drugflow-molstar 0.3.72 → 0.3.73

package/build/drugflow-molstar-plugin-0.3.73.js.LICENSE.txt

@@ -0,0 +1,39 @@
+/**
+ * @license React
+ * react-dom.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * react-jsx-runtime.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * react.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * scheduler.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */

package/lib/drugflow-molstar-component-build-0.3.73.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.73.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.73.js.LICENSE.txt

@@ -0,0 +1,24 @@
+/**
+ * @license
+ * Copyright (c) 2017 The Polymer Project Authors. All rights reserved.
+ * This code may only be used under the BSD style license found at
+ * http://polymer.github.io/LICENSE.txt
+ * The complete set of authors may be found at
+ * http://polymer.github.io/AUTHORS.txt
+ * The complete set of contributors may be found at
+ * http://polymer.github.io/CONTRIBUTORS.txt
+ * Code distributed by Google as part of the polymer project is also
+ * subject to an additional IP rights grant found at
+ * http://polymer.github.io/PATENTS.txt
+ */
+
+/**
+@license
+Copyright (c) 2019 The Polymer Project Authors. All rights reserved.
+This code may only be used under the BSD style license found at
+http://polymer.github.io/LICENSE.txt The complete set of authors may be found at
+http://polymer.github.io/AUTHORS.txt The complete set of contributors may be
+found at http://polymer.github.io/CONTRIBUTORS.txt Code distributed by Google as
+part of the polymer project is also subject to an additional IP rights grant
+found at http://polymer.github.io/PATENTS.txt
+*/

package/lib/index.js

@@ -30,6 +30,7 @@ var linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
 var int_1 = require("molstar/lib/mol-data/int");
 var names_1 = require("molstar/lib/mol-util/color/names");
 var structure_contact3d_1 = require("./structure_contact3d");
+var structure_transparency_1 = require("molstar/lib/mol-plugin-state/helpers/structure-transparency");
 require('molstar/lib/mol-plugin-ui/skin/light.scss');
 var DrugflowMolstarPlugin = /** @class */ (function () {
     function DrugflowMolstarPlugin() {
@@ -495,6 +496,302 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             return [2 /*return*/];
                     }
                 });
+            }); },
+            /**
+             * 使用透明度隐藏指定的链
+             * @param chainId 链ID，例如 'A', 'B'
+             */
+            hideChain: function (chainId) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, components, _b, structures_1, s;
+                var _this = this;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            structures = this.plugin.managers.structure.hierarchy.current.structures;
+                            components = [];
+                            for (_b = 0, structures_1 = structures; _b < structures_1.length; _b++) {
+                                s = structures_1[_b];
+                                components.push.apply(components, s.components);
+                            }
+                            if (components.length === 0) {
+                                console.warn('No components found');
+                                return [2 /*return*/];
+                            }
+                            // 使用透明度为1（完全透明）来隐藏
+                            return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                                    var data, chainQuery;
+                                    var _this = this;
+                                    return tslib_1.__generator(this, function (_b) {
+                                        data = structure;
+                                        chainQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Chain_".concat(chainId), builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                                            'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId])
+                                        }), {
+                                            description: "Chain ".concat(chainId),
+                                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate
+                                        });
+                                        return [2 /*return*/, this.plugin.runTask(mol_task_1.Task.create('Select Chain', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                                                var selection;
+                                                return tslib_1.__generator(this, function (_b) {
+                                                    switch (_b.label) {
+                                                        case 0: return [4 /*yield*/, chainQuery.getSelection(this.plugin, runtime, data)];
+                                                        case 1:
+                                                            selection = _b.sent();
+                                                            return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
+                                                    }
+                                                });
+                                            }); }))];
+                                    });
+                                }); })];
+                        case 1:
+                            // 使用透明度为1（完全透明）来隐藏
+                            _c.sent();
+                            console.log("\u2705 Chain ".concat(chainId, " hidden"));
+                            return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 清除指定链的透明度来显示
+             * @param chainId 链ID，例如 'A', 'B'
+             */
+            showChain: function (chainId) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, components, _b, structures_2, s;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            structures = this.plugin.managers.structure.hierarchy.current.structures;
+                            components = [];
+                            for (_b = 0, structures_2 = structures; _b < structures_2.length; _b++) {
+                                s = structures_2[_b];
+                                components.push.apply(components, s.components);
+                            }
+                            if (components.length === 0) {
+                                console.warn('No components found');
+                                return [2 /*return*/];
+                            }
+                            // 清除透明度来恢复显示
+                            return [4 /*yield*/, (0, structure_transparency_1.clearStructureTransparency)(this.plugin, components)];
+                        case 1:
+                            // 清除透明度来恢复显示
+                            _c.sent();
+                            console.log("\u2705 Chain ".concat(chainId, " shown"));
+                            return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 使用透明度隐藏指定的配体
+             * @param chainId 链ID
+             * @param resId 残基序号（可选）
+             * @param resName 残基名称（可选）
+             */
+            hideLigand: function (chainId, resId, resName) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, components, _b, structures_3, s, queryConditions;
+                var _this = this;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            structures = this.plugin.managers.structure.hierarchy.current.structures;
+                            components = [];
+                            for (_b = 0, structures_3 = structures; _b < structures_3.length; _b++) {
+                                s = structures_3[_b];
+                                components.push.apply(components, s.components);
+                            }
+                            if (components.length === 0) {
+                                console.warn('No components found');
+                                return [2 /*return*/];
+                            }
+                            queryConditions = {
+                                'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId])
+                            };
+                            if (resName) {
+                                queryConditions['residue-test'] = builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_comp_id'), resName.toUpperCase()]);
+                            }
+                            else if (resId !== undefined) {
+                                queryConditions['residue-test'] = builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_seq_id'), resId]);
+                            }
+                            // 使用透明度为1（完全透明）来隐藏
+                            return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                                    var data, ligandQuery;
+                                    var _this = this;
+                                    return tslib_1.__generator(this, function (_b) {
+                                        data = structure;
+                                        ligandQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Ligand_".concat(chainId, "_").concat(resId || resName || 'all'), builder_1.MolScriptBuilder.struct.generator.atomGroups(queryConditions), {
+                                            description: "Ligand at ".concat(chainId, ":").concat(resId || resName || 'all'),
+                                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate
+                                        });
+                                        return [2 /*return*/, this.plugin.runTask(mol_task_1.Task.create('Select Ligand', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                                                var selection;
+                                                return tslib_1.__generator(this, function (_b) {
+                                                    switch (_b.label) {
+                                                        case 0: return [4 /*yield*/, ligandQuery.getSelection(this.plugin, runtime, data)];
+                                                        case 1:
+                                                            selection = _b.sent();
+                                                            return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
+                                                    }
+                                                });
+                                            }); }))];
+                                    });
+                                }); })];
+                        case 1:
+                            // 使用透明度为1（完全透明）来隐藏
+                            _c.sent();
+                            console.log("\u2705 Ligand ".concat(chainId, ":").concat(resId || resName || 'all', " hidden"));
+                            return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 清除指定配体的透明度来显示
+             * @param chainId 链ID
+             * @param resId 残基序号（可选）
+             * @param resName 残基名称（可选）
+             */
+            showLigand: function (chainId, resId, resName) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, components, _b, structures_4, s;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            structures = this.plugin.managers.structure.hierarchy.current.structures;
+                            components = [];
+                            for (_b = 0, structures_4 = structures; _b < structures_4.length; _b++) {
+                                s = structures_4[_b];
+                                components.push.apply(components, s.components);
+                            }
+                            if (components.length === 0) {
+                                console.warn('No components found');
+                                return [2 /*return*/];
+                            }
+                            // 清除透明度来恢复显示
+                            return [4 /*yield*/, (0, structure_transparency_1.clearStructureTransparency)(this.plugin, components)];
+                        case 1:
+                            // 清除透明度来恢复显示
+                            _c.sent();
+                            console.log("\u2705 Ligand ".concat(chainId, ":").concat(resId || resName || 'all', " shown"));
+                            return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 批量隐藏多个链
+             * @param chainIds 链ID数组，例如 ['A', 'B', 'C']
+             */
+            hideChains: function (chainIds) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var _b, chainIds_1, chainId;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            _b = 0, chainIds_1 = chainIds;
+                            _c.label = 1;
+                        case 1:
+                            if (!(_b < chainIds_1.length)) return [3 /*break*/, 4];
+                            chainId = chainIds_1[_b];
+                            return [4 /*yield*/, this.visual.hideChain(chainId)];
+                        case 2:
+                            _c.sent();
+                            _c.label = 3;
+                        case 3:
+                            _b++;
+                            return [3 /*break*/, 1];
+                        case 4: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 批量显示多个链
+             * @param chainIds 链ID数组，例如 ['A', 'B', 'C']
+             */
+            showChains: function (chainIds) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var _b, chainIds_2, chainId;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            _b = 0, chainIds_2 = chainIds;
+                            _c.label = 1;
+                        case 1:
+                            if (!(_b < chainIds_2.length)) return [3 /*break*/, 4];
+                            chainId = chainIds_2[_b];
+                            return [4 /*yield*/, this.visual.showChain(chainId)];
+                        case 2:
+                            _c.sent();
+                            _c.label = 3;
+                        case 3:
+                            _b++;
+                            return [3 /*break*/, 1];
+                        case 4: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 切换链的显示/隐藏状态
+             * @param chainId 链ID
+             * @param visible true显示，false隐藏
+             */
+            toggleChain: function (chainId, visible) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.label) {
+                        case 0:
+                            if (!visible) return [3 /*break*/, 2];
+                            return [4 /*yield*/, this.visual.showChain(chainId)];
+                        case 1:
+                            _b.sent();
+                            return [3 /*break*/, 4];
+                        case 2: return [4 /*yield*/, this.visual.hideChain(chainId)];
+                        case 3:
+                            _b.sent();
+                            _b.label = 4;
+                        case 4: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 切换配体的显示/隐藏状态
+             * @param chainId 链ID
+             * @param visible true显示，false隐藏
+             * @param resId 残基序号（可选）
+             * @param resName 残基名称（可选）
+             */
+            toggleLigand: function (chainId, visible, resId, resName) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.label) {
+                        case 0:
+                            if (!visible) return [3 /*break*/, 2];
+                            return [4 /*yield*/, this.visual.showLigand(chainId, resId, resName)];
+                        case 1:
+                            _b.sent();
+                            return [3 /*break*/, 4];
+                        case 2: return [4 /*yield*/, this.visual.hideLigand(chainId, resId, resName)];
+                        case 3:
+                            _b.sent();
+                            _b.label = 4;
+                        case 4: return [2 /*return*/];
+                    }
+                });
+            }); },
+            /**
+             * 清除所有透明度，恢复所有被隐藏的元素
+             */
+            clearAllTransparency: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, components, _b, structures_5, s;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            structures = this.plugin.managers.structure.hierarchy.current.structures;
+                            components = [];
+                            for (_b = 0, structures_5 = structures; _b < structures_5.length; _b++) {
+                                s = structures_5[_b];
+                                components.push.apply(components, s.components);
+                            }
+                            if (!(components.length > 0)) return [3 /*break*/, 2];
+                            return [4 /*yield*/, (0, structure_transparency_1.clearStructureTransparency)(this.plugin, components)];
+                        case 1:
+                            _c.sent();
+                            _c.label = 2;
+                        case 2:
+                            console.log('✅ All transparency cleared');
+                            return [2 /*return*/];
+                    }
+                });
             }); }
         };
         this.ArbitrarySphereVisuals = {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.72",
+  "version": "0.3.73",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {