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-state/manager/animation.js.map CHANGED Viewed

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1	+ 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package/lib/mol-plugin-state/manager/interactivity.d.ts CHANGED Viewed

@@ -37,7 +37,7 @@ declare class InteractivityManager extends StatefulPluginComponent<Interactivity
 }
 declare namespace InteractivityManager {
     const Params: {
-        granularity: PD.Select<"model" | "structure" | "residue" | "element" | "chain" | "entity" | "operator" | "elementInstances" | "residueInstances" | "chainInstances">;
+        granularity: PD.Select<"residue" | "entity" | "operator" | "model" | "element" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances">;
     };
     type Params = typeof Params;
     type Props = PD.Values<Params>;
@@ -80,7 +80,7 @@ declare namespace InteractivityManager {
         setProps(props: Partial<Props>): void;
         addProvider(provider: LociMarkProvider): void;
         removeProvider(provider: LociMarkProvider): void;
-        protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity?: boolean): {
+        protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity: boolean, alwaysConvertBonds?: boolean): {
             loci: Loci;
             repr: Representation.Any | undefined;
         };

package/lib/mol-plugin-state/manager/interactivity.js CHANGED Viewed

@@ -73,11 +73,11 @@ var InteractivityManager = /** @class */ (function (_super) {
             this.providers = this.providers.filter(function (p) { return p !== provider; });
             // TODO clear, then re-apply remaining providers
         };
-        LociMarkManager.prototype.normalizedLoci = function (reprLoci, applyGranularity) {
-            if (applyGranularity === void 0) { applyGranularity = true; }
+        LociMarkManager.prototype.normalizedLoci = function (reprLoci, applyGranularity, alwaysConvertBonds) {
+            if (alwaysConvertBonds === void 0) { alwaysConvertBonds = false; }
             var loci = reprLoci.loci, repr = reprLoci.repr;
             var granularity = applyGranularity ? this.props.granularity : undefined;
-            return { loci: Loci.normalize(loci, granularity), repr: repr };
+            return { loci: Loci.normalize(loci, granularity, alwaysConvertBonds), repr: repr };
         };
         LociMarkManager.prototype.mark = function (current, action, noRender) {
             if (noRender === void 0) { noRender = false; }
@@ -171,7 +171,7 @@ var InteractivityManager = /** @class */ (function (_super) {
             if (applyGranularity === void 0) { applyGranularity = true; }
             if (Loci.isEmpty(current.loci))
                 return;
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.toggleSel(normalized);
             }
@@ -183,7 +183,7 @@ var InteractivityManager = /** @class */ (function (_super) {
             if (applyGranularity === void 0) { applyGranularity = true; }
             if (Loci.isEmpty(current.loci))
                 return;
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 var loci = this.sel.tryGetRange(normalized.loci) || normalized.loci;
                 this.toggleSel({ loci: loci, repr: normalized.repr });
@@ -191,7 +191,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         LociSelectManager.prototype.select = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('add', normalized.loci);
             }
@@ -199,7 +199,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         LociSelectManager.prototype.selectJoin = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('intersect', normalized.loci);
             }
@@ -207,7 +207,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         LociSelectManager.prototype.selectOnly = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 // only deselect for the structure of the given loci
                 this.deselect({ loci: Structure.toStructureElementLoci(normalized.loci.structure), repr: normalized.repr }, false);
@@ -217,7 +217,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         LociSelectManager.prototype.deselect = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('remove', normalized.loci);
             }
@@ -238,8 +238,9 @@ var InteractivityManager = /** @class */ (function (_super) {
                     // do a full deselect/select for the current structure so visuals that are
                     // marked with granularity unequal to 'element' and join/intersect operations
                     // are handled properly
-                    _super.prototype.mark.call(this, { loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, true);
-                    _super.prototype.mark.call(this, { loci: this.sel.getLoci(loci.structure) }, MarkerAction.Select);
+                    var selLoci = this.sel.getLoci(loci.structure);
+                    _super.prototype.mark.call(this, { loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, !Loci.isEmpty(selLoci));
+                    _super.prototype.mark.call(this, { loci: selLoci }, MarkerAction.Select);
                 }
                 else {
                     _super.prototype.mark.call(this, current, action);

package/lib/mol-plugin-state/manager/interactivity.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-plugin-state/manager/loci-label.js CHANGED Viewed

@@ -80,7 +80,7 @@ var LociLabelManager = /** @class */ (function () {
                 var count = group.length;
                 var entry = count > 1 && group[0] !== group[1]
                     ? hash : group[0];
-                _this.labels.push(count === 1 ? entry : entry + " <small>|| \u00D7 " + count + "</small>");
+                _this.labels.push(count === 1 ? entry : "".concat(entry, " <small>|| \u00D7 ").concat(count, "</small>"));
             });
             this.isDirty = false;
         }

package/lib/mol-plugin-state/manager/loci-label.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-plugin-state/manager/snapshots.js CHANGED Viewed

@@ -236,7 +236,7 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
                         _b = _a[_i], asset = _b.asset, file = _b.file;
                         assets.push([asset.id, asset]);
                         _c = zipDataObj;
-                        _d = "assets/" + asset.id;
+                        _d = "assets/".concat(asset.id);
                         _e = Uint8Array.bind;
                         return [4 /*yield*/, file.arrayBuffer()];
                     case 3:
@@ -314,7 +314,7 @@ var PluginStateSnapshotManager = /** @class */ (function (_super) {
                     case 7: return [3 /*break*/, 9];
                     case 8:
                         e_1 = _d.sent();
-                        this.plugin.log.error("Reading state: " + e_1);
+                        this.plugin.log.error("Reading state: ".concat(e_1));
                         return [3 /*break*/, 9];
                     case 9: return [2 /*return*/];
                 }

package/lib/mol-plugin-state/manager/snapshots.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-plugin-state/manager/structure/component.d.ts CHANGED Viewed

@@ -100,11 +100,11 @@ declare namespace StructureComponentManager {
         selection: PD.Select<StructureSelectionQuery>;
         action: PD.Mapped<PD.NamedParams<PD.Normalize<{
             color: import("../../../mol-util/color").Color;
-        }>, "color"> | PD.NamedParams<PD.Normalize<{
+        }>, "color"> | PD.NamedParams<PD.Normalize<unknown>, "reset"> | PD.NamedParams<PD.Normalize<{
             value: number;
         }>, "transparency"> | PD.NamedParams<PD.Normalize<{
             excludeGroups: ("one" | "two" | "three" | "four" | "five" | "six")[];
-        }>, "clipping"> | PD.NamedParams<PD.Normalize<unknown>, "reset">>;
+        }>, "clipping">>;
         representations: PD.MultiSelect<string>;
     };
     type ThemeParams = PD.Values<ReturnType<typeof getThemeParams>>;

package/lib/mol-plugin-state/manager/structure/hierarchy.js CHANGED Viewed

@@ -327,7 +327,7 @@ export { StructureHierarchyManager };
             if (((_e = (_d = s.model) === null || _d === void 0 ? void 0 : _d.trajectory) === null || _e === void 0 ? void 0 : _e.models) && s.model.trajectory.models.length === 1)
                 return entryId;
             if (s.model)
-                return ((_f = s.model.cell.obj) === null || _f === void 0 ? void 0 : _f.label) + " | " + entryId;
+                return "".concat((_f = s.model.cell.obj) === null || _f === void 0 ? void 0 : _f.label, " | ").concat(entryId);
             return entryId;
         }
         var p = structures[0];
@@ -340,7 +340,7 @@ export { StructureHierarchyManager };
                 break;
             }
         }
-        return sameTraj && t ? ((_j = t.cell.obj) === null || _j === void 0 ? void 0 : _j.label) + " | " + structures.length + " structures" : structures.length + " structures";
+        return sameTraj && t ? "".concat((_j = t.cell.obj) === null || _j === void 0 ? void 0 : _j.label, " | ").concat(structures.length, " structures") : "".concat(structures.length, " structures");
     }
     StructureHierarchyManager.getSelectedStructuresDescription = getSelectedStructuresDescription;
 })(StructureHierarchyManager || (StructureHierarchyManager = {}));

package/lib/mol-plugin-state/manager/structure/hierarchy.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-plugin-state/manager/structure/measurement.d.ts CHANGED Viewed

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { StructureElement } from '../../../mol-model/structure';
 import { PluginContext } from '../../../mol-plugin/context';
@@ -14,6 +15,7 @@ import { LociLabelTextParams } from '../../../mol-repr/shape/loci/common';
 import { LineParams } from '../../../mol-repr/structure/representation/line';
 export { StructureMeasurementManager };
 export declare const MeasurementGroupTag = "measurement-group";
+export declare const MeasurementOrderLabelTag = "measurement-order-label";
 export declare type StructureMeasurementCell = StateObjectCell<PluginStateObject.Shape.Representation3D, StateTransform<StateTransformer<PluginStateObject.Molecule.Structure.Selections, PluginStateObject.Shape.Representation3D, any>>>;
 export declare const StructureMeasurementParams: {
     distanceUnitLabel: PD.Text<string>;
@@ -26,6 +28,7 @@ export interface StructureMeasurementManagerState {
     angles: StructureMeasurementCell[];
     dihedrals: StructureMeasurementCell[];
     orientations: StructureMeasurementCell[];
+    planes: StructureMeasurementCell[];
     options: StructureMeasurementOptions;
 }
 declare type StructureMeasurementManagerAddOptions = {
@@ -55,7 +58,9 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
     addLabel(a: StructureElement.Loci, options?: Omit<StructureMeasurementManagerAddOptions, 'customText' | 'lineParams'> & {
         visualParams?: Partial<StateTransformer.Params<typeof StateTransforms.Representation.StructureSelectionsLabel3D>>;
     }): Promise<void>;
-    addOrientation(a: StructureElement.Loci): Promise<void>;
+    addOrientation(locis: StructureElement.Loci[]): Promise<void>;
+    addPlane(locis: StructureElement.Loci[]): Promise<void>;
+    addOrderLabels(locis: StructureElement.Loci[]): Promise<void>;
     private _empty;
     private getTransforms;
     private sync;

package/lib/mol-plugin-state/manager/structure/measurement.js CHANGED Viewed

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { __assign, __awaiter, __extends, __generator } from "tslib";
 import { StructureElement } from '../../../mol-model/structure';
@@ -9,11 +10,14 @@ import { StateSelection, StateTransform } from '../../../mol-state';
 import { StateTransforms } from '../../transforms';
 import { PluginCommands } from '../../../mol-plugin/commands';
 import { arraySetAdd } from '../../../mol-util/array';
+import { PluginStateObject } from '../../objects';
 import { StatefulPluginComponent } from '../../component';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { MeasurementRepresentationCommonTextParams } from '../../../mol-repr/shape/loci/common';
+import { Color } from '../../../mol-util/color';
 export { StructureMeasurementManager };
 export var MeasurementGroupTag = 'measurement-group';
+export var MeasurementOrderLabelTag = 'measurement-order-label';
 export var StructureMeasurementParams = {
     distanceUnitLabel: PD.Text('\u212B', { isEssential: true }),
     textColor: MeasurementRepresentationCommonTextParams.textColor
@@ -22,7 +26,7 @@ var DefaultStructureMeasurementOptions = PD.getDefaultValues(StructureMeasuremen
 var StructureMeasurementManager = /** @class */ (function (_super) {
     __extends(StructureMeasurementManager, _super);
     function StructureMeasurementManager(plugin) {
-        var _this = _super.call(this, { labels: [], distances: [], angles: [], dihedrals: [], orientations: [], options: DefaultStructureMeasurementOptions }) || this;
+        var _this = _super.call(this, { labels: [], distances: [], angles: [], dihedrals: [], orientations: [], planes: [], options: DefaultStructureMeasurementOptions }) || this;
         _this.plugin = plugin;
         _this.behaviors = {
             state: _this.ev.behavior(_this.state)
@@ -222,22 +226,28 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
             });
         });
     };
-    StructureMeasurementManager.prototype.addOrientation = function (a) {
+    StructureMeasurementManager.prototype.addOrientation = function (locis) {
         return __awaiter(this, void 0, void 0, function () {
-            var cellA, dependsOn, update, state;
+            var selections, dependsOn, i, il, l, cell, update, state;
             return __generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
-                        cellA = this.plugin.helpers.substructureParent.get(a.structure);
-                        if (!cellA)
+                        selections = [];
+                        dependsOn = [];
+                        for (i = 0, il = locis.length; i < il; ++i) {
+                            l = locis[i];
+                            cell = this.plugin.helpers.substructureParent.get(l.structure);
+                            if (!cell)
+                                continue;
+                            arraySetAdd(dependsOn, cell.transform.ref);
+                            selections.push({ key: "l".concat(i), ref: cell.transform.ref, expression: StructureElement.Loci.toExpression(l) });
+                        }
+                        if (selections.length === 0)
                             return [2 /*return*/];
-                        dependsOn = [cellA.transform.ref];
                         update = this.getGroup();
                         update
                             .apply(StateTransforms.Model.MultiStructureSelectionFromExpression, {
-                            selections: [
-                                { key: 'a', ref: cellA.transform.ref, expression: StructureElement.Loci.toExpression(a) },
-                            ],
+                            selections: selections,
                             isTransitive: true,
                             label: 'Orientation'
                         }, { dependsOn: dependsOn })
@@ -251,6 +261,86 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
             });
         });
     };
+    StructureMeasurementManager.prototype.addPlane = function (locis) {
+        return __awaiter(this, void 0, void 0, function () {
+            var selections, dependsOn, i, il, l, cell, update, state;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        selections = [];
+                        dependsOn = [];
+                        for (i = 0, il = locis.length; i < il; ++i) {
+                            l = locis[i];
+                            cell = this.plugin.helpers.substructureParent.get(l.structure);
+                            if (!cell)
+                                continue;
+                            arraySetAdd(dependsOn, cell.transform.ref);
+                            selections.push({ key: "l".concat(i), ref: cell.transform.ref, expression: StructureElement.Loci.toExpression(l) });
+                        }
+                        if (selections.length === 0)
+                            return [2 /*return*/];
+                        update = this.getGroup();
+                        update
+                            .apply(StateTransforms.Model.MultiStructureSelectionFromExpression, {
+                            selections: selections,
+                            isTransitive: true,
+                            label: 'Plane'
+                        }, { dependsOn: dependsOn })
+                            .apply(StateTransforms.Representation.StructureSelectionsPlane3D);
+                        state = this.plugin.state.data;
+                        return [4 /*yield*/, PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
+                    case 1:
+                        _a.sent();
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    StructureMeasurementManager.prototype.addOrderLabels = function (locis) {
+        return __awaiter(this, void 0, void 0, function () {
+            var update, current, _i, current_1, obj, order, _a, locis_1, loci, cell, dependsOn, state;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        update = this.getGroup();
+                        current = this.plugin.state.data.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Selections).withTag(MeasurementOrderLabelTag));
+                        for (_i = 0, current_1 = current; _i < current_1.length; _i++) {
+                            obj = current_1[_i];
+                            update.delete(obj);
+                        }
+                        order = 1;
+                        for (_a = 0, locis_1 = locis; _a < locis_1.length; _a++) {
+                            loci = locis_1[_a];
+                            cell = this.plugin.helpers.substructureParent.get(loci.structure);
+                            if (!cell)
+                                continue;
+                            dependsOn = [cell.transform.ref];
+                            update
+                                .apply(StateTransforms.Model.MultiStructureSelectionFromExpression, {
+                                selections: [
+                                    { key: 'a', ref: cell.transform.ref, expression: StructureElement.Loci.toExpression(loci) },
+                                ],
+                                isTransitive: true,
+                                label: 'Order'
+                            }, { dependsOn: dependsOn, tags: MeasurementOrderLabelTag })
+                                .apply(StateTransforms.Representation.StructureSelectionsLabel3D, {
+                                textColor: Color.fromRgb(255, 255, 255),
+                                borderColor: Color.fromRgb(0, 0, 0),
+                                textSize: 0.33,
+                                borderWidth: 0.3,
+                                offsetZ: 0.75,
+                                customText: "".concat(order++)
+                            }, { tags: MeasurementOrderLabelTag });
+                        }
+                        state = this.plugin.state.data;
+                        return [4 /*yield*/, PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true } })];
+                    case 1:
+                        _b.sent();
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
     StructureMeasurementManager.prototype.getTransforms = function (transformer) {
         var state = this.plugin.state.data;
         var groupRef = StateSelection.findTagInSubtree(state.tree, StateTransform.RootRef, MeasurementGroupTag);
@@ -260,12 +350,20 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         return ret;
     };
     StructureMeasurementManager.prototype.sync = function () {
+        var labels = [];
+        for (var _i = 0, _a = this.getTransforms(StateTransforms.Representation.StructureSelectionsLabel3D); _i < _a.length; _i++) {
+            var cell = _a[_i];
+            var tags = cell.obj['tags'];
+            if (!tags || !tags.includes(MeasurementOrderLabelTag))
+                labels.push(cell);
+        }
         var updated = this.updateState({
-            labels: this.getTransforms(StateTransforms.Representation.StructureSelectionsLabel3D),
+            labels: labels,
             distances: this.getTransforms(StateTransforms.Representation.StructureSelectionsDistance3D),
             angles: this.getTransforms(StateTransforms.Representation.StructureSelectionsAngle3D),
             dihedrals: this.getTransforms(StateTransforms.Representation.StructureSelectionsDihedral3D),
-            orientations: this.getTransforms(StateTransforms.Representation.StructureSelectionsOrientation3D)
+            orientations: this.getTransforms(StateTransforms.Representation.StructureSelectionsOrientation3D),
+            planes: this.getTransforms(StateTransforms.Representation.StructureSelectionsPlane3D),
         });
         if (updated)
             this.stateUpdated();