drugflow-molstar 0.3.68 → 0.3.70

package/build/drugflow-molstar-plugin-0.3.70.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-0.3.69.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.69.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.69.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-0.3.70.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.3.70.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

@@ -2196,53 +2196,124 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
         });
     };
     /**
-     * 为指定的配体和周围环境自动计算并显示相互作用
-     * 这是一个便捷方法，适用于配体对接结果的分析
+     * 为指定组件自动计算并显示相互作用
+     * 这是一个通用方法，可用于任意组件（配体、多肽、聚合物等）
      *
-     * @param ligandId - 配体ID（如 '0', '1' 等）
-     * @param structureId - 结构ID（可选，默认与 ligandId 相同）
+     * @param componentRef - 组件引用（如 'Polymer_p1', 'Ligand_plus_0' 等）
+     * @param structureId - 结构ID（可选，默认'0'）
+     * @param interactionTypes - 相互作用类型（可选）
      * @returns 创建的 interactions 表示引用
      *
      * @example
      * ```javascript
-     * // 为配体0显示相互作用
-     * await viewer.show_ligand_interactions('0');
+     * // 为多肽显示相互作用
+     * await viewer.show_component_interactions('Polymer_p1', '1');
      *
-     * // 为多个配体显示相互作用
-     * await viewer.show_ligand_interactions('1', '1');
+     * // 为配体显示相互作用
+     * await viewer.show_component_interactions('Ligand_plus_0', '0');
+     *
+     * // 自定义相互作用类型
+     * await viewer.show_component_interactions('Polymer_p2', '2', ['hydrogen-bond', 'ionic']);
      * ```
      */
-    DrugflowMolstarPlugin.prototype.show_ligand_interactions = function (ligandId, structureId) {
+    DrugflowMolstarPlugin.prototype.show_component_interactions = function (componentRef, structureId, interactionTypes) {
+        if (structureId === void 0) { structureId = '0'; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var actualStructureId, componentRef, reprRef, error_4;
+            var defaultInteractionTypes, reprRef, error_4;
             return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
-                        actualStructureId = structureId || ligandId;
-                        componentRef = "Ligand_plus_".concat(ligandId);
-                        _b.label = 1;
-                    case 1:
-                        _b.trys.push([1, 3, , 4]);
+                        _b.trys.push([0, 2, , 3]);
+                        defaultInteractionTypes = [
+                            'hydrogen-bond',
+                            'hydrophobic',
+                            'pi-stacking',
+                            'cation-pi',
+                            'ionic',
+                            'halogen-bond'
+                        ];
                         return [4 /*yield*/, this.add_interactions_repr({
                                 componentRef: componentRef,
-                                structureId: actualStructureId,
-                                interactionTypes: [
-                                    'hydrogen-bond',
-                                    'hydrophobic',
-                                    'pi-stacking',
-                                    'cation-pi',
-                                    'ionic',
-                                    'halogen-bond'
-                                ]
+                                structureId: structureId,
+                                interactionTypes: interactionTypes || defaultInteractionTypes
                             })];
-                    case 2:
+                    case 1:
                         reprRef = _b.sent();
-                        console.log("\u2705 Showed interactions for ligand ".concat(ligandId));
+                        console.log("\u2705 Showed interactions for component ".concat(componentRef));
                         return [2 /*return*/, reprRef];
-                    case 3:
+                    case 2:
                         error_4 = _b.sent();
-                        console.error("\u274C Failed to show interactions for ligand ".concat(ligandId, ":"), error_4);
+                        console.error("\u274C Failed to show interactions for component ".concat(componentRef, ":"), error_4);
                         throw error_4;
+                    case 3: return [2 /*return*/];
+                }
+            });
+        });
+    };
+    /**
+     * 创建多肽周围环境组件（类似配体的 Ligand_plus）
+     * 用于计算多肽与周围残基的相互作用
+     *
+     * @param options - 配置选项
+     * @returns 周围环境组件引用
+     *
+     * @example
+     * ```javascript
+     * await viewer.create_peptide_surroundings_component({
+     *     peptideId: '1',
+     *     peptideChainName: 'p',
+     *     structureId: '1',
+     *     radius: 5
+     * });
+     * ```
+     */
+    DrugflowMolstarPlugin.prototype.create_peptide_surroundings_component = function (options) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var peptideId, peptideChainName, structureId, _b, radius, peptideQuery, surroundingsQuery, surroundingsRef, error_5;
+            return tslib_1.__generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        peptideId = options.peptideId, peptideChainName = options.peptideChainName, structureId = options.structureId, _b = options.radius, radius = _b === void 0 ? 5 : _b;
+                        _c.label = 1;
+                    case 1:
+                        _c.trys.push([1, 3, , 4]);
+                        peptideQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Peptide_".concat(peptideId), 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'), peptideChainName])
+                            })
+                        ]), {
+                            description: "Peptide ".concat(peptideId, " (chain ").concat(peptideChainName, ")"),
+                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                            referencesCurrent: true
+                        });
+                        surroundingsQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Peptide_Surroundings_".concat(peptideId), builder_1.MolScriptBuilder.struct.modifier.union([
+                            builder_1.MolScriptBuilder.struct.modifier.exceptBy({
+                                0: builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
+                                    0: peptideQuery.expression,
+                                    radius: radius,
+                                    'as-whole-residues': true
+                                }),
+                                by: peptideQuery.expression
+                            })
+                        ]), {
+                            description: "Surroundings of peptide ".concat(peptideId, " within ").concat(radius, "\u00C5"),
+                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                            referencesCurrent: true
+                        });
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'custom',
+                                expression: surroundingsQuery.expression,
+                                structureId: structureId,
+                                componentRef: "Polymer_p_plus_".concat(peptideId)
+                            })];
+                    case 2:
+                        surroundingsRef = _c.sent();
+                        console.log("\u2705 Created peptide surroundings component: Polymer_p_plus_".concat(peptideId));
+                        return [2 /*return*/, surroundingsRef];
+                    case 3:
+                        error_5 = _c.sent();
+                        console.error("\u274C Failed to create peptide surroundings component for ".concat(peptideId, ":"), error_5);
+                        throw error_5;
                     case 4: return [2 /*return*/];
                 }
             });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.68",
+  "version": "0.3.70",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {