drugflow-molstar 0.3.77 → 0.3.78

package/build/drugflow-molstar-plugin-0.3.78.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-0.3.78.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.78.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.78.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

@@ -2799,24 +2799,25 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      * ```
      */
     DrugflowMolstarPlugin.prototype.exportInteractionsData = function (componentRef, structureId, filterResId) {
+        var _b, _c;
         if (structureId === void 0) { structureId = '0'; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var InteractionsProvider, interactionTypeLabel, Vec3, fullComponentRef, componentCell, fallbackCell, actualCell, componentStructure_1, interactionsProperty_1, interactions, exportedData, addedInteractions, contacts, unitsFeatures, i, edge, unitA, unitB, featuresA, featuresB, atomInfoA, atomInfoB, interactionType, atom1Key, atom2Key, _b, key1, key2, uniqueKey, posA, posB, distance, filterMsg, error_7;
+            var InteractionsProvider, interactionTypeLabel, Vec3, fullComponentRef, componentCell, fallbackCell, actualCell, componentStructure_1, interactionsProperty_1, interactions, exportedData, addedInteractions, unitElementToMolIndex, molAtomCount, _d, _e, unit, elements, indexMap, i, contacts, unitsFeatures, i, edge, unitA, unitB, featuresA, featuresB, atomInfoA, atomInfoB, interactionType, atom1Key, atom2Key, _f, key1, key2, uniqueKey, posA, posB, distance, molIndexA, molIndexB, filterMsg, error_7;
             var _this = this;
-            return tslib_1.__generator(this, function (_c) {
-                switch (_c.label) {
+            return tslib_1.__generator(this, function (_g) {
+                switch (_g.label) {
                     case 0: return [4 /*yield*/, Promise.resolve().then(function () { return tslib_1.__importStar(require('molstar/lib/mol-model-props/computed/interactions')); })];
                     case 1:
-                        InteractionsProvider = (_c.sent()).InteractionsProvider;
+                        InteractionsProvider = (_g.sent()).InteractionsProvider;
                         return [4 /*yield*/, Promise.resolve().then(function () { return tslib_1.__importStar(require('molstar/lib/mol-model-props/computed/interactions/common')); })];
                     case 2:
-                        interactionTypeLabel = (_c.sent()).interactionTypeLabel;
+                        interactionTypeLabel = (_g.sent()).interactionTypeLabel;
                         return [4 /*yield*/, Promise.resolve().then(function () { return tslib_1.__importStar(require('molstar/lib/mol-math/linear-algebra')); })];
                     case 3:
-                        Vec3 = (_c.sent()).Vec3;
-                        _c.label = 4;
+                        Vec3 = (_g.sent()).Vec3;
+                        _g.label = 4;
                     case 4:
-                        _c.trys.push([4, 7, , 8]);
+                        _g.trys.push([4, 7, , 8]);
                         fullComponentRef = componentRef.includes('_') ? componentRef : "".concat(componentRef, "_").concat(structureId);
                         componentCell = this.plugin.state.data.select(fullComponentRef)[0];
                         if (!componentCell) {
@@ -2861,8 +2862,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 });
                             }); }))];
                     case 5:
-                        _c.sent();
-                        _c.label = 6;
+                        _g.sent();
+                        _g.label = 6;
                     case 6:
                         if (!interactionsProperty_1 || !interactionsProperty_1.value) {
                             console.log('No interactions data found after computation. Make sure you have added interactions representation first.');
@@ -2871,6 +2872,20 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                         interactions = interactionsProperty_1.value;
                         exportedData = [];
                         addedInteractions = new Set();
+                        unitElementToMolIndex = new Map();
+                        molAtomCount = 0;
+                        for (_d = 0, _e = componentStructure_1.units; _d < _e.length; _d++) {
+                            unit = _e[_d];
+                            if (unit.kind !== 0)
+                                continue; // 只处理原子单元
+                            elements = unit.elements;
+                            indexMap = new Map();
+                            for (i = 0; i < elements.length; i++) {
+                                molAtomCount++;
+                                indexMap.set(i, molAtomCount); // 索引 -> MOL序号（1-based）
+                            }
+                            unitElementToMolIndex.set(unit.id, indexMap);
+                        }
                         contacts = interactions.contacts;
                         unitsFeatures = interactions.unitsFeatures;
                         for (i = 0; i < contacts.edgeCount; i++) {
@@ -2894,7 +2909,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             interactionType = interactionTypeLabel(edge.props.type);
                             atom1Key = "".concat(atomInfoA.chainId, ":").concat(atomInfoA.resId, ":").concat(atomInfoA.atomName);
                             atom2Key = "".concat(atomInfoB.chainId, ":").concat(atomInfoB.resId, ":").concat(atomInfoB.atomName);
-                            _b = atom1Key < atom2Key ? [atom1Key, atom2Key] : [atom2Key, atom1Key], key1 = _b[0], key2 = _b[1];
+                            _f = atom1Key < atom2Key ? [atom1Key, atom2Key] : [atom2Key, atom1Key], key1 = _f[0], key2 = _f[1];
                             uniqueKey = "".concat(interactionType, "|").concat(key1, "|").concat(key2);
                             // 跳过重复的相互作用
                             if (addedInteractions.has(uniqueKey)) {
@@ -2904,10 +2919,14 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             posA = Vec3.create(featuresA.x[edge.indexA], featuresA.y[edge.indexA], featuresA.z[edge.indexA]);
                             posB = Vec3.create(featuresB.x[edge.indexB], featuresB.y[edge.indexB], featuresB.z[edge.indexB]);
                             distance = Vec3.distance(posA, posB);
+                            molIndexA = ((_b = unitElementToMolIndex.get(edge.unitA)) === null || _b === void 0 ? void 0 : _b.get(atomInfoA.elementIndex)) || -1;
+                            molIndexB = ((_c = unitElementToMolIndex.get(edge.unitB)) === null || _c === void 0 ? void 0 : _c.get(atomInfoB.elementIndex)) || -1;
                             exportedData.push({
                                 type: interactionType,
-                                atomA: atomInfoA,
-                                atomB: atomInfoB,
+                                atomA: tslib_1.__assign(tslib_1.__assign({}, atomInfoA), { molIndex: molIndexA // 添加：MOL/SDF文件中的原子序号（1-based）
+                                 }),
+                                atomB: tslib_1.__assign(tslib_1.__assign({}, atomInfoB), { molIndex: molIndexB // 添加：MOL/SDF文件中的原子序号（1-based）
+                                 }),
                                 distance: Math.round(distance * 100) / 100,
                                 // 额外的原始数据
                                 _raw: {
@@ -2923,7 +2942,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                         console.log("\u2705 Exported ".concat(exportedData.length, " unique interactions from ").concat(fullComponentRef).concat(filterMsg));
                         return [2 /*return*/, exportedData];
                     case 7:
-                        error_7 = _c.sent();
+                        error_7 = _g.sent();
                         console.error('❌ Failed to export interactions data:', error_7);
                         throw error_7;
                     case 8: return [2 /*return*/];
@@ -2958,7 +2977,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                 resId: 0,
                 resName: 'UNK',
                 atomName: 'unknown',
-                atomId: null
+                atomId: null,
+                elementIndex: -1
             };
         }
         try {
@@ -2969,17 +2989,17 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             var offset = features.offsets[featureIndex];
             if (offset === undefined) {
                 console.log('Feature offset undefined for index:', featureIndex);
-                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null };
+                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null, elementIndex: -1 };
             }
             var elementIndex = features.members[offset];
             if (elementIndex === undefined || elementIndex < 0) {
                 console.log('Element index undefined for offset:', offset);
-                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null };
+                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null, elementIndex: -1 };
             }
             // 检查索引是否在有效范围内
             if (elementIndex >= unit.elements.length) {
                 console.log('Element index out of range:', elementIndex, 'max:', unit.elements.length);
-                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null };
+                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null, elementIndex: -1 };
             }
             // 创建 Location 对象（必须传入 structure）
             var location_2 = structure_2.StructureElement.Location.create(structure, unit);
@@ -2997,7 +3017,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                 resId: resId,
                 resName: resName,
                 atomName: atomName,
-                atomId: atomId
+                atomId: atomId,
+                elementIndex: elementIndex // 添加：原子在unit.elements中的索引
             };
         }
         catch (error) {
@@ -3007,7 +3028,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                 resId: 0,
                 resName: 'UNK',
                 atomName: 'unknown',
-                atomId: null
+                atomId: null,
+                elementIndex: -1
             };
         }
     };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.77",
+  "version": "0.3.78",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {