drugflow-molstar 0.2.1 → 0.2.2

package/lib/superposition-focus-representation.js

@@ -1,153 +1,153 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SuperpositionFocusRepresentation = exports.SuperpositionFocusRepresentationTags = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("Molstar/mol-model/structure");
-var structure_representation_params_1 = require("Molstar/mol-plugin-state/helpers/structure-representation-params");
-var transforms_1 = require("Molstar/mol-plugin-state/transforms");
-var behavior_1 = require("Molstar/mol-plugin/behavior");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var mol_state_1 = require("Molstar/mol-state");
-var param_definition_1 = require("Molstar/mol-util/param-definition");
-var commands_1 = require("Molstar/mol-plugin/commands");
-var loci_details_1 = require("./loci-details");
-var SuperpositionFocusRepresentationParams = function (plugin) {
-    var reprParams = transforms_1.StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
-    return {
-        expandRadius: param_definition_1.ParamDefinition.Numeric(5, { min: 1, max: 10, step: 1 }),
-        surroundingsParams: param_definition_1.ParamDefinition.Group(reprParams, {
-            label: 'Surroundings',
-            customDefault: (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 }, sizeParams: { scale: 0.3 } })
-        })
-    };
-};
-var SuperpositionFocusRepresentationTags;
-(function (SuperpositionFocusRepresentationTags) {
-    SuperpositionFocusRepresentationTags["SurrSel"] = "superposition-focus-surr-sel";
-    SuperpositionFocusRepresentationTags["SurrRepr"] = "superposition-focus-surr-repr";
-})(SuperpositionFocusRepresentationTags = exports.SuperpositionFocusRepresentationTags || (exports.SuperpositionFocusRepresentationTags = {}));
-var TagSet = new Set([SuperpositionFocusRepresentationTags.SurrSel, SuperpositionFocusRepresentationTags.SurrRepr]);
-var SuperpositionFocusRepresentationBehavior = /** @class */ (function (_super) {
-    tslib_1.__extends(SuperpositionFocusRepresentationBehavior, _super);
-    function SuperpositionFocusRepresentationBehavior() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    Object.defineProperty(SuperpositionFocusRepresentationBehavior.prototype, "surrLabel", {
-        get: function () { return "[Focus] Surroundings (".concat(this.params.expandRadius, " \u00C5)"); },
-        enumerable: false,
-        configurable: true
-    });
-    SuperpositionFocusRepresentationBehavior.prototype.ensureShape = function (cell) {
-        var state = this.plugin.state.data, tree = state.tree;
-        var builder = state.build();
-        var refs = mol_state_1.StateSelection.findUniqueTagsInSubtree(tree, cell.transform.ref, TagSet);
-        // Selections
-        if (!refs[SuperpositionFocusRepresentationTags.SurrSel]) {
-            refs[SuperpositionFocusRepresentationTags.SurrSel] = builder
-                .to(cell)
-                .apply(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, { expression: builder_1.MolScriptBuilder.struct.generator.empty(), label: this.surrLabel }, { tags: SuperpositionFocusRepresentationTags.SurrSel }).ref;
-        }
-        // Representations
-        if (!refs[SuperpositionFocusRepresentationTags.SurrRepr]) {
-            refs[SuperpositionFocusRepresentationTags.SurrRepr] = builder
-                .to(refs[SuperpositionFocusRepresentationTags.SurrSel])
-                .apply(transforms_1.StateTransforms.Representation.StructureRepresentation3D, this.params.surroundingsParams, { tags: SuperpositionFocusRepresentationTags.SurrRepr }).ref;
-        }
-        return { state: state, builder: builder, refs: refs };
-    };
-    SuperpositionFocusRepresentationBehavior.prototype.clear = function (root) {
-        var state = this.plugin.state.data;
-        var surrs = state.select(mol_state_1.StateSelection.Generators.byRef(root).subtree().withTag(SuperpositionFocusRepresentationTags.SurrSel));
-        if (surrs.length === 0)
-            return;
-        var update = state.build();
-        var expression = builder_1.MolScriptBuilder.struct.generator.empty();
-        for (var _i = 0, surrs_1 = surrs; _i < surrs_1.length; _i++) {
-            var s = surrs_1[_i];
-            update.to(s).update(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, function (old) { return (tslib_1.__assign(tslib_1.__assign({}, old), { expression: expression })); });
-        }
-        return commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
-    };
-    SuperpositionFocusRepresentationBehavior.prototype.focus = function (sourceLoci) {
-        return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var parent, loci, residueLoci, residueBundle, target, surroundings, lociDeatils, _a, state, builder, refs;
-            var _this = this;
-            return tslib_1.__generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        parent = this.plugin.helpers.substructureParent.get(sourceLoci.structure);
-                        if (!parent || !parent.obj)
-                            return [2 /*return*/];
-                        loci = structure_1.StructureElement.Loci.remap(sourceLoci, parent.obj.data);
-                        residueLoci = structure_1.StructureElement.Loci.extendToWholeResidues(loci);
-                        residueBundle = structure_1.StructureElement.Bundle.fromLoci(residueLoci);
-                        target = structure_1.StructureElement.Bundle.toExpression(residueBundle);
-                        surroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
-                            0: target,
-                            radius: this.params.expandRadius,
-                            'as-whole-residues': true
-                        });
-                        lociDeatils = (0, loci_details_1.lociDetails)(sourceLoci);
-                        if (!lociDeatils) {
-                            surroundings = builder_1.MolScriptBuilder.struct.modifier.exceptBy({
-                                0: surroundings,
-                                by: target
-                            });
-                        }
-                        _a = this.ensureShape(parent), state = _a.state, builder = _a.builder, refs = _a.refs;
-                        builder.to(refs[SuperpositionFocusRepresentationTags.SurrSel]).update(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, function (old) { return (tslib_1.__assign(tslib_1.__assign({}, old), { expression: surroundings, label: _this.surrLabel })); });
-                        return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
-                    case 1:
-                        _b.sent();
-                        return [2 /*return*/];
-                }
-            });
-        });
-    };
-    SuperpositionFocusRepresentationBehavior.prototype.register = function (ref) {
-        var _this = this;
-        this.subscribeObservable(this.plugin.managers.structure.focus.behaviors.current, function (entry) {
-            // if (entry) this.focus(entry.loci);
-            // else this.clear(StateTransform.RootRef);
-            _this.clear(mol_state_1.StateTransform.RootRef);
-            if (entry)
-                _this.focus(entry.loci);
-        });
-    };
-    SuperpositionFocusRepresentationBehavior.prototype.update = function (params) {
-        return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var old, state, builder, all, _i, _a, repr;
-            return tslib_1.__generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        old = this.params;
-                        this.params = params;
-                        state = this.plugin.state.data;
-                        builder = state.build();
-                        all = mol_state_1.StateSelection.Generators.root.subtree();
-                        for (_i = 0, _a = state.select(all.withTag(SuperpositionFocusRepresentationTags.SurrRepr)); _i < _a.length; _i++) {
-                            repr = _a[_i];
-                            builder.to(repr).update(this.params.surroundingsParams);
-                        }
-                        return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
-                    case 1:
-                        _b.sent();
-                        if (!(params.expandRadius !== old.expandRadius)) return [3 /*break*/, 3];
-                        return [4 /*yield*/, this.clear(mol_state_1.StateTransform.RootRef)];
-                    case 2:
-                        _b.sent();
-                        _b.label = 3;
-                    case 3: return [2 /*return*/, true];
-                }
-            });
-        });
-    };
-    return SuperpositionFocusRepresentationBehavior;
-}(behavior_1.PluginBehavior.WithSubscribers));
-exports.SuperpositionFocusRepresentation = behavior_1.PluginBehavior.create({
-    name: 'create-superposition-focus-representation',
-    display: { name: 'Superposition Focus Representation' },
-    category: 'interaction',
-    ctor: SuperpositionFocusRepresentationBehavior,
-    params: function (_, plugin) { return SuperpositionFocusRepresentationParams(plugin); }
-});
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SuperpositionFocusRepresentation = exports.SuperpositionFocusRepresentationTags = void 0;
+var tslib_1 = require("tslib");
+var structure_1 = require("Molstar/mol-model/structure");
+var structure_representation_params_1 = require("Molstar/mol-plugin-state/helpers/structure-representation-params");
+var transforms_1 = require("Molstar/mol-plugin-state/transforms");
+var behavior_1 = require("Molstar/mol-plugin/behavior");
+var builder_1 = require("Molstar/mol-script/language/builder");
+var mol_state_1 = require("Molstar/mol-state");
+var param_definition_1 = require("Molstar/mol-util/param-definition");
+var commands_1 = require("Molstar/mol-plugin/commands");
+var loci_details_1 = require("./loci-details");
+var SuperpositionFocusRepresentationParams = function (plugin) {
+    var reprParams = transforms_1.StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
+    return {
+        expandRadius: param_definition_1.ParamDefinition.Numeric(5, { min: 1, max: 10, step: 1 }),
+        surroundingsParams: param_definition_1.ParamDefinition.Group(reprParams, {
+            label: 'Surroundings',
+            customDefault: (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 }, sizeParams: { scale: 0.3 } })
+        })
+    };
+};
+var SuperpositionFocusRepresentationTags;
+(function (SuperpositionFocusRepresentationTags) {
+    SuperpositionFocusRepresentationTags["SurrSel"] = "superposition-focus-surr-sel";
+    SuperpositionFocusRepresentationTags["SurrRepr"] = "superposition-focus-surr-repr";
+})(SuperpositionFocusRepresentationTags = exports.SuperpositionFocusRepresentationTags || (exports.SuperpositionFocusRepresentationTags = {}));
+var TagSet = new Set([SuperpositionFocusRepresentationTags.SurrSel, SuperpositionFocusRepresentationTags.SurrRepr]);
+var SuperpositionFocusRepresentationBehavior = /** @class */ (function (_super) {
+    tslib_1.__extends(SuperpositionFocusRepresentationBehavior, _super);
+    function SuperpositionFocusRepresentationBehavior() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    Object.defineProperty(SuperpositionFocusRepresentationBehavior.prototype, "surrLabel", {
+        get: function () { return "[Focus] Surroundings (".concat(this.params.expandRadius, " \u00C5)"); },
+        enumerable: false,
+        configurable: true
+    });
+    SuperpositionFocusRepresentationBehavior.prototype.ensureShape = function (cell) {
+        var state = this.plugin.state.data, tree = state.tree;
+        var builder = state.build();
+        var refs = mol_state_1.StateSelection.findUniqueTagsInSubtree(tree, cell.transform.ref, TagSet);
+        // Selections
+        if (!refs[SuperpositionFocusRepresentationTags.SurrSel]) {
+            refs[SuperpositionFocusRepresentationTags.SurrSel] = builder
+                .to(cell)
+                .apply(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, { expression: builder_1.MolScriptBuilder.struct.generator.empty(), label: this.surrLabel }, { tags: SuperpositionFocusRepresentationTags.SurrSel }).ref;
+        }
+        // Representations
+        if (!refs[SuperpositionFocusRepresentationTags.SurrRepr]) {
+            refs[SuperpositionFocusRepresentationTags.SurrRepr] = builder
+                .to(refs[SuperpositionFocusRepresentationTags.SurrSel])
+                .apply(transforms_1.StateTransforms.Representation.StructureRepresentation3D, this.params.surroundingsParams, { tags: SuperpositionFocusRepresentationTags.SurrRepr }).ref;
+        }
+        return { state: state, builder: builder, refs: refs };
+    };
+    SuperpositionFocusRepresentationBehavior.prototype.clear = function (root) {
+        var state = this.plugin.state.data;
+        var surrs = state.select(mol_state_1.StateSelection.Generators.byRef(root).subtree().withTag(SuperpositionFocusRepresentationTags.SurrSel));
+        if (surrs.length === 0)
+            return;
+        var update = state.build();
+        var expression = builder_1.MolScriptBuilder.struct.generator.empty();
+        for (var _i = 0, surrs_1 = surrs; _i < surrs_1.length; _i++) {
+            var s = surrs_1[_i];
+            update.to(s).update(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, function (old) { return (tslib_1.__assign(tslib_1.__assign({}, old), { expression: expression })); });
+        }
+        return commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
+    };
+    SuperpositionFocusRepresentationBehavior.prototype.focus = function (sourceLoci) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var parent, loci, residueLoci, residueBundle, target, surroundings, lociDeatils, _a, state, builder, refs;
+            var _this = this;
+            return tslib_1.__generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        parent = this.plugin.helpers.substructureParent.get(sourceLoci.structure);
+                        if (!parent || !parent.obj)
+                            return [2 /*return*/];
+                        loci = structure_1.StructureElement.Loci.remap(sourceLoci, parent.obj.data);
+                        residueLoci = structure_1.StructureElement.Loci.extendToWholeResidues(loci);
+                        residueBundle = structure_1.StructureElement.Bundle.fromLoci(residueLoci);
+                        target = structure_1.StructureElement.Bundle.toExpression(residueBundle);
+                        surroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
+                            0: target,
+                            radius: this.params.expandRadius,
+                            'as-whole-residues': true
+                        });
+                        lociDeatils = (0, loci_details_1.lociDetails)(sourceLoci);
+                        if (!lociDeatils) {
+                            surroundings = builder_1.MolScriptBuilder.struct.modifier.exceptBy({
+                                0: surroundings,
+                                by: target
+                            });
+                        }
+                        _a = this.ensureShape(parent), state = _a.state, builder = _a.builder, refs = _a.refs;
+                        builder.to(refs[SuperpositionFocusRepresentationTags.SurrSel]).update(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, function (old) { return (tslib_1.__assign(tslib_1.__assign({}, old), { expression: surroundings, label: _this.surrLabel })); });
+                        return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
+                    case 1:
+                        _b.sent();
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    SuperpositionFocusRepresentationBehavior.prototype.register = function (ref) {
+        var _this = this;
+        this.subscribeObservable(this.plugin.managers.structure.focus.behaviors.current, function (entry) {
+            // if (entry) this.focus(entry.loci);
+            // else this.clear(StateTransform.RootRef);
+            _this.clear(mol_state_1.StateTransform.RootRef);
+            if (entry)
+                _this.focus(entry.loci);
+        });
+    };
+    SuperpositionFocusRepresentationBehavior.prototype.update = function (params) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var old, state, builder, all, _i, _a, repr;
+            return tslib_1.__generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        old = this.params;
+                        this.params = params;
+                        state = this.plugin.state.data;
+                        builder = state.build();
+                        all = mol_state_1.StateSelection.Generators.root.subtree();
+                        for (_i = 0, _a = state.select(all.withTag(SuperpositionFocusRepresentationTags.SurrRepr)); _i < _a.length; _i++) {
+                            repr = _a[_i];
+                            builder.to(repr).update(this.params.surroundingsParams);
+                        }
+                        return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
+                    case 1:
+                        _b.sent();
+                        if (!(params.expandRadius !== old.expandRadius)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, this.clear(mol_state_1.StateTransform.RootRef)];
+                    case 2:
+                        _b.sent();
+                        _b.label = 3;
+                    case 3: return [2 /*return*/, true];
+                }
+            });
+        });
+    };
+    return SuperpositionFocusRepresentationBehavior;
+}(behavior_1.PluginBehavior.WithSubscribers));
+exports.SuperpositionFocusRepresentation = behavior_1.PluginBehavior.create({
+    name: 'create-superposition-focus-representation',
+    display: { name: 'Superposition Focus Representation' },
+    category: 'interaction',
+    ctor: SuperpositionFocusRepresentationBehavior,
+    params: function (_, plugin) { return SuperpositionFocusRepresentationParams(plugin); }
+});

package/lib/superposition-sifts-mapping.d.ts

@@ -1,22 +1,22 @@
-import { MinimizeRmsd } from 'Molstar/mol-math/linear-algebra/3d/minimize-rmsd';
-import { ElementIndex, ResidueIndex } from 'Molstar/mol-model/structure/model/indexing';
-import { StructureElement } from 'Molstar/mol-model/structure/structure/element';
-import { Structure } from 'Molstar/mol-model/structure';
-import { Unit } from 'Molstar/mol-model/structure/structure/unit';
-export interface AlignmentResultEntry {
-    transform: MinimizeRmsd.Result;
-    pivot: number;
-    other: number;
-}
-export interface AlignmentResult {
-    entries: AlignmentResultEntry[];
-    zeroOverlapPairs: [number, number][];
-    failedPairs: [number, number][];
-}
-declare type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location<Unit.Atomic>, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean;
-export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
-    traceOnly?: boolean;
-    includeResidueTest?: IncludeResidueTest;
-    applyTestIndex?: number[];
-}): AlignmentResult;
-export {};
+import { MinimizeRmsd } from 'Molstar/mol-math/linear-algebra/3d/minimize-rmsd';
+import { ElementIndex, ResidueIndex } from 'Molstar/mol-model/structure/model/indexing';
+import { StructureElement } from 'Molstar/mol-model/structure/structure/element';
+import { Structure } from 'Molstar/mol-model/structure';
+import { Unit } from 'Molstar/mol-model/structure/structure/unit';
+export interface AlignmentResultEntry {
+    transform: MinimizeRmsd.Result;
+    pivot: number;
+    other: number;
+}
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[];
+    zeroOverlapPairs: [number, number][];
+    failedPairs: [number, number][];
+}
+declare type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location<Unit.Atomic>, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean;
+export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
+    traceOnly?: boolean;
+    includeResidueTest?: IncludeResidueTest;
+    applyTestIndex?: number[];
+}): AlignmentResult;
+export {};