molstar 2.3.3 → 2.3.8

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

@@ -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();

package/lib/commonjs/mol-plugin-state/manager/structure/measurement.js.map

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

@@ -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): {
+    getLoci(structure: Structure): StructureElement.Loci | {
         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

@@ -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

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

@@ -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[] | ArrayBuffer | Uint8Array;
+    data: string | ArrayBuffer | Uint8Array | number[];
     label: string | undefined;
 }>>;
 declare type ReadFile = typeof ReadFile;

package/lib/commonjs/mol-plugin-state/transforms/data.js

@@ -81,7 +81,7 @@ var DownloadBlob = objects_1.PluginStateTransform.BuiltIn({
             url: param_definition_1.ParamDefinition.Url('https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif', { description: 'Resource URL. Must be the same domain or support CORS.' }),
             isBinary: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false, { description: 'If true, download data as binary (string otherwise)' })),
             canFail: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false, { description: 'Indicate whether the download can fail and not be included in the blob as a result.' }))
-        }, function (e) { return e.id + ": " + e.url; }),
+        }, function (e) { return "".concat(e.id, ": ").concat(e.url); }),
         maxConcurrency: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Numeric(4, { min: 1, max: 12, step: 1 }, { description: 'The maximum number of concurrent downloads.' }))
     }
 })({
@@ -101,7 +101,7 @@ var DownloadBlob = objects_1.PluginStateTransform.BuiltIn({
                         for (i = 0; i < data.length; i++) {
                             r = data[i], src = params.sources[i];
                             if (r.kind === 'error')
-                                plugin.log.warn("Download " + r.id + " (" + src.url + ") failed: " + r.error);
+                                plugin.log.warn("Download ".concat(r.id, " (").concat(src.url, ") failed: ").concat(r.error));
                             else {
                                 assets.push(r.result);
                                 entries.push(src.isBinary
@@ -110,7 +110,7 @@ var DownloadBlob = objects_1.PluginStateTransform.BuiltIn({
                             }
                         }
                         cache.assets = assets;
-                        return [2 /*return*/, new objects_1.PluginStateObject.Data.Blob(entries, { label: 'Data Blob', description: entries.length + " " + (entries.length === 1 ? 'entry' : 'entries') })];
+                        return [2 /*return*/, new objects_1.PluginStateObject.Data.Blob(entries, { label: 'Data Blob', description: "".concat(entries.length, " ").concat(entries.length === 1 ? 'entry' : 'entries') })];
                 }
             });
         }); });
@@ -268,7 +268,7 @@ var ParseBlob = objects_1.PluginStateTransform.BuiltIn({
         formats: param_definition_1.ParamDefinition.ObjectList({
             id: param_definition_1.ParamDefinition.Text('', { label: 'Unique ID' }),
             format: param_definition_1.ParamDefinition.Select('cif', [['cif', 'cif']])
-        }, function (e) { return e.id + ": " + e.format; })
+        }, function (e) { return "".concat(e.id, ": ").concat(e.format); })
     }
 })({
     apply: function (_a, plugin) {
@@ -296,13 +296,13 @@ var ParseBlob = objects_1.PluginStateTransform.BuiltIn({
                     case 2:
                         parsed = _e.sent();
                         if (parsed.isError)
-                            throw new Error(e.id + ": " + parsed.message);
+                            throw new Error("".concat(e.id, ": ").concat(parsed.message));
                         entries.push({ id: e.id, kind: 'cif', data: parsed.result });
                         _e.label = 3;
                     case 3:
                         _c++;
                         return [3 /*break*/, 1];
-                    case 4: return [2 /*return*/, new objects_1.PluginStateObject.Format.Blob(entries, { label: 'Format Blob', description: entries.length + " " + (entries.length === 1 ? 'entry' : 'entries') })];
+                    case 4: return [2 /*return*/, new objects_1.PluginStateObject.Format.Blob(entries, { label: 'Format Blob', description: "".concat(entries.length, " ").concat(entries.length === 1 ? 'entry' : 'entries') })];
                 }
             });
         }); });
@@ -587,7 +587,7 @@ var LazyVolume = objects_1.PluginStateTransform.BuiltIn({
             color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.black),
             alpha: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 1, step: 0.01 }),
             volumeIndex: param_definition_1.ParamDefinition.Numeric(0),
-        }, function (e) { return e.type + " " + e.value; })
+        }, function (e) { return "".concat(e.type, " ").concat(e.value); })
     }
 })({
     apply: function (_a) {
@@ -597,7 +597,7 @@ var LazyVolume = objects_1.PluginStateTransform.BuiltIn({
             var entryId;
             return (0, tslib_1.__generator)(this, function (_a) {
                 entryId = Array.isArray(params.entryId) ? params.entryId.join(', ') : params.entryId;
-                return [2 /*return*/, new objects_1.PluginStateObject.Volume.Lazy(params, { label: "" + (entryId || params.url), description: 'Lazy Volume' })];
+                return [2 /*return*/, new objects_1.PluginStateObject.Volume.Lazy(params, { label: "".concat(entryId || params.url), description: 'Lazy Volume' })];
             });
         }); });
     }

package/lib/commonjs/mol-plugin-state/transforms/data.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-plugin-state/transforms/helpers.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,8 +9,10 @@ import { LabelData } from '../../mol-repr/shape/loci/label';
 import { OrientationData } from '../../mol-repr/shape/loci/orientation';
 import { AngleData } from '../../mol-repr/shape/loci/angle';
 import { DihedralData } from '../../mol-repr/shape/loci/dihedral';
+import { PlaneData } from '../../mol-repr/shape/loci/plane';
 export declare function getDistanceDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): DistanceData;
 export declare function getAngleDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): AngleData;
 export declare function getDihedralDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): DihedralData;
 export declare function getLabelDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): LabelData;
 export declare function getOrientationDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): OrientationData;
+export declare function getPlaneDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): PlaneData;