drugflow-molstar 0.3.53 → 0.3.54

package/build/drugflow-molstar-plugin-0.3.54.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-0.3.54.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.54.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.54.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

@@ -986,15 +986,17 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     // ============================================
     // Structure Component Creators - 创建结构组件
     // ============================================
+    // 注意：这些方法已弃用，请使用 createComponent() 方法
+    // 保留这些方法仅用于向后兼容
     /**
-     * 添加聚合物组件
+     * @deprecated 请使用 createComponent({ type: 'polymer' })
      */
     DrugflowMolstarPlugin.prototype.addPolymerComponent = function (builder, ref) {
         if (ref === void 0) { ref = 'Polymer'; }
         builder.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'static', params: 'polymer' } }, { ref: ref });
     };
     /**
-     * 添加配体组件
+     * @deprecated 请使用 createComponent({ type: 'ligand' })
      */
     DrugflowMolstarPlugin.prototype.addLigandComponent = function (builder, ref) {
         if (ref === void 0) { ref = 'Ligand'; }
@@ -1002,7 +1004,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
         builder.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'expression', params: ligandQuery.expression } }, { ref: ref });
     };
     /**
-     * 添加水分子组件
+     * @deprecated 请使用 createComponent({ type: 'water' })
      */
     DrugflowMolstarPlugin.prototype.addWaterComponent = function (builder, ref) {
         if (ref === void 0) { ref = 'Water'; }
@@ -1049,6 +1051,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     };
     /**
      * 渲染完整蛋白（polymer + ligand + water）
+     * @deprecated 建议使用 buildFullProteinStructureAsync
      */
     DrugflowMolstarPlugin.prototype.buildFullProteinStructure = function (builder, options) {
         if (options === void 0) { options = {}; }
@@ -1061,8 +1064,64 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             this.addWaterComponent(builder);
         return builder;
     };
+    /**
+     * 异步构建完整蛋白结构（推荐使用）
+     * 使用 createComponent API，结构更清晰
+     */
+    DrugflowMolstarPlugin.prototype.buildFullProteinStructureAsync = function (structureId, options) {
+        if (structureId === void 0) { structureId = '0'; }
+        if (options === void 0) { options = {}; }
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var _b, polymer, _c, ligand, _d, water, componentRefs, ref, ref, ref;
+            return tslib_1.__generator(this, function (_e) {
+                switch (_e.label) {
+                    case 0:
+                        _b = options.polymer, polymer = _b === void 0 ? true : _b, _c = options.ligand, ligand = _c === void 0 ? true : _c, _d = options.water, water = _d === void 0 ? true : _d;
+                        componentRefs = [];
+                        if (!polymer) return [3 /*break*/, 2];
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'polymer',
+                                structureId: structureId,
+                                componentRef: 'Polymer'
+                            })];
+                    case 1:
+                        ref = _e.sent();
+                        if (ref)
+                            componentRefs.push(ref);
+                        _e.label = 2;
+                    case 2:
+                        if (!ligand) return [3 /*break*/, 4];
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'ligand',
+                                structureId: structureId,
+                                componentRef: 'Ligand'
+                            })];
+                    case 3:
+                        ref = _e.sent();
+                        if (ref)
+                            componentRefs.push(ref);
+                        _e.label = 4;
+                    case 4:
+                        if (!water) return [3 /*break*/, 6];
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'water',
+                                structureId: structureId,
+                                componentRef: 'Water'
+                            })];
+                    case 5:
+                        ref = _e.sent();
+                        if (ref)
+                            componentRefs.push(ref);
+                        _e.label = 6;
+                    case 6: 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
+     * @private
      */
     DrugflowMolstarPlugin.prototype.buildLigandPocketStructure = function (builder, ligandId, options) {
         if (options === void 0) { options = {}; }
@@ -1072,6 +1131,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     };
     /**
      * 渲染多肽背景（non-peptide polymer + peptide + ligand + water）
+     * @deprecated 旧的同步builder方式，建议使用 createComponent()
+     * @private
      */
     DrugflowMolstarPlugin.prototype.buildPeptideBackgroundStructure = function (builder, options) {
         if (options === void 0) { options = {}; }
@@ -1087,6 +1148,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     };
     /**
      * 渲染多肽链
+     * @deprecated 旧的同步builder方式，建议使用 createComponent()
+     * @private
      */
     DrugflowMolstarPlugin.prototype.buildPeptideStructure = function (builder, ligandId) {
         this.addPeptideComponent(builder, 'Polymer_p' + ligandId);
@@ -1094,6 +1157,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     };
     /**
      * 渲染小分子（用于SDF格式）
+     * @deprecated 旧的同步builder方式，建议使用 createComponent()
+     * @private
      */
     DrugflowMolstarPlugin.prototype.buildSmallMoleculeStructure = function (builder, ligandId) {
         this.addSmallMoleculeComponent(builder, 'SmallMolecule_' + ligandId);
@@ -1101,6 +1166,13 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     };
     /**
      * 统一的结构创建接口
+     *
+     * @deprecated 该方法使用旧的同步builder方式。
+     * 新代码应使用：
+     * - `createComponent()` - 创建单个组件
+     * - `buildFullProteinStructureAsync()` - 异步构建完整结构
+     *
+     * @private 仅供内部使用（load_tree 方法）
      */
     DrugflowMolstarPlugin.prototype.create_structure_and_component = function (model, type, ligand_id, add_polymer, add_ligand, add_water, no_structure, ligand_name, ligand_site) {
         if (add_polymer === void 0) { add_polymer = true; }
@@ -1217,6 +1289,30 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     };
     /**
      * 主加载方法 - 加载并渲染结构
+     *
+     * @deprecated 推荐使用以下新API替代：
+     * - `loadFullProtein()` - 加载完整蛋白
+     * - `loadLigandPocket()` - 加载配体口袋
+     * - `loadPeptide()` - 加载多肽链
+     *
+     * 新API提供更清晰的流程和更好的控制：
+     * @example
+     * ```javascript
+     * // 旧方式
+     * await viewer.load_tree({
+     *     url,
+     *     format: 'pdb',
+     *     render_type: 'default'
+     * });
+     *
+     * // 新方式（推荐）
+     * const components = await viewer.loadFullProtein(url, 'pdb', {
+     *     showPolymer: true,
+     *     showLigand: true,
+     *     showWater: false
+     * });
+     * // 返回组件引用：['Polymer', 'Ligand']
+     * ```
      */
     DrugflowMolstarPlugin.prototype.load_tree = function (_b, fullLoad) {
         var url = _b.url, _c = _b.format, format = _c === void 0 ? 'mmcif' : _c, _d = _b.isBinary, isBinary = _d === void 0 ? false : _d, _e = _b.assemblyId, assemblyId = _e === void 0 ? '' : _e, _f = _b.pdb_string, pdb_string = _f === void 0 ? '' : _f, _g = _b.if_render, if_render = _g === void 0 ? true : _g, _h = _b.render_type, render_type = _h === void 0 ? 'default' : _h, _k = _b.render_id, render_id = _k === void 0 ? '0' : _k, _l = _b.ligand_name, ligand_name = _l === void 0 ? '' : _l, _m = _b.modelIndex, modelIndex = _m === void 0 ? 0 : _m, _o = _b.ligand_site, ligand_site = _o === void 0 ? '' : _o;
@@ -1406,6 +1502,64 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             });
         });
     };
+    /**
+     * 创建新组件
+     * @param options - 组件配置选项
+     * @returns 组件引用
+     */
+    DrugflowMolstarPlugin.prototype.createComponent = function (options) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var type, componentRef, _b, structureId, expression, label, finalComponentRef, state, structureRef, structureCell, update, ligandQuery;
+            return tslib_1.__generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        type = options.type, componentRef = options.componentRef, _b = options.structureId, structureId = _b === void 0 ? '0' : _b, expression = options.expression, label = options.label;
+                        finalComponentRef = componentRef || "".concat(type, "_").concat(Date.now());
+                        state = this.plugin.state.data;
+                        structureRef = "Structure_".concat(structureId);
+                        structureCell = state.select(structureRef)[0];
+                        if (!structureCell) {
+                            console.warn("Structure ".concat(structureRef, " not found"));
+                            return [2 /*return*/, null];
+                        }
+                        update = state.build().to(structureRef);
+                        // 根据类型创建组件
+                        switch (type) {
+                            case 'polymer':
+                                update.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'static', params: 'polymer' } }, { ref: finalComponentRef });
+                                break;
+                            case 'ligand':
+                                ligandQuery = this.createLigandQuery(label || 'Ligand');
+                                update.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'expression', params: ligandQuery.expression } }, { ref: finalComponentRef });
+                                break;
+                            case 'water':
+                                update.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'static', params: 'water' } }, { ref: finalComponentRef });
+                                break;
+                            case 'ion':
+                                update.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'static', params: 'ion' } }, { ref: finalComponentRef });
+                                break;
+                            case 'all':
+                                update.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'static', params: 'all' } }, { ref: finalComponentRef });
+                                break;
+                            case 'custom':
+                                if (!expression) {
+                                    console.error('Custom type requires expression parameter');
+                                    return [2 /*return*/, null];
+                                }
+                                update.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'expression', params: expression } }, { ref: finalComponentRef });
+                                break;
+                            default:
+                                console.error("Unknown component type: ".concat(type));
+                                return [2 /*return*/, null];
+                        }
+                        return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update })];
+                    case 1:
+                        _c.sent();
+                        return [2 /*return*/, finalComponentRef];
+                }
+            });
+        });
+    };
     /**
      * 修改表示的显示类型
      * @param reprRef - 表示引用
@@ -1474,35 +1628,73 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      * @param format - 文件格式 (mmcif, pdb, sdf等)
      * @param options - 可选参数
      */
+    /**
+     * 加载完整蛋白结构
+     * 流程：Load Data → Parse Model → Add Structure → Create Components
+     *
+     * @param url - 蛋白文件URL
+     * @param format - 文件格式
+     * @param options - 加载选项
+     * @returns 创建的组件引用列表
+     */
     DrugflowMolstarPlugin.prototype.loadFullProtein = 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, showPolymer, _f, showLigand, _g, showWater, _h, pdbString;
+            var _b, _c, isBinary, _d, modelIndex, _e, showPolymer, _f, showLigand, _g, showWater, _h, pdbString, structureId, state, data, model, structureBuilder, componentRefs, error_1;
             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.showPolymer, showPolymer = _e === void 0 ? true : _e, _f = _b.showLigand, showLigand = _f === void 0 ? true : _f, _g = _b.showWater, showWater = _g === void 0 ? true : _g, _h = _b.pdbString, pdbString = _h === void 0 ? '' : _h;
-                        return [4 /*yield*/, this.load_tree({
+                        structureId = '0';
+                        _k.label = 1;
+                    case 1:
+                        _k.trys.push([1, 7, , 8]);
+                        state = this.plugin.state.data;
+                        return [4 /*yield*/, commands_1.PluginCommands.State.RemoveObject(this.plugin, {
+                                state: state,
+                                ref: state.tree.root.ref
+                            })];
+                    case 2:
+                        _k.sent();
+                        // 🔹 Step 2: 加载数据
+                        console.log('📥 Loading data...');
+                        return [4 /*yield*/, this.loadData({
                                 url: url,
-                                format: format,
-                                isBinary: isBinary,
-                                pdb_string: pdbString,
-                                render_type: 'default',
-                                render_id: '0',
-                                modelIndex: modelIndex
+                                pdbString: pdbString,
+                                isBinary: isBinary
                             })];
-                    case 1:
+                    case 3:
+                        data = _k.sent();
+                        // 🔹 Step 3: 解析并创建模型
+                        console.log('🧬 Parsing model...');
+                        return [4 /*yield*/, this.parseAndCreateModel(data, format, modelIndex)];
+                    case 4:
+                        model = _k.sent();
+                        // 🔹 Step 4: 创建结构
+                        console.log('🏗️ Creating structure...');
+                        structureBuilder = this.createBaseStructure(model, structureId);
+                        return [4 /*yield*/, this.applyState(structureBuilder)];
+                    case 5:
                         _k.sent();
-                        if (!(!showPolymer || !showLigand || !showWater)) return [3 /*break*/, 3];
-                        return [4 /*yield*/, this.recreate_s_c({
+                        // 🔹 Step 5: 创建组件
+                        console.log('📦 Creating components...');
+                        return [4 /*yield*/, this.buildFullProteinStructureAsync(structureId, {
                                 polymer: showPolymer,
                                 ligand: showLigand,
                                 water: showWater
                             })];
-                    case 2:
-                        _k.sent();
-                        _k.label = 3;
-                    case 3: return [2 /*return*/];
+                    case 6:
+                        componentRefs = _k.sent();
+                        // 🔹 Step 6: 更新引用并触发事件
+                        this.updateAssemblyRef();
+                        this.events.loadComplete.next(true);
+                        console.log("\u2705 Loaded protein with ".concat(componentRefs.length, " components:"), componentRefs);
+                        return [2 /*return*/, componentRefs];
+                    case 7:
+                        error_1 = _k.sent();
+                        console.error('❌ Error loading protein:', error_1);
+                        throw error_1;
+                    case 8: return [2 /*return*/];
                 }
             });
         });
@@ -1587,6 +1779,77 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             return void 0;
         return cell.obj.data;
     };
+    /**
+     * 为组件添加3D表示
+     *
+     * @example
+     * ```javascript
+     * // 添加cartoon表示
+     * await viewer.add_repr({
+     *     componentRef: 'Polymer',
+     *     type: 'cartoon',
+     *     colorTheme: 'secondary-structure'
+     * });
+     *
+     * // 添加半透明surface
+     * await viewer.add_repr({
+     *     componentRef: 'Polymer',
+     *     type: 'molecular-surface',
+     *     colorTheme: 'hydrophobicity',
+     *     alpha: 0.5
+     * });
+     * ```
+     *
+     * @param options - 表示配置选项
+     * @returns 表示引用
+     */
+    DrugflowMolstarPlugin.prototype.add_repr = function (options) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var componentRef, reprRef, type, colorTheme, alpha, _b, visible, _c, structureId, _d, params, finalReprRef, structure, reprParams, tree;
+            return tslib_1.__generator(this, function (_e) {
+                switch (_e.label) {
+                    case 0:
+                        componentRef = options.componentRef, reprRef = options.reprRef, type = options.type, colorTheme = options.colorTheme, alpha = options.alpha, _b = options.visible, visible = _b === void 0 ? true : _b, _c = options.structureId, structureId = _c === void 0 ? '0' : _c, _d = options.params, params = _d === void 0 ? {} : _d;
+                        finalReprRef = reprRef || "".concat(componentRef, "_").concat(type, "_").concat(Date.now());
+                        structure = this.getObj('Structure_' + structureId);
+                        if (!structure) {
+                            console.warn("Structure_".concat(structureId, " not found"));
+                            return [2 /*return*/, null];
+                        }
+                        reprParams = tslib_1.__assign({ type: type }, params);
+                        // 设置颜色主题
+                        if (colorTheme) {
+                            reprParams.color = colorTheme; // 应该是 'color' 而不是 'colorTheme'
+                        }
+                        // 设置透明度（作为 type 的参数）
+                        if (alpha !== undefined) {
+                            reprParams.typeParams = reprParams.typeParams || {};
+                            reprParams.typeParams.alpha = alpha;
+                        }
+                        tree = this.visual_tree(structure, componentRef, finalReprRef, reprParams);
+                        if (!tree) {
+                            console.error('Failed to build visual tree');
+                            return [2 /*return*/, null];
+                        }
+                        return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, {
+                                state: this.plugin.state.data,
+                                tree: tree
+                            })];
+                    case 1:
+                        _e.sent();
+                        // 控制可见性
+                        if (!visible) {
+                            this.set_visibility(finalReprRef);
+                        }
+                        return [2 /*return*/, finalReprRef];
+                }
+            });
+        });
+    };
+    /**
+     * @deprecated 使用 add_repr 替代
+     * 旧的表示更新方法，保留用于向后兼容
+     */
     DrugflowMolstarPlugin.prototype.update_comp_repr = function (comp_ref, repr_ref, if_show, params, ligand_id) {
         return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structure, tree;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.53",
+  "version": "0.3.54",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {