npm - molstar - Versions diffs - 2.3.5 → 2.3.9 - Mend

molstar 2.3.5 → 2.3.9

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 (1658) hide show

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

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.js CHANGED Viewed

@@ -330,7 +330,7 @@ exports.StructureHierarchyManager = 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];
@@ -343,7 +343,7 @@ exports.StructureHierarchyManager = 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 = exports.StructureHierarchyManager || (exports.StructureHierarchyManager = {}));

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

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

@@ -1,21 +1,25 @@
 "use strict";
 /**
- * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureMeasurementParams = exports.MeasurementGroupTag = exports.StructureMeasurementManager = void 0;
+exports.StructureMeasurementParams = exports.MeasurementOrderLabelTag = exports.MeasurementGroupTag = exports.StructureMeasurementManager = void 0;
 var tslib_1 = require("tslib");
 var structure_1 = require("../../../mol-model/structure");
 var mol_state_1 = require("../../../mol-state");
 var transforms_1 = require("../../transforms");
 var commands_1 = require("../../../mol-plugin/commands");
 var array_1 = require("../../../mol-util/array");
+var objects_1 = require("../../objects");
 var component_1 = require("../../component");
 var param_definition_1 = require("../../../mol-util/param-definition");
 var common_1 = require("../../../mol-repr/shape/loci/common");
+var color_1 = require("../../../mol-util/color");
 exports.MeasurementGroupTag = 'measurement-group';
+exports.MeasurementOrderLabelTag = 'measurement-order-label';
 exports.StructureMeasurementParams = {
     distanceUnitLabel: param_definition_1.ParamDefinition.Text('\u212B', { isEssential: true }),
     textColor: common_1.MeasurementRepresentationCommonTextParams.textColor
@@ -24,7 +28,7 @@ var DefaultStructureMeasurementOptions = param_definition_1.ParamDefinition.getD
 var StructureMeasurementManager = /** @class */ (function (_super) {
     (0, tslib_1.__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)
@@ -224,22 +228,28 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
             });
         });
     };
-    StructureMeasurementManager.prototype.addOrientation = function (a) {
+    StructureMeasurementManager.prototype.addOrientation = function (locis) {
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var cellA, dependsOn, update, state;
+            var selections, dependsOn, i, il, l, cell, update, state;
             return (0, tslib_1.__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;
+                            (0, array_1.arraySetAdd)(dependsOn, cell.transform.ref);
+                            selections.push({ key: "l".concat(i), ref: cell.transform.ref, expression: structure_1.StructureElement.Loci.toExpression(l) });
+                        }
+                        if (selections.length === 0)
                             return [2 /*return*/];
-                        dependsOn = [cellA.transform.ref];
                         update = this.getGroup();
                         update
                             .apply(transforms_1.StateTransforms.Model.MultiStructureSelectionFromExpression, {
-                            selections: [
-                                { key: 'a', ref: cellA.transform.ref, expression: structure_1.StructureElement.Loci.toExpression(a) },
-                            ],
+                            selections: selections,
                             isTransitive: true,
                             label: 'Orientation'
                         }, { dependsOn: dependsOn })
@@ -253,6 +263,86 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
             });
         });
     };
+    StructureMeasurementManager.prototype.addPlane = function (locis) {
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var selections, dependsOn, i, il, l, cell, update, state;
+            return (0, tslib_1.__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;
+                            (0, array_1.arraySetAdd)(dependsOn, cell.transform.ref);
+                            selections.push({ key: "l".concat(i), ref: cell.transform.ref, expression: structure_1.StructureElement.Loci.toExpression(l) });
+                        }
+                        if (selections.length === 0)
+                            return [2 /*return*/];
+                        update = this.getGroup();
+                        update
+                            .apply(transforms_1.StateTransforms.Model.MultiStructureSelectionFromExpression, {
+                            selections: selections,
+                            isTransitive: true,
+                            label: 'Plane'
+                        }, { dependsOn: dependsOn })
+                            .apply(transforms_1.StateTransforms.Representation.StructureSelectionsPlane3D);
+                        state = this.plugin.state.data;
+                        return [4 /*yield*/, commands_1.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 (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var update, current, _i, current_1, obj, order, _a, locis_1, loci, cell, dependsOn, state;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        update = this.getGroup();
+                        current = this.plugin.state.data.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Selections).withTag(exports.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(transforms_1.StateTransforms.Model.MultiStructureSelectionFromExpression, {
+                                selections: [
+                                    { key: 'a', ref: cell.transform.ref, expression: structure_1.StructureElement.Loci.toExpression(loci) },
+                                ],
+                                isTransitive: true,
+                                label: 'Order'
+                            }, { dependsOn: dependsOn, tags: exports.MeasurementOrderLabelTag })
+                                .apply(transforms_1.StateTransforms.Representation.StructureSelectionsLabel3D, {
+                                textColor: color_1.Color.fromRgb(255, 255, 255),
+                                borderColor: color_1.Color.fromRgb(0, 0, 0),
+                                textSize: 0.33,
+                                borderWidth: 0.3,
+                                offsetZ: 0.75,
+                                customText: "".concat(order++)
+                            }, { tags: exports.MeasurementOrderLabelTag });
+                        }
+                        state = this.plugin.state.data;
+                        return [4 /*yield*/, commands_1.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 = mol_state_1.StateSelection.findTagInSubtree(state.tree, mol_state_1.StateTransform.RootRef, exports.MeasurementGroupTag);
@@ -262,12 +352,20 @@ var StructureMeasurementManager = /** @class */ (function (_super) {
         return ret;
     };
     StructureMeasurementManager.prototype.sync = function () {
+        var labels = [];
+        for (var _i = 0, _a = this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsLabel3D); _i < _a.length; _i++) {
+            var cell = _a[_i];
+            var tags = cell.obj['tags'];
+            if (!tags || !tags.includes(exports.MeasurementOrderLabelTag))
+                labels.push(cell);
+        }
         var updated = this.updateState({
-            labels: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsLabel3D),
+            labels: labels,
             distances: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsDistance3D),
             angles: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsAngle3D),
             dihedrals: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsDihedral3D),
-            orientations: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsOrientation3D)
+            orientations: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsOrientation3D),
+            planes: this.getTransforms(transforms_1.StateTransforms.Representation.StructureSelectionsPlane3D),
         });
         if (updated)
             this.stateUpdated();

