drugflow-molstar 0.3.56 → 0.3.58

package/lib/drugflow-molstar-component-build-0.3.57.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.57.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.57.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/drugflow-molstar-component-build-0.3.58.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.3.58.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

@@ -1103,6 +1103,95 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             });
         });
     };
+    /**
+     * 异步构建配体口袋组件
+     * 创建配体和周围环境两个组件
+     */
+    DrugflowMolstarPlugin.prototype.buildLigandPocketComponentsAsync = function (structureId, ligandId, ligandInfo, radius) {
+        if (radius === void 0) { radius = 5; }
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var componentRefs, chainId, resId, parts, ligandQuery, surroundingsQuery, ligandRef, surroundingsRef;
+            return tslib_1.__generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        componentRefs = [];
+                        chainId = 'A';
+                        if (ligandInfo.site) {
+                            parts = ligandInfo.site.split(':');
+                            if (parts.length >= 1)
+                                chainId = parts[0];
+                            if (parts.length >= 2)
+                                resId = parseInt(parts[1]);
+                        }
+                        if (ligandInfo.name) {
+                            // 通过配体名称查询
+                            ligandQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Ligand_".concat(ligandInfo.name), builder_1.MolScriptBuilder.struct.modifier.union([
+                                builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                                    'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId]),
+                                    'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_comp_id'), ligandInfo.name.toUpperCase()])
+                                })
+                            ]), {
+                                description: "Ligand ".concat(ligandInfo.name),
+                                category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                                referencesCurrent: true
+                            });
+                        }
+                        else if (resId !== undefined) {
+                            // 通过残基ID查询
+                            ligandQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Ligand_".concat(resId), builder_1.MolScriptBuilder.struct.modifier.union([
+                                builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                                    'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId]),
+                                    'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_seq_id'), resId])
+                                })
+                            ]), {
+                                description: "Ligand at ".concat(chainId, ":").concat(resId),
+                                category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                                referencesCurrent: true
+                            });
+                        }
+                        else {
+                            // 使用默认配体查询（所有配体）
+                            ligandQuery = structure_selection_query_1.StructureSelectionQueries.ligand;
+                        }
+                        surroundingsQuery = (0, structure_selection_query_1.StructureSelectionQuery)('Surroundings', builder_1.MolScriptBuilder.struct.modifier.union([
+                            builder_1.MolScriptBuilder.struct.modifier.exceptBy({
+                                0: builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
+                                    0: ligandQuery.expression,
+                                    radius: radius,
+                                    'as-whole-residues': true
+                                }),
+                                by: ligandQuery.expression
+                            })
+                        ]), {
+                            description: "Surroundings within ".concat(radius, "\u00C5"),
+                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                            referencesCurrent: true
+                        });
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'custom',
+                                expression: ligandQuery.expression,
+                                structureId: structureId,
+                                componentRef: "Ligand_".concat(ligandId)
+                            })];
+                    case 1:
+                        ligandRef = _b.sent();
+                        if (ligandRef)
+                            componentRefs.push(ligandRef);
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'custom',
+                                expression: surroundingsQuery.expression,
+                                structureId: structureId,
+                                componentRef: "Ligand_plus_".concat(ligandId)
+                            })];
+                    case 2:
+                        surroundingsRef = _b.sent();
+                        if (surroundingsRef)
+                            componentRefs.push(surroundingsRef);
+                        return [2 /*return*/, componentRefs];
+                }
+            });
+        });
+    };
     /**
      * 渲染配体口袋（ligand + surrounding）
      * @deprecated 旧的同步builder方式，建议使用 createComponent() 结合自定义查询
@@ -1634,75 +1723,130 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             });
         });
     };
-    // async loadLigandPocket(
-    //     url: string,
-    //     ligandInfo: {
-    //         name?: string;
-    //         site?: string; // 格式: "A:123" (chainId:resId)
-    //     },
-    //     format: 'mmcif' | 'pdb' | 'sdf' | 'mol' | 'mol2' | 'xyz' | 'gro' | 'pdbqt' | 'cifCore' = 'mmcif',
-    //     options?: {
-    //         isBinary?: boolean;
-    //         modelIndex?: number;
-    //         pdbString?: string;
-    //     }
-    // ) {
-    //     const {
-    //         isBinary = false,
-    //         modelIndex = 0,
-    //         pdbString = ''
-    //     } = options || {};
-    //     await this.load_tree({
-    //         url,
-    //         format,
-    //         isBinary,
-    //         pdb_string: pdbString,
-    //         render_type: 'ligand_view',
-    //         render_id: '0',
-    //         ligand_name: ligandInfo.name || '',
-    //         ligand_site: ligandInfo.site || '',
-    //         modelIndex
-    //     });
-    // }
-    // async loadPeptide(
-    //     url: string,
-    //     format: 'mmcif' | 'pdb' | 'sdf' | 'mol' | 'mol2' | 'xyz' | 'gro' | 'pdbqt' | 'cifCore' = 'mmcif',
-    //     options?: {
-    //         isBinary?: boolean;
-    //         modelIndex?: number;
-    //         showBackground?: boolean; // 是否显示背景（非多肽聚合物）
-    //         showLigand?: boolean;
-    //         showWater?: boolean;
-    //         pdbString?: string;
-    //     }
-    // ) {
-    //     const {
-    //         isBinary = false,
-    //         modelIndex = 0,
-    //         showBackground = false,
-    //         showLigand = true,
-    //         showWater = false,
-    //         pdbString = ''
-    //     } = options || {};
-    //     const renderType = showBackground ? 'peptide_background' : 'peptide';
-    //     await this.load_tree({
-    //         url,
-    //         format,
-    //         isBinary,
-    //         pdb_string: pdbString,
-    //         render_type: renderType,
-    //         render_id: '0',
-    //         modelIndex
-    //     });
-    //     // 如果是peptide_background模式，根据选项调整显示
-    //     if (showBackground && (!showLigand || !showWater)) {
-    //         await this.recreate_s_c({
-    //             polymer: true,
-    //             ligand: showLigand,
-    //             water: showWater
-    //         });
-    //     }
-    // }
+    /**
+     * 加载并渲染配体口袋
+     * 流程：Load Data → Parse Model → Add Structure → Create Ligand Pocket Components
+     *
+     * 支持多次调用创建多个配体口袋叠加视图进行比较
+     *
+     * @param url - PDB文件URL
+     * @param ligandInfo - 配体信息
+     * @param format - 文件格式
+     * @param options - 可选参数
+     * @returns 创建的组件引用列表 [ligandRef, surroundingsRef]
+     *
+     */
+    DrugflowMolstarPlugin.prototype.loadLigandPocket = function (url, ligandInfo, format, options) {
+        if (format === void 0) { format = 'mmcif'; }
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var _b, _c, isBinary, _d, modelIndex, _e, pdbString, _f, clearPrevious, _g, radius, ligandId, structureId, state, data, model, structureBuilder, componentRefs, error_2;
+            return tslib_1.__generator(this, function (_h) {
+                switch (_h.label) {
+                    case 0:
+                        _b = options || {}, _c = _b.isBinary, isBinary = _c === void 0 ? false : _c, _d = _b.modelIndex, modelIndex = _d === void 0 ? 0 : _d, _e = _b.pdbString, pdbString = _e === void 0 ? '' : _e, _f = _b.clearPrevious, clearPrevious = _f === void 0 ? true : _f, _g = _b.radius, radius = _g === void 0 ? 5 : _g;
+                        ligandId = ligandInfo.ligandId || ligandInfo.name || '0';
+                        structureId = clearPrevious ? '0' : ligandId || '0';
+                        _h.label = 1;
+                    case 1:
+                        _h.trys.push([1, 8, , 9]);
+                        if (!clearPrevious) return [3 /*break*/, 3];
+                        state = this.plugin.state.data;
+                        return [4 /*yield*/, commands_1.PluginCommands.State.RemoveObject(this.plugin, {
+                                state: state,
+                                ref: state.tree.root.ref
+                            })];
+                    case 2:
+                        _h.sent();
+                        _h.label = 3;
+                    case 3:
+                        // 🔹 Step 2: 加载数据
+                        console.log('📥 Loading data for ligand pocket...');
+                        return [4 /*yield*/, this.loadData({
+                                url: url,
+                                pdbString: pdbString,
+                                isBinary: isBinary
+                            })];
+                    case 4:
+                        data = _h.sent();
+                        // 🔹 Step 3: 解析并创建模型
+                        console.log('🧬 Parsing model...');
+                        return [4 /*yield*/, this.parseAndCreateModel(data, format, modelIndex)];
+                    case 5:
+                        model = _h.sent();
+                        // 🔹 Step 4: 创建结构
+                        console.log('🏗️ Creating structure...');
+                        structureBuilder = this.createBaseStructure(model, structureId);
+                        return [4 /*yield*/, this.applyState(structureBuilder)];
+                    case 6:
+                        _h.sent();
+                        // 🔹 Step 5: 创建配体口袋组件
+                        console.log('📦 Creating ligand pocket components...');
+                        return [4 /*yield*/, this.buildLigandPocketComponentsAsync(structureId, ligandId, ligandInfo, radius)];
+                    case 7:
+                        componentRefs = _h.sent();
+                        // 🔹 Step 6: 更新引用并触发事件
+                        if (clearPrevious) {
+                            this.updateAssemblyRef();
+                        }
+                        this.events.loadComplete.next(true);
+                        console.log("\u2705 Loaded ligand pocket with ".concat(componentRefs.length, " components:"), componentRefs);
+                        return [2 /*return*/, componentRefs];
+                    case 8:
+                        error_2 = _h.sent();
+                        console.error('❌ Error loading ligand pocket:', error_2);
+                        throw error_2;
+                    case 9: return [2 /*return*/];
+                }
+            });
+        });
+    };
+    /**
+     * 加载并渲染多肽链
+     *
+     * @deprecated 该方法仍使用旧的 load_tree 流程，将来会重构为新架构
+     *
+     * @param url - PDB文件URL
+     * @param format - 文件格式
+     * @param options - 可选参数
+     */
+    DrugflowMolstarPlugin.prototype.loadPeptide = function (url, format, options) {
+        if (format === void 0) { format = 'mmcif'; }
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var _b, _c, isBinary, _d, modelIndex, _e, showBackground, _f, showLigand, _g, showWater, _h, pdbString, renderType;
+            return tslib_1.__generator(this, function (_k) {
+                switch (_k.label) {
+                    case 0:
+                        _b = options || {}, _c = _b.isBinary, isBinary = _c === void 0 ? false : _c, _d = _b.modelIndex, modelIndex = _d === void 0 ? 0 : _d, _e = _b.showBackground, showBackground = _e === void 0 ? false : _e, _f = _b.showLigand, showLigand = _f === void 0 ? true : _f, _g = _b.showWater, showWater = _g === void 0 ? false : _g, _h = _b.pdbString, pdbString = _h === void 0 ? '' : _h;
+                        renderType = showBackground ? 'peptide_background' : 'peptide';
+                        // @ts-ignore - 使用旧的load_tree方法，将来会重构
+                        return [4 /*yield*/, this.load_tree({
+                                url: url,
+                                format: format,
+                                isBinary: isBinary,
+                                pdb_string: pdbString,
+                                render_type: renderType,
+                                render_id: '0',
+                                modelIndex: modelIndex
+                            })];
+                    case 1:
+                        // @ts-ignore - 使用旧的load_tree方法，将来会重构
+                        _k.sent();
+                        if (!(showBackground && (!showLigand || !showWater))) return [3 /*break*/, 3];
+                        // @ts-ignore - 使用旧的recreate_s_c方法
+                        return [4 /*yield*/, this.recreate_s_c({
+                                polymer: true,
+                                ligand: showLigand,
+                                water: showWater
+                            })];
+                    case 2:
+                        // @ts-ignore - 使用旧的recreate_s_c方法
+                        _k.sent();
+                        _k.label = 3;
+                    case 3: return [2 /*return*/];
+                }
+            });
+        });
+    };
     DrugflowMolstarPlugin.prototype.getObj = function (ref) {
         var state = this.plugin.state.data;
         var cell = state.select(ref)[0];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.56",
+  "version": "0.3.58",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {