2 /*return*/, update.commit()];
                 }
                 return [2 /*return*/, plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
-                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso;
+                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso, volume, volumeData;
                         var _a, _b, _c, _d;
                         return __generator(this, function (_e) {
                             switch (_e.label) {
@@ -367,11 +378,13 @@ var Viewer = /** @class */ (function () {
                                     repr = plugin.build();
                                     for (_i = 0, isovalues_1 = isovalues; _i < isovalues_1.length; _i++) {
                                         iso = isovalues_1[_i];
+                                        volume = (_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume;
+                                        volumeData = volume.cell.obj.data;
                                         repr
-                                            .to((_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume)
+                                            .to(volume)
                                             .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data, {
                                             type: 'isosurface',
-                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
                                             color: 'uniform',
                                             colorParams: { value: iso.color }
                                         }));

package/lib/apps/viewer/index.html

@@ -57,7 +57,7 @@
             var pickScale = getParam('pick-scale', '[^&]+').trim();
             var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
 
             molstar.Viewer.create('app', {
                 layoutShowControls: !hideControls,
@@ -71,7 +71,7 @@
                 pixelScale: parseFloat(pixelScale) || 1,
                 pickScale: parseFloat(pickScale) || 0.25,
                 pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: !disableWboit,
+                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
                 preferWebgl1: preferWebgl1,
             }).then(viewer => {
                 var snapshotId = getParam('snapshot-id', '[^&]+').trim();

package/lib/commonjs/apps/docking-viewer/viewport.d.ts

@@ -9,6 +9,7 @@ import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
 export declare const StructurePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;
@@ -31,6 +32,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/commonjs/apps/viewer/app.d.ts

@@ -21,7 +21,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -202,6 +202,7 @@ export interface LoadTrajectoryParams {
 }
 export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/commonjs/apps/viewer/app.js

@@ -16,11 +16,13 @@ var geo_export_1 = require("../../extensions/geo-export");
 var behavior_2 = require("../../extensions/model-archive/quality-assessment/behavior");
 var behavior_3 = require("../../extensions/model-archive/quality-assessment/behavior");
 var prop_1 = require("../../extensions/model-archive/quality-assessment/prop");
+var model_export_1 = require("../../extensions/model-export");
 var mp4_export_1 = require("../../extensions/mp4-export");
 var pdbe_1 = require("../../extensions/pdbe");
 var rcsb_1 = require("../../extensions/rcsb");
+var volume_1 = require("../../mol-model/volume");
 var structure_1 = require("../../mol-plugin-state/actions/structure");
-var volume_1 = require("../../mol-plugin-state/actions/volume");
+var volume_2 = require("../../mol-plugin-state/actions/volume");
 var representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
 var volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
@@ -50,6 +52,7 @@ var Extensions = {
     'rcsb-validation-report': spec_2.PluginSpec.Behavior(rcsb_1.RCSBValidationReport),
     'anvil-membrane-orientation': spec_2.PluginSpec.Behavior(behavior_1.ANVILMembraneOrientation),
     'g3d': spec_2.PluginSpec.Behavior(format_1.G3DFormat),
+    'model-export': spec_2.PluginSpec.Behavior(model_export_1.ModelExport),
     'mp4-export': spec_2.PluginSpec.Behavior(mp4_export_1.Mp4Export),
     'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport),
     'ma-quality-assessment': spec_2.PluginSpec.Behavior(behavior_2.MAQualityAssessment),
@@ -91,11 +94,19 @@ var Viewer = /** @class */ (function () {
         var _a;
         if (options === void 0) { options = {}; }
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var o, defaultSpec, spec, element, plugin;
-            return (0, tslib_1.__generator)(this, function (_b) {
-                switch (_b.label) {
+            var definedOptions, _i, _b, p, o, defaultSpec, spec, element, plugin;
+            return (0, tslib_1.__generator)(this, function (_c) {
+                switch (_c.label) {
                     case 0:
-                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), options);
+                        definedOptions = {};
+                        // filter for defined properies only so the default values
+                        // are property applied
+                        for (_i = 0, _b = Object.keys(options); _i < _b.length; _i++) {
+                            p = _b[_i];
+                            if (options[p] !== void 0)
+                                definedOptions[p] = options[p];
+                        }
+                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), definedOptions);
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
                         spec = {
                             actions: defaultSpec.actions,
@@ -151,7 +162,7 @@ var Viewer = /** @class */ (function () {
                                 }
                             })];
                     case 1:
-                        plugin = _b.sent();
+                        plugin = _c.sent();
                         return [2 /*return*/, new Viewer(plugin)];
                 }
             });
@@ -259,7 +270,7 @@ var Viewer = /** @class */ (function () {
     Viewer.prototype.loadEmdb = function (emdb, options) {
         var _a;
         var provider = this.plugin.config.get(config_1.PluginConfig.Download.DefaultEmdbProvider);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(volume_1.DownloadDensity, {
+        return this.plugin.runTask(this.plugin.state.data.applyAction(volume_2.DownloadDensity, {
             source: {
                 name: 'pdb-emd-ds',
                 params: {
@@ -357,7 +368,7 @@ var Viewer = /** @class */ (function () {
                     return [2 /*return*/, update.commit()];
                 }
                 return [2 /*return*/, plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso;
+                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso, volume, volumeData;
                         var _a, _b, _c, _d;
                         return (0, tslib_1.__generator)(this, function (_e) {
                             switch (_e.label) {
@@ -373,11 +384,13 @@ var Viewer = /** @class */ (function () {
                                     repr = plugin.build();
                                     for (_i = 0, isovalues_1 = isovalues; _i < isovalues_1.length; _i++) {
                                         iso = isovalues_1[_i];
+                                        volume = (_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume;
+                                        volumeData = volume.cell.obj.data;
                                         repr
-                                            .to((_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume)
+                                            .to(volume)
                                             .apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.createVolumeRepresentationParams)(this.plugin, firstVolume.data, {
                                             type: 'isosurface',
-                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: volume_1.Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
                                             color: 'uniform',
                                             colorParams: { value: iso.color }
                                         }));

package/lib/commonjs/examples/basic-wrapper/index.js

@@ -244,13 +244,17 @@ var BasicWrapper = /** @class */ (function () {
     BasicWrapper.prototype.toggleSpin = function () {
         if (!this.plugin.canvas3d)
             return;
+        var trackball = this.plugin.canvas3d.props.trackball;
         commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, {
-            settings: function (props) {
-                props.trackball.spin = !props.trackball.spin;
+            settings: {
+                trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } } })
             }
         });
-        if (!this.plugin.canvas3d.props.trackball.spin)
+        if (this.plugin.canvas3d.props.trackball.animate.name !== 'spin') {
             commands_1.PluginCommands.Camera.Reset(this.plugin, {});
+        }
     };
     BasicWrapper.prototype.animateModelIndexTargetFps = function () {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);

package/lib/commonjs/examples/proteopedia-wrapper/index.js

@@ -479,7 +479,13 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         if (!this.plugin.canvas3d)
             return;
         var trackball = this.plugin.canvas3d.props.trackball;
-        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { spin: !trackball.spin }) } });
+        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: {
+                trackball: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, trackball), { animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } } })
+            }
+        });
     };
     MolStarProteopediaWrapper.prototype.animateModelIndexTargetFps = function () {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -47,6 +47,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
 }>>;
 export declare const MembraneOrientationPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/anvil/representation.js

@@ -30,7 +30,7 @@ var SharedParams = {
     radiusFactor: param_definition_1.ParamDefinition.Numeric(1.2, { min: 0.1, max: 3.0, step: 0.01 }, { description: 'Scale the radius of the membrane layer' })
 };
 var BilayerPlanesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), SharedParams), { sectorOpacity: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }) });
-var BilayerRimsParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0.01, max: 50, step: 0.01 }), dashedLines: param_definition_1.ParamDefinition.Boolean(true) });
+var BilayerRimsParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), linesSize: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 50, step: 0.01 }), dashedLines: param_definition_1.ParamDefinition.Boolean(false) });
 var MembraneOrientationVisuals = {
     'bilayer-planes': function (ctx, getParams) { return (0, representation_3.ShapeRepresentation)(getBilayerPlanes, mesh_1.Mesh.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); }, modifyProps: function (p) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, p), { alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false })); } }); },
     'bilayer-rims': function (ctx, getParams) { return (0, representation_3.ShapeRepresentation)(getBilayerRims, lines_1.Lines.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); }

package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts

@@ -9,6 +9,7 @@ import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 export declare const DnatcoConfalPyramidsPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts

@@ -12,6 +12,7 @@ export declare const MAQualityAssessment: import("../../../mol-state/transformer
 }>;
 export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
@@ -40,6 +41,7 @@ export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPreset
 }>;
 export declare const QualityAssessmentQmeanPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/model-export/export.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>
+ */
+import { PluginContext } from '../../mol-plugin/context';
+export declare function exportHierarchy(plugin: PluginContext, options?: {
+    format?: 'cif' | 'bcif';
+}): Promise<void>;

package/lib/commonjs/extensions/model-export/export.js

@@ -0,0 +1,129 @@
+"use strict";
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.exportHierarchy = void 0;
+var tslib_1 = require("tslib");
+var utf8_1 = require("../../mol-io/common/utf8");
+var structure_1 = require("../../mol-model/structure");
+var mol_task_1 = require("../../mol-task");
+var date_1 = require("../../mol-util/date");
+var download_1 = require("../../mol-util/download");
+var zip_1 = require("../../mol-util/zip/zip");
+function exportHierarchy(plugin, options) {
+    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        var e_1;
+        return (0, tslib_1.__generator)(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    _a.trys.push([0, 2, , 3]);
+                    return [4 /*yield*/, plugin.runTask(_exportHierarchy(plugin, options), { useOverlay: true })];
+                case 1:
+                    _a.sent();
+                    return [3 /*break*/, 3];
+                case 2:
+                    e_1 = _a.sent();
+                    console.error(e_1);
+                    plugin.log.error("Model export failed. See console for details.");
+                    return [3 /*break*/, 3];
+                case 3: return [2 /*return*/];
+            }
+        });
+    });
+}
+exports.exportHierarchy = exportHierarchy;
+function _exportHierarchy(plugin, options) {
+    var _this = this;
+    return mol_task_1.Task.create('Export', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        var format, structures, files, entryMap, _i, structures_1, _s, s, name_1, zipData, _a, files_1, _b, fn, data, bytes, buffer;
+        var _c, _d, _e, _f, _g, _h, _j, _k;
+        return (0, tslib_1.__generator)(this, function (_l) {
+            switch (_l.label) {
+                case 0: return [4 /*yield*/, ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false })];
+                case 1:
+                    _l.sent();
+                    format = (_c = options === null || options === void 0 ? void 0 : options.format) !== null && _c !== void 0 ? _c : 'cif';
+                    structures = plugin.managers.structure.hierarchy.current.structures;
+                    files = [];
+                    entryMap = new Map();
+                    _i = 0, structures_1 = structures;
+                    _l.label = 2;
+                case 2:
+                    if (!(_i < structures_1.length)) return [3 /*break*/, 7];
+                    _s = structures_1[_i];
+                    s = (_f = (_e = (_d = _s.transform) === null || _d === void 0 ? void 0 : _d.cell.obj) === null || _e === void 0 ? void 0 : _e.data) !== null && _f !== void 0 ? _f : (_g = _s.cell.obj) === null || _g === void 0 ? void 0 : _g.data;
+                    if (!s)
+                        return [3 /*break*/, 6];
+                    if (s.models.length > 1) {
+                        plugin.log.warn("[Export] Skipping ".concat((_h = _s.cell.obj) === null || _h === void 0 ? void 0 : _h.label, ": Multimodel exports not supported."));
+                        return [3 /*break*/, 6];
+                    }
+                    if (s.units.some(function (u) { return !structure_1.Unit.isAtomic(u); })) {
+                        plugin.log.warn("[Export] Skipping ".concat((_j = _s.cell.obj) === null || _j === void 0 ? void 0 : _j.label, ": Non-atomic model exports not supported."));
+                        return [3 /*break*/, 6];
+                    }
+                    name_1 = entryMap.has(s.model.entryId)
+                        ? "".concat(s.model.entryId, "_").concat(entryMap.get(s.model.entryId) + 1, ".").concat(format)
+                        : "".concat(s.model.entryId, ".").concat(format);
+                    entryMap.set(s.model.entryId, ((_k = entryMap.get(s.model.entryId)) !== null && _k !== void 0 ? _k : 0) + 1);
+                    return [4 /*yield*/, ctx.update({ message: "Exporting ".concat(s.model.entryId, "..."), isIndeterminate: true, canAbort: false })];
+                case 3:
+                    _l.sent();
+                    if (!(s.elementCount > 100000)) return [3 /*break*/, 5];
+                    // Give UI chance to update, only needed for larger structures.
+                    return [4 /*yield*/, new Promise(function (res) { return setTimeout(res, 50); })];
+                case 4:
+                    // Give UI chance to update, only needed for larger structures.
+                    _l.sent();
+                    _l.label = 5;
+                case 5:
+                    try {
+                        files.push([name_1, (0, structure_1.to_mmCIF)(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+                    }
+                    catch (e) {
+                        if (format === 'cif' && s.elementCount > 2000000) {
+                            plugin.log.warn("[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.");
+                        }
+                        throw e;
+                    }
+                    _l.label = 6;
+                case 6:
+                    _i++;
+                    return [3 /*break*/, 2];
+                case 7:
+                    if (!(files.length === 1)) return [3 /*break*/, 8];
+                    (0, download_1.download)(new Blob([files[0][1]]), files[0][0]);
+                    return [3 /*break*/, 11];
+                case 8:
+                    if (!(files.length > 1)) return [3 /*break*/, 11];
+                    zipData = {};
+                    for (_a = 0, files_1 = files; _a < files_1.length; _a++) {
+                        _b = files_1[_a], fn = _b[0], data = _b[1];
+                        if (data instanceof Uint8Array) {
+                            zipData[fn] = data;
+                        }
+                        else {
+                            bytes = new Uint8Array((0, utf8_1.utf8ByteCount)(data));
+                            (0, utf8_1.utf8Write)(bytes, 0, data);
+                            zipData[fn] = bytes;
+                        }
+                    }
+                    return [4 /*yield*/, ctx.update({ message: "Compressing Data...", isIndeterminate: true, canAbort: false })];
+                case 9:
+                    _l.sent();
+                    return [4 /*yield*/, (0, zip_1.zip)(ctx, zipData)];
+                case 10:
+                    buffer = _l.sent();
+                    (0, download_1.download)(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), "structures_".concat((0, date_1.getFormattedTime)(), ".zip"));
+                    _l.label = 11;
+                case 11:
+                    plugin.log.info("[Export] Done.");
+                    return [2 /*return*/];
+            }
+        });
+    }); });
+}
+//# sourceMappingURL=export.js.map

package/lib/commonjs/extensions/model-export/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+export declare const ModelExport: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/commonjs/extensions/model-export/index.js

@@ -0,0 +1,36 @@
+"use strict";
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ModelExport = void 0;
+var tslib_1 = require("tslib");
+var behavior_1 = require("../../mol-plugin/behavior/behavior");
+var ui_1 = require("./ui");
+exports.ModelExport = behavior_1.PluginBehavior.create({
+    name: 'extension-model-export',
+    category: 'misc',
+    display: {
+        name: 'Model Export'
+    },
+    ctor: /** @class */ (function (_super) {
+        (0, tslib_1.__extends)(class_1, _super);
+        function class_1() {
+            return _super !== null && _super.apply(this, arguments) || this;
+        }
+        class_1.prototype.register = function () {
+            this.ctx.customStructureControls.set('model-export', ui_1.ModelExportUI);
+        };
+        class_1.prototype.update = function () {
+            return false;
+        };
+        class_1.prototype.unregister = function () {
+            this.ctx.customStructureControls.delete('model-export');
+        };
+        return class_1;
+    }(behavior_1.PluginBehavior.Handler)),
+    params: function () { return ({}); }
+});
+//# sourceMappingURL=index.js.map

package/lib/commonjs/extensions/model-export/ui.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+/// <reference types="react" />
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+export declare class ModelExportUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState;
+    protected renderControls(): JSX.Element | null;
+}

package/lib/commonjs/extensions/model-export/ui.js

@@ -0,0 +1,77 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ModelExportUI = void 0;
+var tslib_1 = require("tslib");
+var jsx_runtime_1 = require("react/jsx-runtime");
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+var react_1 = require("react");
+var base_1 = require("../../mol-plugin-ui/base");
+var common_1 = require("../../mol-plugin-ui/controls/common");
+var icons_1 = require("../../mol-plugin-ui/controls/icons");
+var parameters_1 = require("../../mol-plugin-ui/controls/parameters");
+var use_behavior_1 = require("../../mol-plugin-ui/hooks/use-behavior");
+var param_definition_1 = require("../../mol-util/param-definition");
+var export_1 = require("./export");
+var ModelExportUI = /** @class */ (function (_super) {
+    (0, tslib_1.__extends)(ModelExportUI, _super);
+    function ModelExportUI() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    ModelExportUI.prototype.defaultState = function () {
+        return {
+            header: 'Export Models',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: icons_1.GetAppSvg }
+        };
+    };
+    ModelExportUI.prototype.renderControls = function () {
+        return (0, jsx_runtime_1.jsx)(ExportControls, { plugin: this.plugin }, void 0);
+    };
+    return ModelExportUI;
+}(base_1.CollapsableControls));
+exports.ModelExportUI = ModelExportUI;
+var Params = {
+    format: param_definition_1.ParamDefinition.Select('cif', [['cif', 'mmCIF'], ['bcif', 'Binary mmCIF']])
+};
+var DefaultParams = param_definition_1.ParamDefinition.getDefaultValues(Params);
+function ExportControls(_a) {
+    var _this = this;
+    var plugin = _a.plugin;
+    var _b = (0, react_1.useState)(DefaultParams), params = _b[0], setParams = _b[1];
+    var _c = (0, react_1.useState)(false), exporting = _c[0], setExporting = _c[1];
+    (0, use_behavior_1.useBehavior)(plugin.managers.structure.hierarchy.behaviors.selection); // triggers UI update
+    var isBusy = (0, use_behavior_1.useBehavior)(plugin.behaviors.state.isBusy);
+    var hierarchy = plugin.managers.structure.hierarchy.current;
+    var label = 'Nothing to Export';
+    if (hierarchy.structures.length === 1) {
+        label = 'Export';
+    }
+    if (hierarchy.structures.length > 1) {
+        label = 'Export (as ZIP)';
+    }
+    var onExport = function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return (0, tslib_1.__generator)(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    setExporting(true);
+                    _a.label = 1;
+                case 1:
+                    _a.trys.push([1, , 3, 4]);
+                    return [4 /*yield*/, (0, export_1.exportHierarchy)(plugin, { format: params.format })];
+                case 2:
+                    _a.sent();
+                    return [3 /*break*/, 4];
+                case 3:
+                    setExporting(false);
+                    return [7 /*endfinally*/];
+                case 4: return [2 /*return*/];
+            }
+        });
+    }); };
+    return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: Params, values: params, onChangeValues: setParams, isDisabled: isBusy || exporting }, void 0), (0, jsx_runtime_1.jsx)(common_1.Button, (0, tslib_1.__assign)({ onClick: onExport, style: { marginTop: 1 }, disabled: isBusy || hierarchy.structures.length === 0 || exporting, commit: hierarchy.structures.length ? 'on' : 'off' }, { children: label }), void 0)] }, void 0);
+}
+//# sourceMappingURL=ui.js.map

package/lib/commonjs/extensions/mp4-export/encoder.js

@@ -67,7 +67,7 @@ function encodeMp4Animation(plugin, ctx, params) {
                     _d.label = 6;
                 case 6:
                     if (!(i <= N)) return [3 /*break*/, 10];
-                    return [4 /*yield*/, loop.tick(i * dt, { isSynchronous: true, manualDraw: true })];
+                    return [4 /*yield*/, loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true })];
                 case 7:
                     _d.sent();
                     image = params.pass.getImageData(width, height, normalizedViewport);