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/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();

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

	@@ -1 +1 @@
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package/lib/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>

package/lib/mol-plugin-state/manager/structure/selection.js 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>
@@ -8,7 +8,6 @@ import { __awaiter, __extends, __generator } from "tslib";
 import { OrderedSet } from '../../../mol-data/int';
 import { BoundaryHelper } from '../../../mol-math/geometry/boundary-helper';
 import { Vec3 } from '../../../mol-math/linear-algebra';
-import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal-axes';
 import { EmptyLoci, Loci } from '../../../mol-model/loci';
 import { QueryContext, Structure, StructureElement, StructureSelection } from '../../../mol-model/structure';
 import { StateObjectRef } from '../../../mol-state';
@@ -18,6 +17,7 @@ import { arrayRemoveAtInPlace } from '../../../mol-util/array';
 import { StatefulPluginComponent } from '../../component';
 import { PluginStateObject as PSO } from '../../objects';
 import { UUID } from '../../../mol-util';
+import { iterableToArray } from '../../../mol-data/util';
 var boundaryHelper = new BoundaryHelper('98');
 var HISTORY_CAPACITY = 24;
 var StructureSelectionManager = /** @class */ (function (_super) {
@@ -394,14 +394,8 @@ 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) {
-            StructureElement.Loci.toPositionsArray(v.selection, positions, offset);
-            offset += StructureElement.Loci.size(v.selection) * 3;
-        });
-        return PrincipalAxes.ofPositions(positions);
+        var values = iterableToArray(this.entries.values());
+        return StructureElement.Loci.getPrincipalAxesMany(values.map(function (v) { return v.selection; }));
     };
     StructureSelectionManager.prototype.modify = function (modifier, loci) {
         var changed = false;

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

	@@ -1 +1 @@
1	- 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package/lib/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;

package/lib/mol-plugin-state/transforms/data.js CHANGED Viewed

@@ -93,7 +93,7 @@ var DownloadBlob = PluginStateTransform.BuiltIn({
             url: PD.Url('https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif', { description: 'Resource URL. Must be the same domain or support CORS.' }),
             isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' })),
             canFail: PD.Optional(PD.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: PD.Optional(PD.Numeric(4, { min: 1, max: 12, step: 1 }, { description: 'The maximum number of concurrent downloads.' }))
     }
 })({
@@ -113,7 +113,7 @@ var DownloadBlob = 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
@@ -122,7 +122,7 @@ var DownloadBlob = PluginStateTransform.BuiltIn({
                             }
                         }
                         cache.assets = assets;
-                        return [2 /*return*/, new SO.Data.Blob(entries, { label: 'Data Blob', description: entries.length + " " + (entries.length === 1 ? 'entry' : 'entries') })];
+                        return [2 /*return*/, new SO.Data.Blob(entries, { label: 'Data Blob', description: "".concat(entries.length, " ").concat(entries.length === 1 ? 'entry' : 'entries') })];
                 }
             });
         }); });
@@ -277,7 +277,7 @@ var ParseBlob = PluginStateTransform.BuiltIn({
         formats: PD.ObjectList({
             id: PD.Text('', { label: 'Unique ID' }),
             format: PD.Select('cif', [['cif', 'cif']])
-        }, function (e) { return e.id + ": " + e.format; })
+        }, function (e) { return "".concat(e.id, ": ").concat(e.format); })
     }
 })({
     apply: function (_a, plugin) {
@@ -305,13 +305,13 @@ var ParseBlob = 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 SO.Format.Blob(entries, { label: 'Format Blob', description: entries.length + " " + (entries.length === 1 ? 'entry' : 'entries') })];
+                    case 4: return [2 /*return*/, new SO.Format.Blob(entries, { label: 'Format Blob', description: "".concat(entries.length, " ").concat(entries.length === 1 ? 'entry' : 'entries') })];
                 }
             });
         }); });
@@ -585,7 +585,7 @@ var LazyVolume = PluginStateTransform.BuiltIn({
             color: PD.Color(ColorNames.black),
             alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
             volumeIndex: PD.Numeric(0),
-        }, function (e) { return e.type + " " + e.value; })
+        }, function (e) { return "".concat(e.type, " ").concat(e.value); })
     }
 })({
     apply: function (_a) {
@@ -595,7 +595,7 @@ var LazyVolume = PluginStateTransform.BuiltIn({
             var entryId;
             return __generator(this, function (_a) {
                 entryId = Array.isArray(params.entryId) ? params.entryId.join(', ') : params.entryId;
-                return [2 /*return*/, new SO.Volume.Lazy(params, { label: "" + (entryId || params.url), description: 'Lazy Volume' })];
+                return [2 /*return*/, new SO.Volume.Lazy(params, { label: "".concat(entryId || params.url), description: 'Lazy Volume' })];
             });
         }); });
     }

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

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

@@ -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;

package/lib/mol-plugin-state/transforms/helpers.js CHANGED Viewed

@@ -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>
  */
@@ -26,7 +26,9 @@ export function getLabelDataFromStructureSelections(s) {
     return { infos: [{ loci: loci }] };
 }
 export function getOrientationDataFromStructureSelections(s) {
-    var loci = s[0].loci;
-    return { locis: [loci] };
+    return { locis: s.map(function (v) { return v.loci; }) };
+}
+export function getPlaneDataFromStructureSelections(s) {
+    return { locis: s.map(function (v) { return v.loci; }) };
 }
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