npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1829) hide show

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

@@ -15,7 +15,7 @@ import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observ
 import { Binding } from '../../../mol-util/binding';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
+import { Bond, Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
 import { arrayMax } from '../../../mol-util/array';
 var B = ButtonsType;
 var M = ModifiersKeys;
@@ -28,6 +28,7 @@ var DefaultHighlightLociBindings = {
 var HighlightLociParams = {
     bindings: PD.Value(DefaultHighlightLociBindings, { isHidden: true }),
     ignore: PD.Value([], { isHidden: true }),
+    preferAtoms: PD.Boolean(false, { description: 'Always prefer atoms over bonds' }),
     mark: PD.Boolean(true)
 };
 export var HighlightLoci = PluginBehavior.create({
@@ -44,6 +45,11 @@ export var HighlightLoci = PluginBehavior.create({
             };
             return _this;
         }
+        class_1.prototype.getLoci = function (loci) {
+            return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
+                ? Bond.toFirstStructureElementLoci(loci)
+                : loci;
+        };
         class_1.prototype.register = function () {
             var _this = this;
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, function (_a) {
@@ -51,19 +57,20 @@ export var HighlightLoci = PluginBehavior.create({
                 var current = _a.current, buttons = _a.buttons, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy)
                     return;
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(current.loci.kind)) >= 0) {
+                var loci = _this.getLoci(current.loci);
+                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0) {
                     _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EmptyLoci });
                     return;
                 }
                 var matched = false;
                 if (Binding.match(_this.params.bindings.hoverHighlightOnly, buttons, modifiers)) {
                     // remove repr to highlight loci everywhere on hover
-                    _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci: current.loci });
+                    _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci: loci });
                     matched = true;
                 }
                 if (Binding.match(_this.params.bindings.hoverHighlightOnlyExtend, buttons, modifiers)) {
                     // remove repr to highlight loci everywhere on hover
-                    _this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci: current.loci });
+                    _this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci: loci });
                     matched = true;
                 }
                 if (!matched) {
@@ -92,6 +99,7 @@ var DefaultSelectLociBindings = {
 var SelectLociParams = {
     bindings: PD.Value(DefaultSelectLociBindings, { isHidden: true }),
     ignore: PD.Value([], { isHidden: true }),
+    preferAtoms: PD.Boolean(false, { description: 'Always prefer atoms over bonds' }),
     mark: PD.Boolean(true)
 };
 export var SelectLoci = PluginBehavior.create({
@@ -109,6 +117,11 @@ export var SelectLoci = PluginBehavior.create({
             _this.spine = new StateTreeSpine.Impl(ctx.state.data.cells);
             return _this;
         }
+        class_2.prototype.getLoci = function (loci) {
+            return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
+                ? Bond.toFirstStructureElementLoci(loci)
+                : loci;
+        };
         class_2.prototype.applySelectMark = function (ref, clear) {
             var cell = this.ctx.state.data.cells.get(ref);
             if (cell && SO.isRepresentation3D(cell.obj)) {
@@ -125,8 +138,8 @@ export var SelectLoci = PluginBehavior.create({
         };
         class_2.prototype.register = function () {
             var _this = this;
-            var lociIsEmpty = function (current) { return Loci.isEmpty(current.loci); };
-            var lociIsNotEmpty = function (current) { return !Loci.isEmpty(current.loci); };
+            var lociIsEmpty = function (loci) { return Loci.isEmpty(loci); };
+            var lociIsNotEmpty = function (loci) { return !Loci.isEmpty(loci); };
             var actions = [
                 ['clickSelect', function (current) { return _this.ctx.managers.interactivity.lociSelects.select(current); }, lociIsNotEmpty],
                 ['clickToggle', function (current) { return _this.ctx.managers.interactivity.lociSelects.toggle(current); }, lociIsNotEmpty],
@@ -147,13 +160,14 @@ export var SelectLoci = PluginBehavior.create({
                 var current = _a.current, button = _a.button, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy || !_this.ctx.selectionMode)
                     return;
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(current.loci.kind)) >= 0)
+                var loci = _this.getLoci(current.loci);
+                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0)
                     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];
-                    if (Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(current))) {
-                        action(current);
+                    if (Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
+                        action({ repr: current.repr, loci: loci });
                         break;
                     }
                 }

package/lib/mol-plugin/behavior/dynamic/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts CHANGED Viewed

@@ -18,7 +18,7 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     nciParams: PD.Group<PD.Normalize<{
         [x: string]: any;
     }>>;
-    components: PD.MultiSelect<"target" | "interactions" | "surroundings">;
+    components: PD.MultiSelect<"target" | "surroundings" | "interactions">;
     excludeTargetFromSurroundings: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
 };

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

@@ -22,7 +22,7 @@ var StructureFocusRepresentationParams = function (plugin) {
         expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
         targetParams: PD.Group(reprParams, {
             label: 'Target',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51 } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
         }),
         surroundingsParams: PD.Group(reprParams, {
             label: 'Surroundings',
@@ -59,7 +59,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
         return _this;
     }
     Object.defineProperty(StructureFocusRepresentationBehavior.prototype, "surrLabel", {
-        get: function () { return "[Focus] Surroundings (" + this.params.expandRadius + " \u00C5)"; },
+        get: function () { return "[Focus] Surroundings (".concat(this.params.expandRadius, " \u00C5)"); },
         enumerable: false,
         configurable: true
     });

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

	@@ -1 +1 @@
1	- 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package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.js CHANGED Viewed

@@ -82,13 +82,13 @@ export { VolumeStreaming };
                 // Show selection-box if available and cell otherwise.
                 'auto': PD.Group({
                     radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }, { description: 'Radius in \u212B within which the volume is shown.' }),
-                    selectionDetailLevel: PD.Select(Math.min(6, info.header.availablePrecisions.length - 1), info.header.availablePrecisions.map(function (p, i) { return [i, i + 1 + " [ " + (Math.pow(p.maxVoxels, 1 / 3) | 0) + "^3 cells ]"]; }), { label: 'Selection Detail', description: 'Determines the maximum number of voxels. Depending on the size of the volume options are in the range from 0 (0.52M voxels) to 6 (25.17M voxels).' }),
+                    selectionDetailLevel: PD.Select(Math.min(6, info.header.availablePrecisions.length - 1), info.header.availablePrecisions.map(function (p, i) { return [i, "".concat(i + 1, " [ ").concat(Math.pow(p.maxVoxels, 1 / 3) | 0, "^3 cells ]")]; }), { label: 'Selection Detail', description: 'Determines the maximum number of voxels. Depending on the size of the volume options are in the range from 0 (0.52M voxels) to 6 (25.17M voxels).' }),
                     isSelection: PD.Boolean(false, { isHidden: true }),
                     bottomLeft: PD.Vec3(box.min, {}, { isHidden: true }),
                     topRight: PD.Vec3(box.max, {}, { isHidden: true }),
                 }, { description: 'Box around focused element.', isFlat: true })
             }, { options: VolumeStreaming.ViewTypeOptions, description: 'Controls what of the volume is displayed. "Off" hides the volume alltogether. "Bounded box" shows the volume inside the given box. "Around Interaction" shows the volume around the focused element/atom. "Whole Structure" shows the volume for the whole structure.' }),
-            detailLevel: PD.Select(Math.min(3, info.header.availablePrecisions.length - 1), info.header.availablePrecisions.map(function (p, i) { return [i, i + 1 + " [ " + (Math.pow(p.maxVoxels, 1 / 3) | 0) + "^3 cells ]"]; }), { description: 'Determines the maximum number of voxels. Depending on the size of the volume options are in the range from 0 (0.52M voxels) to 6 (25.17M voxels).' }),
+            detailLevel: PD.Select(Math.min(3, info.header.availablePrecisions.length - 1), info.header.availablePrecisions.map(function (p, i) { return [i, "".concat(i + 1, " [ ").concat(Math.pow(p.maxVoxels, 1 / 3) | 0, "^3 cells ]")]; }), { description: 'Determines the maximum number of voxels. Depending on the size of the volume options are in the range from 0 (0.52M voxels) to 6 (25.17M voxels).' }),
             channels: info.kind === 'em'
                 ? PD.Group({
                     'em': channelParam('EM', Color(0x638F8F), info.emDefaultContourLevel || Volume.IsoValue.relative(1), info.header.sampling[0].valuesInfo[0], channelParams['em'])
@@ -132,12 +132,12 @@ export { VolumeStreaming };
                 return __generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
-                            url = urlCombine(this.data.serverUrl, this.info.kind + "/" + this.info.dataId.toLowerCase());
+                            url = urlCombine(this.data.serverUrl, "".concat(this.info.kind, "/").concat(this.info.dataId.toLowerCase()));
                             if (box) {
                                 a = box.min, b = box.max;
                                 url += "/box"
-                                    + ("/" + a.map(function (v) { return Math.round(1000 * v) / 1000; }).join(','))
-                                    + ("/" + b.map(function (v) { return Math.round(1000 * v) / 1000; }).join(','));
+                                    + "/".concat(a.map(function (v) { return Math.round(1000 * v) / 1000; }).join(','))
+                                    + "/".concat(b.map(function (v) { return Math.round(1000 * v) / 1000; }).join(','));
                             }
                             else {
                                 url += "/cell";
@@ -146,7 +146,7 @@ export { VolumeStreaming };
                             if (this.params.entry.params.view.name === 'auto' && this.params.entry.params.view.params.isSelection) {
                                 detail = this.params.entry.params.view.params.selectionDetailLevel;
                             }
-                            url += "?detail=" + detail;
+                            url += "?detail=".concat(detail);
                             entry = LRUCache.get(this.cache, url);
                             if (entry)
                                 return [2 /*return*/, entry.data];

package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts CHANGED Viewed

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        /** Precision data the server can show. */
-        label: string;
+        label: string; /** Precision data the server can show. */
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
+        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,6 +23,7 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
+        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts CHANGED Viewed

@@ -29,9 +29,9 @@ declare const CreateVolumeStreamingInfo: StateTransformer<SO.Molecule.Structure,
     serverUrl: string;
     entries: PD.Normalize<PD.Values<{
         dataId: PD.Text<string>;
-        source: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "x-ray"> | PD.NamedParams<PD.Normalize<{
+        source: PD.Mapped<PD.NamedParams<PD.Normalize<{
             isoValue: any;
-        }>, "em">>;
+        }>, "em"> | PD.NamedParams<PD.Normalize<unknown>, "x-ray">>;
     }>>[];
 }>>;
 export { CreateVolumeStreamingBehavior };

package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.js CHANGED Viewed

@@ -94,7 +94,7 @@ export var InitVolumeStreaming = StateAction.build({
                     return [3 /*break*/, 8];
                 case 7:
                     e_1 = _a.sent();
-                    console.info("Could not get map info for " + emdbId + ": " + e_1);
+                    console.info("Could not get map info for ".concat(emdbId, ": ").concat(e_1));
                     return [3 /*break*/, 9];
                 case 8:
                     addEntry(entries, params.method, emdbId, contourLevel || 0);
@@ -111,7 +111,7 @@ export var InitVolumeStreaming = StateAction.build({
                     return [3 /*break*/, 14];
                 case 13:
                     e_2 = _a.sent();
-                    console.info("Could not get map info for " + dataId + ": " + e_2);
+                    console.info("Could not get map info for ".concat(dataId, ": ").concat(e_2));
                     return [3 /*break*/, 15];
                 case 14:
                     addEntry(entries, params.method, dataId, emDefaultContourLevel || 0);
@@ -225,7 +225,7 @@ var CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
                         return [4 /*yield*/, taskCtx.update('Getting server header...')];
                     case 2:
                         _a.sent();
-                        return [4 /*yield*/, plugin.fetch({ url: urlCombine(params.serverUrl, e.source.name + "/" + dataId.toLocaleLowerCase()), type: 'json' }).runInContext(taskCtx)];
+                        return [4 /*yield*/, plugin.fetch({ url: urlCombine(params.serverUrl, "".concat(e.source.name, "/").concat(dataId.toLocaleLowerCase())), type: 'json' }).runInContext(taskCtx)];
                     case 3:
                         header = _a.sent();
                         entries.push({
@@ -244,7 +244,7 @@ var CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
                             entries: entries,
                             structure: a.data
                         };
-                        return [2 /*return*/, new VolumeServerInfo(data, { label: 'Volume Server', description: "" + entries.map(function (e) { return e.dataId; }).join(', ') })];
+                        return [2 /*return*/, new VolumeServerInfo(data, { label: 'Volume Server', description: "".concat(entries.map(function (e) { return e.dataId; }).join(', ')) })];
                 }
             });
         }); });
@@ -341,7 +341,7 @@ var VolumeStreamingVisual = PluginStateTransform.BuiltIn({
                         _c.sent();
                         if (transform)
                             repr.setState({ transform: transform });
-                        return [2 /*return*/, new SO.Volume.Representation3D({ repr: repr, sourceData: channel.data }, { label: Math.round(channel.isoValue.relativeValue * 100) / 100 + " \u03C3 [" + srcParams.channel + "]" })];
+                        return [2 /*return*/, new SO.Volume.Representation3D({ repr: repr, sourceData: channel.data }, { label: "".concat(Math.round(channel.isoValue.relativeValue * 100) / 100, " \u03C3 [").concat(srcParams.channel, "]") })];
                 }
             });
         }); });

package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-plugin/behavior/dynamic/volume-streaming/util.js CHANGED Viewed

@@ -73,7 +73,7 @@ export function getContourLevelEmdb(plugin, taskCtx, emdbId) {
             switch (_a.label) {
                 case 0:
                     emdbHeaderServer = plugin.config.get(PluginConfig.VolumeStreaming.EmdbHeaderServer);
-                    return [4 /*yield*/, plugin.fetch({ url: emdbHeaderServer + "/" + emdbId.toUpperCase() + "/header/" + emdbId.toLowerCase() + ".xml", type: 'xml' }).runInContext(taskCtx)];
+                    return [4 /*yield*/, plugin.fetch({ url: "".concat(emdbHeaderServer, "/").concat(emdbId.toUpperCase(), "/header/").concat(emdbId.toLowerCase(), ".xml"), type: 'xml' }).runInContext(taskCtx)];
                 case 1:
                     header = _a.sent();
                     map = header.getElementsByTagName('map')[0];
@@ -92,7 +92,7 @@ export function getContourLevelPdbe(plugin, taskCtx, emdbId) {
                 case 0:
                     // TODO: parametrize URL in plugin settings?
                     emdbId = emdbId.toUpperCase();
-                    return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/emdb/api/entry/map/" + emdbId, type: 'json' }).runInContext(taskCtx)];
+                    return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/emdb/api/entry/map/".concat(emdbId), type: 'json' }).runInContext(taskCtx)];
                 case 1:
                     header = _e.sent();
                     contours = (_b = (_a = header === null || header === void 0 ? void 0 : header.map) === null || _a === void 0 ? void 0 : _a.contour_list) === null || _b === void 0 ? void 0 : _b.contour;
@@ -114,7 +114,7 @@ function getContourLevelPdbeLegacy(plugin, taskCtx, emdbId) {
                 case 0:
                     // TODO: parametrize URL in plugin settings?
                     emdbId = emdbId.toUpperCase();
-                    return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/" + emdbId, type: 'json' }).runInContext(taskCtx)];
+                    return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/".concat(emdbId), type: 'json' }).runInContext(taskCtx)];
                 case 1:
                     header = _d.sent();
                     emdbEntry = header === null || header === void 0 ? void 0 : header[emdbId];
@@ -133,7 +133,7 @@ export function getEmdbIds(plugin, taskCtx, pdbId) {
         var summary, summaryEntry, emdbIds, emdb;
         return __generator(this, function (_b) {
             switch (_b.label) {
-                case 0: return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/" + pdbId, type: 'json' }).runInContext(taskCtx)];
+                case 0: return [4 /*yield*/, plugin.fetch({ url: "https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/".concat(pdbId), type: 'json' }).runInContext(taskCtx)];
                 case 1:
                     summary = _b.sent();
                     summaryEntry = summary === null || summary === void 0 ? void 0 : summary[pdbId];
@@ -141,12 +141,12 @@ export function getEmdbIds(plugin, taskCtx, pdbId) {
                     if ((_a = summaryEntry === null || summaryEntry === void 0 ? void 0 : summaryEntry[0]) === null || _a === void 0 ? void 0 : _a.related_structures) {
                         emdb = summaryEntry[0].related_structures.filter(function (s) { return s.resource === 'EMDB' && s.relationship === 'associated EM volume'; });
                         if (!emdb.length) {
-                            throw new Error("No related EMDB entry found for '" + pdbId + "'.");
+                            throw new Error("No related EMDB entry found for '".concat(pdbId, "'."));
                         }
                         emdbIds.push.apply(emdbIds, emdb.map(function (e) { return e.accession; }));
                     }
                     else {
-                        throw new Error("No related EMDB entry found for '" + pdbId + "'.");
+                        throw new Error("No related EMDB entry found for '".concat(pdbId, "'."));
                     }
                     return [2 /*return*/, emdbIds];
             }