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package/lib/commonjs/mol-plugin-state/manager/structure/selection.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * 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>
@@ -50,9 +50,9 @@ export declare class StructureSelectionManager extends StatefulPluginComponent<S
     private onUpdate;
     /** Removes all selections and returns them */
     clear(): StructureElement.Loci[];
-    getLoci(structure: Structure): StructureElement.Loci | {
+    getLoci(structure: Structure): {
         kind: "empty-loci";
-    };
+    } | StructureElement.Loci;
     getStructure(structure: Structure): Structure | undefined;
     structureHasSelection(structure: StructureRef): boolean;
     has(loci: Loci): boolean;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -11,7 +11,6 @@ var tslib_1 = require("tslib");
 var int_1 = require("../../../mol-data/int");
 var boundary_helper_1 = require("../../../mol-math/geometry/boundary-helper");
 var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var principal_axes_1 = require("../../../mol-math/linear-algebra/matrix/principal-axes");
 var loci_1 = require("../../../mol-model/loci");
 var structure_1 = require("../../../mol-model/structure");
 var mol_state_1 = require("../../../mol-state");
@@ -21,6 +20,7 @@ var array_1 = require("../../../mol-util/array");
 var component_1 = require("../../component");
 var objects_1 = require("../../objects");
 var mol_util_1 = require("../../../mol-util");
+var util_1 = require("../../../mol-data/util");
 var boundaryHelper = new boundary_helper_1.BoundaryHelper('98');
 var HISTORY_CAPACITY = 24;
 var StructureSelectionManager = /** @class */ (function (_super) {
@@ -397,14 +397,8 @@ var StructureSelectionManager = /** @class */ (function (_super) {
         return { box: { min: min, max: max }, sphere: boundaryHelper.getSphere() };
     };
     StructureSelectionManager.prototype.getPrincipalAxes = function () {
-        var elementCount = this.elementCount();
-        var positions = new Float32Array(3 * elementCount);
-        var offset = 0;
-        this.entries.forEach(function (v) {
-            structure_1.StructureElement.Loci.toPositionsArray(v.selection, positions, offset);
-            offset += structure_1.StructureElement.Loci.size(v.selection) * 3;
-        });
-        return principal_axes_1.PrincipalAxes.ofPositions(positions);
+        var values = (0, util_1.iterableToArray)(this.entries.values());
+        return structure_1.StructureElement.Loci.getPrincipalAxesMany(values.map(function (v) { return v.selection; }));
     };
     StructureSelectionManager.prototype.modify = function (modifier, loci) {
         var changed = false;

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

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-plugin-state/transforms/data.d.ts CHANGED Viewed

@@ -42,7 +42,7 @@ declare const DownloadBlob: StateTransformer<SO.Root, SO.Data.Blob, PD.Normalize
 }>>;
 declare type RawData = typeof RawData;
 declare const RawData: StateTransformer<SO.Root, SO.Data.String | SO.Data.Binary, PD.Normalize<{
-    data: string | number[] | Uint8Array | ArrayBuffer;
+    data: string | Uint8Array | number[] | ArrayBuffer;
     label: string | undefined;
 }>>;
 declare type ReadFile = typeof ReadFile;