drugflow-molstar 0.3.73 → 0.3.74

package/build/drugflow-molstar-plugin-0.3.74.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-0.3.74.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.74.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.74.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

@@ -47,6 +47,11 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             "now": { "polymer": [], "ligand": [], "other": [] }
         };
         this.isHighlightColorUpdated = false;
+        // 隐藏状态追踪器
+        this.hiddenState = {
+            chains: new Set(),
+            ligands: new Set() // 隐藏的配体（格式: "chainId:resId" 或 "chainId:resName"）
+        };
         this.canvas = {
             toggleControls: function (isVisible) {
                 if (typeof isVisible === 'undefined')
@@ -498,11 +503,10 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                 });
             }); },
             /**
-             * 使用透明度隐藏指定的链
-             * @param chainId 链ID，例如 'A', 'B'
+             * 应用所有隐藏状态（内部方法）
              */
-            hideChain: function (chainId) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
-                var structures, components, _b, structures_1, s;
+            _applyHiddenState: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                var structures, components, _b, structures_1, s, chainArray, _loop_1, this_1, i, ligandArray, _loop_2, this_2, i;
                 var _this = this;
                 return tslib_1.__generator(this, function (_c) {
                     switch (_c.label) {
@@ -514,37 +518,145 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 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)];
-                                                    }
-                                                });
-                                            }); }))];
-                                    });
-                                }); })];
+                            // 先清除所有透明度
+                            return [4 /*yield*/, (0, structure_transparency_1.clearStructureTransparency)(this.plugin, components)];
                         case 1:
-                            // 使用透明度为1（完全透明）来隐藏
+                            // 先清除所有透明度
+                            _c.sent();
+                            // 如果没有需要隐藏的，直接返回
+                            if (this.hiddenState.chains.size === 0 && this.hiddenState.ligands.size === 0) {
+                                return [2 /*return*/];
+                            }
+                            chainArray = Array.from(this.hiddenState.chains);
+                            _loop_1 = function (i) {
+                                var chainId;
+                                return tslib_1.__generator(this, function (_d) {
+                                    switch (_d.label) {
+                                        case 0:
+                                            chainId = chainArray[i];
+                                            return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this_1.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                                                    var chainQuery;
+                                                    var _this = this;
+                                                    return tslib_1.__generator(this, function (_b) {
+                                                        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, structure)];
+                                                                        case 1:
+                                                                            selection = _b.sent();
+                                                                            return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
+                                                                    }
+                                                                });
+                                                            }); }))];
+                                                    });
+                                                }); })];
+                                        case 1:
+                                            _d.sent();
+                                            return [2 /*return*/];
+                                    }
+                                });
+                            };
+                            this_1 = this;
+                            i = 0;
+                            _c.label = 2;
+                        case 2:
+                            if (!(i < chainArray.length)) return [3 /*break*/, 5];
+                            return [5 /*yield**/, _loop_1(i)];
+                        case 3:
                             _c.sent();
+                            _c.label = 4;
+                        case 4:
+                            i++;
+                            return [3 /*break*/, 2];
+                        case 5:
+                            ligandArray = Array.from(this.hiddenState.ligands);
+                            _loop_2 = function (i) {
+                                var ligandKey, parts, chainId, identifier, resId, resName, queryConditions;
+                                return tslib_1.__generator(this, function (_e) {
+                                    switch (_e.label) {
+                                        case 0:
+                                            ligandKey = ligandArray[i];
+                                            parts = ligandKey.split(':');
+                                            chainId = parts[0];
+                                            identifier = parts[1];
+                                            resId = isNaN(Number(identifier)) ? undefined : Number(identifier);
+                                            resName = isNaN(Number(identifier)) ? identifier : undefined;
+                                            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]);
+                                            }
+                                            return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this_2.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                                                    var ligandQuery;
+                                                    var _this = this;
+                                                    return tslib_1.__generator(this, function (_b) {
+                                                        ligandQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Ligand_".concat(ligandKey), builder_1.MolScriptBuilder.struct.generator.atomGroups(queryConditions), {
+                                                            description: "Ligand at ".concat(ligandKey),
+                                                            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, structure)];
+                                                                        case 1:
+                                                                            selection = _b.sent();
+                                                                            return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
+                                                                    }
+                                                                });
+                                                            }); }))];
+                                                    });
+                                                }); })];
+                                        case 1:
+                                            _e.sent();
+                                            return [2 /*return*/];
+                                    }
+                                });
+                            };
+                            this_2 = this;
+                            i = 0;
+                            _c.label = 6;
+                        case 6:
+                            if (!(i < ligandArray.length)) return [3 /*break*/, 9];
+                            return [5 /*yield**/, _loop_2(i)];
+                        case 7:
+                            _c.sent();
+                            _c.label = 8;
+                        case 8:
+                            i++;
+                            return [3 /*break*/, 6];
+                        case 9: 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 () {
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.label) {
+                        case 0:
+                            // 添加到隐藏状态
+                            this.hiddenState.chains.add(chainId);
+                            // 重新应用所有隐藏状态
+                            return [4 /*yield*/, this.visual._applyHiddenState()];
+                        case 1:
+                            // 重新应用所有隐藏状态
+                            _b.sent();
                             console.log("\u2705 Chain ".concat(chainId, " hidden"));
                             return [2 /*return*/];
                     }
@@ -555,25 +667,16 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
              * @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) {
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.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)];
+                            // 从隐藏状态中移除
+                            this.hiddenState.chains.delete(chainId);
+                            // 重新应用所有隐藏状态
+                            return [4 /*yield*/, this.visual._applyHiddenState()];
                         case 1:
-                            // 清除透明度来恢复显示
-                            _c.sent();
+                            // 重新应用所有隐藏状态
+                            _b.sent();
                             console.log("\u2705 Chain ".concat(chainId, " shown"));
                             return [2 /*return*/];
                     }
@@ -586,57 +689,20 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
              * @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) {
+                var identifier, ligandKey;
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.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)];
-                                                    }
-                                                });
-                                            }); }))];
-                                    });
-                                }); })];
+                            identifier = resId !== undefined ? resId.toString() : (resName || 'all');
+                            ligandKey = "".concat(chainId, ":").concat(identifier);
+                            // 添加到隐藏状态
+                            this.hiddenState.ligands.add(ligandKey);
+                            // 重新应用所有隐藏状态
+                            return [4 /*yield*/, this.visual._applyHiddenState()];
                         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"));
+                            // 重新应用所有隐藏状态
+                            _b.sent();
+                            console.log("\u2705 Ligand ".concat(ligandKey, " hidden"));
                             return [2 /*return*/];
                     }
                 });
@@ -648,26 +714,20 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
              * @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) {
+                var identifier, ligandKey;
+                return tslib_1.__generator(this, function (_b) {
+                    switch (_b.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)];
+                            identifier = resId !== undefined ? resId.toString() : (resName || 'all');
+                            ligandKey = "".concat(chainId, ":").concat(identifier);
+                            // 从隐藏状态中移除
+                            this.hiddenState.ligands.delete(ligandKey);
+                            // 重新应用所有隐藏状态
+                            return [4 /*yield*/, this.visual._applyHiddenState()];
                         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"));
+                            // 重新应用所有隐藏状态
+                            _b.sent();
+                            console.log("\u2705 Ligand ".concat(ligandKey, " shown"));
                             return [2 /*return*/];
                     }
                 });
@@ -772,14 +832,17 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
              * 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;
+                var structures, components, _b, structures_2, s;
                 return tslib_1.__generator(this, function (_c) {
                     switch (_c.label) {
                         case 0:
+                            // 清空隐藏状态
+                            this.hiddenState.chains.clear();
+                            this.hiddenState.ligands.clear();
                             structures = this.plugin.managers.structure.hierarchy.current.structures;
                             components = [];
-                            for (_b = 0, structures_5 = structures; _b < structures_5.length; _b++) {
-                                s = structures_5[_b];
+                            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)) return [3 /*break*/, 2];
@@ -792,7 +855,16 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             return [2 /*return*/];
                     }
                 });
-            }); }
+            }); },
+            /**
+             * 获取当前隐藏状态
+             */
+            getHiddenState: function () {
+                return {
+                    chains: Array.from(_this.hiddenState.chains),
+                    ligands: Array.from(_this.hiddenState.ligands)
+                };
+            }
         };
         this.ArbitrarySphereVisuals = {
             'arbitrary-sphere': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Arbitrary sphere mesh', ctx, getParams, _this.ArbitrarySphereVisual); }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.73",
+  "version": "0.3.74",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {