drugflow-molstar 0.3.75 → 0.3.77

package/lib/drugflow-molstar-component-build-0.3.76.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.76.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.76.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-0.3.77.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.3.77.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

@@ -1330,10 +1330,15 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                     radius: radius,
                                     'as-whole-residues': true
                                 }),
-                                by: ligandQuery.expression
+                                by: builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                                    'residue-test': builder_1.MolScriptBuilder.core.rel.eq([
+                                        builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_comp_id(),
+                                        'HOH'
+                                    ])
+                                })
                             })
                         ]), {
-                            description: "Surroundings within ".concat(radius, "\u00C5"),
+                            description: "Surroundings within ".concat(radius, "\u00C5 (excluding water)"),
                             category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
                             referencesCurrent: true
                         });
@@ -2532,12 +2537,13 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      * ```
      */
     DrugflowMolstarPlugin.prototype.add_interactions_repr = function (options) {
+        var _b;
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            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) {
+            var componentRef, reprRef, _c, structureId, interactionTypes, _d, interChainOnly, _e, visible, _f, params, finalReprRef, structure, reprParams, tree;
+            return tslib_1.__generator(this, function (_g) {
+                switch (_g.label) {
                     case 0:
-                        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;
+                        componentRef = options.componentRef, reprRef = options.reprRef, _c = options.structureId, structureId = _c === void 0 ? '0' : _c, interactionTypes = options.interactionTypes, _d = options.interChainOnly, interChainOnly = _d === void 0 ? false : _d, _e = options.visible, visible = _e === void 0 ? true : _e, _f = options.params, params = _f === void 0 ? {} : _f;
                         finalReprRef = reprRef || "".concat(componentRef, "_interactions_").concat(Date.now());
                         structure = this.getObj('Structure_' + structureId);
                         if (!structure) {
@@ -2556,6 +2562,11 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                             // 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'];
                         }
+                        // includeParent 参数：false = 只计算组件内的相互作用，true = 包含父结构
+                        // 默认为 false，这样只显示组件范围内的相互作用
+                        if (reprParams.typeParams) {
+                            reprParams.typeParams.includeParent = (_b = reprParams.typeParams.includeParent) !== null && _b !== void 0 ? _b : false;
+                        }
                         tree = this.visual_tree(structure, componentRef, finalReprRef, reprParams);
                         if (!tree) {
                             console.error('Failed to build visual tree for interactions');
@@ -2566,7 +2577,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 tree: tree
                             })];
                     case 1:
-                        _f.sent();
+                        _g.sent();
                         // 控制可见性
                         if (!visible) {
                             this.set_visibility(finalReprRef);
@@ -2765,49 +2776,59 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
      *
      * @param componentRef - 组件引用（如 'Ligand_plus_0'）
      * @param structureId - 结构ID（可选，默认'0'）
+     * @param filterResId - 可选的残基ID，如果提供则只返回与该残基相关的相互作用
      * @returns Interaction 数据数组
      *
      * @example
      * ```javascript
-     * // 导出配体周围的相互作用数据
+     * // 导出配体周围的所有相互作用数据
      * const interactions = await viewer.exportInteractionsData('Ligand_plus_0');
-     * console.log(interactions);
+     *
+     * // 只导出与残基 1102 相关的相互作用
+     * const ligandInteractions = await viewer.exportInteractionsData('Ligand_plus_0', '0', 1102);
+     * console.log(ligandInteractions);
      * // [
      * //   {
      * //     type: 'hydrogen-bond',
-     * //     atomA: { chainId: 'A', resId: 123, resName: 'ASP', atomName: 'OD1' },
-     * //     atomB: { chainId: 'B', resId: 456, resName: 'LIG', atomName: 'O1' },
-     * //     distance: 2.8
+     * //     atomA: { chainId: 'A', resId: 1102, resName: 'KY9', atomName: 'O38', atomId: 38 },
+     * //     atomB: { chainId: 'A', resId: 745, resName: 'LYS', atomName: 'NZ', atomId: null },
+     * //     distance: 2.87
      * //   },
      * //   ...
      * // ]
      * ```
      */
-    DrugflowMolstarPlugin.prototype.exportInteractionsData = function (componentRef, structureId) {
+    DrugflowMolstarPlugin.prototype.exportInteractionsData = function (componentRef, structureId, filterResId) {
         if (structureId === void 0) { structureId = '0'; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var InteractionsProvider, interactionTypeLabel, Vec3, componentCell, componentStructure_1, interactionsProperty_1, interactions, exportedData, contacts, unitsFeatures, i, edge, unitA, unitB, featuresA, featuresB, atomInfoA, atomInfoB, posA, posB, distance, error_7;
+            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 _this = this;
-            return tslib_1.__generator(this, function (_b) {
-                switch (_b.label) {
+            return tslib_1.__generator(this, function (_c) {
+                switch (_c.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 = (_b.sent()).InteractionsProvider;
+                        InteractionsProvider = (_c.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 = (_b.sent()).interactionTypeLabel;
+                        interactionTypeLabel = (_c.sent()).interactionTypeLabel;
                         return [4 /*yield*/, Promise.resolve().then(function () { return tslib_1.__importStar(require('molstar/lib/mol-math/linear-algebra')); })];
                     case 3:
-                        Vec3 = (_b.sent()).Vec3;
-                        _b.label = 4;
+                        Vec3 = (_c.sent()).Vec3;
+                        _c.label = 4;
                     case 4:
-                        _b.trys.push([4, 7, , 8]);
-                        componentCell = this.plugin.state.data.select(componentRef)[0];
+                        _c.trys.push([4, 7, , 8]);
+                        fullComponentRef = componentRef.includes('_') ? componentRef : "".concat(componentRef, "_").concat(structureId);
+                        componentCell = this.plugin.state.data.select(fullComponentRef)[0];
                         if (!componentCell) {
-                            console.log("Component ".concat(componentRef, " not found"));
-                            return [2 /*return*/, []];
+                            console.log("Component ".concat(fullComponentRef, " not found, trying original ref ").concat(componentRef));
+                            fallbackCell = this.plugin.state.data.select(componentRef)[0];
+                            if (!fallbackCell) {
+                                console.log("Component ".concat(componentRef, " not found either"));
+                                return [2 /*return*/, []];
+                            }
                         }
-                        componentStructure_1 = componentCell.obj.data;
+                        actualCell = this.plugin.state.data.select(fullComponentRef)[0] || this.plugin.state.data.select(componentRef)[0];
+                        componentStructure_1 = actualCell.obj.data;
                         if (!componentStructure_1) {
                             console.log("Structure data not found for ".concat(componentRef));
                             return [2 /*return*/, []];
@@ -2840,8 +2861,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 });
                             }); }))];
                     case 5:
-                        _b.sent();
-                        _b.label = 6;
+                        _c.sent();
+                        _c.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.');
@@ -2849,6 +2870,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                         }
                         interactions = interactionsProperty_1.value;
                         exportedData = [];
+                        addedInteractions = new Set();
                         contacts = interactions.contacts;
                         unitsFeatures = interactions.unitsFeatures;
                         for (i = 0; i < contacts.edgeCount; i++) {
@@ -2863,11 +2885,27 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 continue;
                             atomInfoA = this.getAtomInfoFromFeature(componentStructure_1, unitA, featuresA, edge.indexA);
                             atomInfoB = this.getAtomInfoFromFeature(componentStructure_1, unitB, featuresB, edge.indexB);
+                            // 如果提供了 filterResId，则只保留与该残基相关的相互作用
+                            if (filterResId !== undefined) {
+                                if (atomInfoA.resId !== filterResId && atomInfoB.resId !== filterResId) {
+                                    continue; // 两端都不是目标残基，跳过
+                                }
+                            }
+                            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];
+                            uniqueKey = "".concat(interactionType, "|").concat(key1, "|").concat(key2);
+                            // 跳过重复的相互作用
+                            if (addedInteractions.has(uniqueKey)) {
+                                continue;
+                            }
+                            addedInteractions.add(uniqueKey);
                             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);
                             exportedData.push({
-                                type: interactionTypeLabel(edge.props.type),
+                                type: interactionType,
                                 atomA: atomInfoA,
                                 atomB: atomInfoB,
                                 distance: Math.round(distance * 100) / 100,
@@ -2881,10 +2919,11 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                 }
                             });
                         }
-                        console.log("\u2705 Exported ".concat(exportedData.length, " interactions from ").concat(componentRef));
+                        filterMsg = filterResId !== undefined ? " (filtered by resId=".concat(filterResId, ")") : '';
+                        console.log("\u2705 Exported ".concat(exportedData.length, " unique interactions from ").concat(fullComponentRef).concat(filterMsg));
                         return [2 /*return*/, exportedData];
                     case 7:
-                        error_7 = _b.sent();
+                        error_7 = _c.sent();
                         console.error('❌ Failed to export interactions data:', error_7);
                         throw error_7;
                     case 8: return [2 /*return*/];
@@ -2892,6 +2931,22 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             });
         });
     };
+    /**
+     * 从原子名称中提取数字作为 atomId
+     * @param atomName - 原子名称，如 "O38", "NZ", "CA"
+     * @returns 提取的数字，如果没有数字则返回 null
+     * @private
+     */
+    DrugflowMolstarPlugin.prototype.extractAtomIdFromName = function (atomName) {
+        if (!atomName)
+            return null;
+        // 提取原子名称中的所有数字
+        var match = atomName.match(/\d+/);
+        if (match) {
+            return parseInt(match[0], 10);
+        }
+        return null;
+    };
     /**
      * 辅助方法：从 structure、unit、features 和 feature index 获取原子信息
      * @private
@@ -2902,32 +2957,41 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                 chainId: 'unknown',
                 resId: 0,
                 resName: 'UNK',
-                atomName: 'unknown'
+                atomName: 'unknown',
+                atomId: null
             };
         }
         try {
-            // 根据 Molstar 源码 (features.js)：
+            // 根据 Molstar 源码 (features.js 和 interactions-intra-unit-cylinder.js)：
             // - offsets[featureIndex] 指向该 feature 的第一个成员在 members 数组中的位置
-            // - members[offset] 是原子在 unit.elements 中的索引
+            // - members[offset] 是原子在 unit.elements 中的索引（注意：是索引，不是元素ID）
+            // - 需要通过 unit.elements[index] 来获取实际的元素ID
             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' };
+                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null };
             }
             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' };
+                return { chainId: 'unknown', resId: 0, resName: 'UNK', atomName: 'unknown', atomId: null };
+            }
+            // 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 };
             }
             // 创建 Location 对象（必须传入 structure）
             var location_2 = structure_2.StructureElement.Location.create(structure, unit);
-            location_2.element = elementIndex;
+            // 关键修复：使用 unit.elements[elementIndex] 获取实际的元素ID
+            location_2.element = unit.elements[elementIndex];
             // 使用 StructureProperties 获取信息
             var chainId = structure_1.StructureProperties.chain.auth_asym_id(location_2);
             var resId = structure_1.StructureProperties.residue.auth_seq_id(location_2);
             var resName = structure_1.StructureProperties.atom.label_comp_id(location_2);
             var atomName = structure_1.StructureProperties.atom.auth_atom_id(location_2);
-            var atomId = structure_1.StructureProperties.atom.id(location_2);
+            // 从 atomName 中提取数字作为 atomId（如 "O38" -> 38）
+            var atomId = this.extractAtomIdFromName(atomName);
             return {
                 chainId: chainId,
                 resId: resId,
@@ -2942,7 +3006,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                 chainId: 'unknown',
                 resId: 0,
                 resName: 'UNK',
-                atomName: 'unknown'
+                atomName: 'unknown',
+                atomId: null
             };
         }
     };
@@ -3003,8 +3068,8 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
     DrugflowMolstarPlugin.prototype.exportLigandAsMOL = function (ligandComponentRef, structureId) {
         if (structureId === void 0) { structureId = '0'; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var componentCell, structure, molString_1, atomCount, atomLines, bondLines, atomIndexMap, addedBonds, _b, _c, unit, elements, conformation, atoms, i, eI, pos, x, y, z, element, xStr, yStr, zStr, elemStr, atomLine, bondProps, offset, b, edgeProps, unitBondCount, i, eI, molIndexA, bondStart, bondEnd, bondIdx, elementIndexB, atomB, molIndexB, minIdx, maxIdx, bondKey, bondOrder, bondStereo, bondLine;
-            return tslib_1.__generator(this, function (_d) {
+            var componentCell, structure, molString_1, atomCount, atomLines, bondLines, atomIndexMap, addedBonds, bondStats, aromaticBondSet, _b, _c, unit, rings, _d, _e, ringIndex, ring, _f, offset, b, ringIdx, indexA, bondStart, bondEnd, bondIdx, indexB, isInRing, k, kl, key, _g, _h, unit, elements, conformation, atoms, i, eI, pos, x, y, z, element, xStr, yStr, zStr, elemStr, atomLine, bondProps, offset, b, edgeProps, i, eI, molIndexA, bondStart, bondEnd, bondIdx, elementIndexB, atomB, molIndexB, minIdx, maxIdx, bondKey, bondOrder, bondType, bondFlags, isAromatic, atomIndexKey, wasInSet, bondStereo, bondLine;
+            return tslib_1.__generator(this, function (_k) {
                 try {
                     componentCell = this.plugin.state.data.select(ligandComponentRef)[0];
                     if (!componentCell) {
@@ -3024,15 +3089,55 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                     bondLines = [];
                     atomIndexMap = new Map();
                     addedBonds = new Set();
-                    console.log("\uD83D\uDD0D Structure has ".concat(structure.units.length, " units"));
-                    // 遍历结构获取原子信息
+                    bondStats = {
+                        single: 0,
+                        double: 0,
+                        triple: 0,
+                        aromatic: 0,
+                        other: 0
+                    };
+                    aromaticBondSet = new Set();
                     for (_b = 0, _c = structure.units; _b < _c.length; _b++) {
                         unit = _c[_b];
+                        if (unit.kind !== 0)
+                            continue;
+                        rings = unit.rings;
+                        if (rings && rings.aromaticRings && rings.aromaticRings.length > 0) {
+                            // 遍历每个芳香环
+                            for (_d = 0, _e = rings.aromaticRings; _d < _e.length; _d++) {
+                                ringIndex = _e[_d];
+                                ring = rings.all[ringIndex];
+                                _f = unit.bonds, offset = _f.offset, b = _f.b;
+                                // 对环内每个原子，检查它的键是否连接到环内其他原子
+                                for (ringIdx = 0; ringIdx < ring.length; ringIdx++) {
+                                    indexA = ring[ringIdx];
+                                    bondStart = offset[indexA];
+                                    bondEnd = offset[indexA + 1];
+                                    for (bondIdx = bondStart; bondIdx < bondEnd; bondIdx++) {
+                                        indexB = b[bondIdx];
+                                        isInRing = false;
+                                        for (k = 0, kl = ring.length; k < kl; k++) {
+                                            if (ring[k] === indexB) {
+                                                isInRing = true;
+                                                break;
+                                            }
+                                        }
+                                        if (isInRing) {
+                                            key = indexA < indexB ? "".concat(indexA, "-").concat(indexB) : "".concat(indexB, "-").concat(indexA);
+                                            aromaticBondSet.add(key);
+                                        }
+                                    }
+                                }
+                            }
+                        }
+                    }
+                    // 遍历结构获取原子信息
+                    for (_g = 0, _h = structure.units; _g < _h.length; _g++) {
+                        unit = _h[_g];
                         if (unit.kind !== 0)
                             continue; // 只处理原子单元
                         elements = unit.elements, conformation = unit.conformation;
                         atoms = unit.model.atomicHierarchy.atoms;
-                        console.log("  \uD83D\uDCE6 Unit has ".concat(elements.length, " atoms"));
                         // 收集原子
                         for (i = 0; i < elements.length; i++) {
                             eI = elements[i];
@@ -3055,7 +3160,6 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                         if (unit.bonds) {
                             bondProps = unit.bonds;
                             offset = bondProps.offset, b = bondProps.b, edgeProps = bondProps.edgeProps;
-                            unitBondCount = 0;
                             // 遍历所有原子的键
                             for (i = 0; i < elements.length; i++) {
                                 eI = elements[i];
@@ -3080,19 +3184,50 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                                     }
                                     addedBonds.add(bondKey);
                                     bondOrder = 1;
-                                    if (edgeProps && edgeProps.order) {
-                                        bondOrder = edgeProps.order[bondIdx] || 1;
+                                    bondType = 1;
+                                    bondFlags = (edgeProps && edgeProps.flags) ? edgeProps.flags[bondIdx] : 0;
+                                    isAromatic = (bondFlags & 16) !== 0;
+                                    // 方法2：如果方法1失败，从环分析结果检查
+                                    // 注意：需要使用索引而不是原子ID
+                                    if (!isAromatic) {
+                                        atomIndexKey = i < elementIndexB ? "".concat(i, "-").concat(elementIndexB) : "".concat(elementIndexB, "-").concat(i);
+                                        wasInSet = aromaticBondSet.has(atomIndexKey);
+                                        if (wasInSet) {
+                                            isAromatic = true;
+                                            // 从集合中移除，用于追踪哪些键被使用了
+                                            aromaticBondSet.delete(atomIndexKey);
+                                        }
+                                    }
+                                    if (isAromatic) {
+                                        // 芳香键在MOL格式中用 type=4 表示
+                                        bondType = 4;
+                                        bondOrder = 1; // 芳香键的order通常记为1，但type表明它是芳香的
+                                        bondStats.aromatic++;
+                                    }
+                                    else {
+                                        // 非芳香键：从 edgeProps.order 获取键级
+                                        if (edgeProps && edgeProps.order) {
+                                            bondOrder = edgeProps.order[bondIdx] || 1;
+                                        }
+                                        bondType = bondOrder; // 单键=1, 双键=2, 三键=3
+                                        // 更新统计
+                                        if (bondOrder === 1)
+                                            bondStats.single++;
+                                        else if (bondOrder === 2)
+                                            bondStats.double++;
+                                        else if (bondOrder === 3)
+                                            bondStats.triple++;
+                                        else
+                                            bondStats.other++;
                                     }
                                     bondStereo = 0;
-                                    bondLine = "".concat(minIdx.toString().padStart(3)).concat(maxIdx.toString().padStart(3)).concat(bondOrder.toString().padStart(3)).concat(bondStereo.toString().padStart(3));
+                                    bondLine = "".concat(minIdx.toString().padStart(3)).concat(maxIdx.toString().padStart(3)).concat(bondType.toString().padStart(3)).concat(bondStereo.toString().padStart(3));
                                     bondLines.push(bondLine);
-                                    unitBondCount++;
                                 }
                             }
-                            console.log("  \uD83D\uDD17 Unit exported ".concat(unitBondCount, " bonds"));
                         }
                         else {
-                            console.log("  \u26A0\uFE0F Unit has no bond information");
+                            console.warn('⚠️ Unit has no bond information');
                         }
                     }
                     // Counts line: atoms(3) bonds(3) ... V2000
@@ -3105,9 +3240,12 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                     bondLines.forEach(function (line) {
                         molString_1 += line + '\n';
                     });
+                    // 检查是否有芳香键被标记但未导出（可能的问题）
+                    if (aromaticBondSet.size > 0) {
+                        console.warn("\u26A0\uFE0F ".concat(aromaticBondSet.size, " aromatic bonds detected in rings but not exported (this may be expected for some ring topologies)"));
+                    }
                     molString_1 += 'M  END\n';
                     molString_1 += '$$$$\n';
-                    console.log("\u2705 Exported ligand as MOL: ".concat(atomCount, " atoms, ").concat(bondLines.length, " bonds"));
                     return [2 /*return*/, molString_1];
                 }
                 catch (error) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.75",
+  "version": "0.3.77",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {