drugflow-molstar 0.3.69 → 0.3.71

package/build/drugflow-molstar-plugin-0.3.71.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-0.3.70.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.70.js.LICENSE.txt */
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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/drugflow-molstar-component-build-0.3.71.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.3.71.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

@@ -2153,15 +2153,22 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      *     structureId: '0',
      *     interactionTypes: ['hydrogen-bond', 'hydrophobic', 'pi-stacking']
      * });
+     *
+     * // 只显示跨链相互作用（多肽场景）
+     * await viewer.add_interactions_repr({
+     *     componentRef: 'Polymer_p_plus_1',
+     *     structureId: '1',
+     *     interChainOnly: true  // 只显示不同链之间的相互作用
+     * });
      * ```
      */
     DrugflowMolstarPlugin.prototype.add_interactions_repr = function (options) {
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var componentRef, reprRef, _b, structureId, interactionTypes, _c, visible, _d, params, finalReprRef, structure, reprParams, tree;
-            return tslib_1.__generator(this, function (_e) {
-                switch (_e.label) {
+            var componentRef, reprRef, _b, structureId, interactionTypes, _c, interChainOnly, _d, visible, _e, params, finalReprRef, structure, reprParams, tree;
+            return tslib_1.__generator(this, function (_f) {
+                switch (_f.label) {
                     case 0:
-                        componentRef = options.componentRef, reprRef = options.reprRef, _b = options.structureId, structureId = _b === void 0 ? '0' : _b, interactionTypes = options.interactionTypes, _c = options.visible, visible = _c === void 0 ? true : _c, _d = options.params, params = _d === void 0 ? {} : _d;
+                        componentRef = options.componentRef, reprRef = options.reprRef, _b = options.structureId, structureId = _b === void 0 ? '0' : _b, interactionTypes = options.interactionTypes, _c = options.interChainOnly, interChainOnly = _c === void 0 ? false : _c, _d = options.visible, visible = _d === void 0 ? true : _d, _e = options.params, params = _e === void 0 ? {} : _e;
                         finalReprRef = reprRef || "".concat(componentRef, "_interactions_").concat(Date.now());
                         structure = this.getObj('Structure_' + structureId);
                         if (!structure) {
@@ -2174,6 +2181,12 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             reprParams.typeParams = reprParams.typeParams || {};
                             reprParams.typeParams.interactions = interactionTypes;
                         }
+                        // 如果只显示跨链相互作用（inter-unit interactions）
+                        if (interChainOnly) {
+                            reprParams.typeParams = reprParams.typeParams || {};
+                            // 只显示 inter-unit（跨单元/跨链）相互作用，不显示 intra-unit（单元内/链内）相互作用
+                            reprParams.typeParams.visuals = ['inter-unit'];
+                        }
                         tree = this.visual_tree(structure, componentRef, finalReprRef, reprParams);
                         if (!tree) {
                             console.error('Failed to build visual tree for interactions');
@@ -2184,12 +2197,12 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 tree: tree
                             })];
                     case 1:
-                        _e.sent();
+                        _f.sent();
                         // 控制可见性
                         if (!visible) {
                             this.set_visibility(finalReprRef);
                         }
-                        console.log("\u2705 Added interactions representation: ".concat(finalReprRef));
+                        console.log("\u2705 Added interactions representation: ".concat(finalReprRef, " (interChainOnly: ").concat(interChainOnly, ")"));
                         return [2 /*return*/, finalReprRef];
                 }
             });
@@ -2202,12 +2215,13 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      * @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）
+     * @param interChainOnly - 是否只显示跨链相互作用（可选，默认自动判断）
      * @returns 创建的 interactions 表示引用
      *
      * @example
      * ```javascript
-     * // 为多肽显示相互作用
-     * await viewer.show_component_interactions('Polymer_p1', '1');
+     * // 为多肽显示相互作用（自动启用跨链过滤）
+     * await viewer.show_component_interactions('Polymer_p_plus_1', '1');
      *
      * // 为配体显示相互作用
      * await viewer.show_component_interactions('Ligand_plus_0', '0');
@@ -2216,10 +2230,10 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      * await viewer.show_component_interactions('Polymer_p2', '2', ['hydrogen-bond', 'ionic']);
      * ```
      */
-    DrugflowMolstarPlugin.prototype.show_component_interactions = function (componentRef, structureId, interactionTypes) {
+    DrugflowMolstarPlugin.prototype.show_component_interactions = function (componentRef, structureId, interactionTypes, interChainOnly) {
         if (structureId === void 0) { structureId = '0'; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var defaultInteractionTypes, reprRef, error_4;
+            var defaultInteractionTypes, shouldFilterInterChain, reprRef, error_4;
             return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
@@ -2232,14 +2246,18 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             'ionic',
                             'halogen-bond'
                         ];
+                        shouldFilterInterChain = interChainOnly !== undefined
+                            ? interChainOnly
+                            : componentRef.includes('Polymer_p_plus');
                         return [4 /*yield*/, this.add_interactions_repr({
                                 componentRef: componentRef,
                                 structureId: structureId,
-                                interactionTypes: interactionTypes || defaultInteractionTypes
+                                interactionTypes: interactionTypes || defaultInteractionTypes,
+                                interChainOnly: shouldFilterInterChain
                             })];
                     case 1:
                         reprRef = _b.sent();
-                        console.log("\u2705 Showed interactions for component ".concat(componentRef));
+                        console.log("\u2705 Showed interactions for component ".concat(componentRef, " (interChainOnly: ").concat(shouldFilterInterChain, ")"));
                         return [2 /*return*/, reprRef];
                     case 2:
                         error_4 = _b.sent();
@@ -2250,6 +2268,72 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             });
         });
     };
+    /**
+     * 创建多肽周围环境组件（包含多肽本身+周围残基）
+     * 用于计算多肽与周围残基之间的相互作用
+     *
+     * @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, combinedQuery, combinedRef, 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
+                        });
+                        combinedQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Peptide_with_Surroundings_".concat(peptideId), builder_1.MolScriptBuilder.struct.modifier.union([
+                            builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
+                                0: peptideQuery.expression,
+                                radius: radius,
+                                'as-whole-residues': true
+                            })
+                        ]), {
+                            description: "Peptide ".concat(peptideId, " with surroundings within ").concat(radius, "\u00C5"),
+                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                            referencesCurrent: true
+                        });
+                        return [4 /*yield*/, this.createComponent({
+                                type: 'custom',
+                                expression: combinedQuery.expression,
+                                structureId: structureId,
+                                componentRef: "Polymer_p_plus_".concat(peptideId)
+                            })];
+                    case 2:
+                        combinedRef = _c.sent();
+                        console.log("\u2705 Created peptide with surroundings component: Polymer_p_plus_".concat(peptideId));
+                        return [2 /*return*/, combinedRef];
+                    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*/];
+                }
+            });
+        });
+    };
     /**
      * 删除指定的 contact/interaction 表示
      * @param contactId - contact 的 ID（通常是 prolif_id）

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.69",
+  "version": "0.3.71",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {