drugflow-molstar 0.3.76 → 0.3.77

package/lib/drugflow-molstar-component-build-0.3.77.js

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

@@ -3068,8 +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) {
@@ -3089,15 +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];
@@ -3120,7 +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];
@@ -3145,19 +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
@@ -3170,9 +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": "0.3.76",
+  "version": "0.3.77",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {

package/build/drugflow-molstar-0.3.76.css

@@ -1 +0,0 @@
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)}.msp-plugin 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