drugflow-molstar 0.4.5 → 0.4.7

package/lib/drugflow-molstar-component-build-0.4.6.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.4.6.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.4.6.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-0.4.7.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.4.7.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

@@ -51,7 +51,8 @@ class DrugflowMolstarPlugin {
         // 隐藏状态追踪器
         this.hiddenState = {
             chains: new Set(), // 隐藏的链ID
-            ligands: new Set() // 隐藏的配体（格式: "chainId:resId" 或 "chainId:resName"）
+            ligands: new Set(), // 隐藏的配体（格式: "chainId:resId" 或 "chainId:resName"）
+            residues: new Set() // 隐藏的残基（格式: "chainId:resId"）
         };
         this.canvas = {
             toggleControls: (isVisible) => {
@@ -324,7 +325,7 @@ class DrugflowMolstarPlugin {
                 // 先清除所有透明度
                 await (0, structure_transparency_1.clearStructureTransparency)(this.plugin, components);
                 // 如果没有需要隐藏的，直接返回
-                if (this.hiddenState.chains.size === 0 && this.hiddenState.ligands.size === 0) {
+                if (this.hiddenState.chains.size === 0 && this.hiddenState.ligands.size === 0 && this.hiddenState.residues.size === 0) {
                     return;
                 }
                 // 重新应用所有隐藏的链
@@ -374,6 +375,35 @@ class DrugflowMolstarPlugin {
                         }));
                     });
                 }
+                // 重新应用所有隐藏的残基
+                // 按链分组残基，批量处理以提高性能
+                const residuesByChain = new Map();
+                for (const residueKey of this.hiddenState.residues) {
+                    const [chainId, resIdStr] = residueKey.split(':');
+                    const resId = Number(resIdStr);
+                    if (!residuesByChain.has(chainId)) {
+                        residuesByChain.set(chainId, []);
+                    }
+                    residuesByChain.get(chainId).push(resId);
+                }
+                for (const [chainId, residueIds] of residuesByChain) {
+                    await (0, structure_transparency_1.setStructureTransparency)(this.plugin, components, 1, async (structure) => {
+                        const residueQuery = (0, structure_selection_query_1.StructureSelectionQuery)(`Residues_${chainId}`, builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                            'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId]),
+                            'residue-test': builder_1.MolScriptBuilder.core.set.has([
+                                builder_1.MolScriptBuilder.set(...residueIds),
+                                builder_1.MolScriptBuilder.ammp('auth_seq_id')
+                            ])
+                        }), {
+                            description: `Residues in chain ${chainId}`,
+                            category: structure_selection_query_1.StructureSelectionCategory.Manipulate
+                        });
+                        return this.plugin.runTask(mol_task_1.Task.create('Select Residues', async (runtime) => {
+                            const selection = await residueQuery.getSelection(this.plugin, runtime, structure);
+                            return structure_1.StructureSelection.toLociWithSourceUnits(selection);
+                        }));
+                    });
+                }
             },
             /**
              * 使用透明度隐藏指定的链
@@ -397,6 +427,56 @@ class DrugflowMolstarPlugin {
                 await this.visual._applyHiddenState();
                 console.log(`✅ Chain ${chainId} shown`);
             },
+            /**
+             * 使用透明度隐藏指定链中的残基
+             * @param chainId 链ID，例如 'A', 'B'
+             * @param residueIds 残基序号数组，例如 [10, 15, 20] 或范围 { start: 10, end: 20 }
+             */
+            hideResidues: async (chainId, residueIds) => {
+                // 处理范围格式
+                const ids = Array.isArray(residueIds)
+                    ? residueIds
+                    : Array.from({ length: residueIds.end - residueIds.start + 1 }, (_, i) => residueIds.start + i);
+                // 添加到隐藏状态
+                for (const resId of ids) {
+                    this.hiddenState.residues.add(`${chainId}:${resId}`);
+                }
+                // 重新应用所有隐藏状态
+                await this.visual._applyHiddenState();
+                console.log(`✅ Residues ${ids.join(', ')} in chain ${chainId} hidden`);
+            },
+            /**
+             * 清除指定链中残基的透明度来显示
+             * @param chainId 链ID，例如 'A', 'B'
+             * @param residueIds 残基序号数组，例如 [10, 15, 20] 或范围 { start: 10, end: 20 }
+             */
+            showResidues: async (chainId, residueIds) => {
+                // 处理范围格式
+                const ids = Array.isArray(residueIds)
+                    ? residueIds
+                    : Array.from({ length: residueIds.end - residueIds.start + 1 }, (_, i) => residueIds.start + i);
+                // 从隐藏状态中移除
+                for (const resId of ids) {
+                    this.hiddenState.residues.delete(`${chainId}:${resId}`);
+                }
+                // 重新应用所有隐藏状态
+                await this.visual._applyHiddenState();
+                console.log(`✅ Residues ${ids.join(', ')} in chain ${chainId} shown`);
+            },
+            /**
+             * 切换残基的显示/隐藏状态
+             * @param chainId 链ID
+             * @param residueIds 残基序号数组或范围
+             * @param visible true显示，false隐藏
+             */
+            toggleResidues: async (chainId, residueIds, visible) => {
+                if (visible) {
+                    await this.visual.showResidues(chainId, residueIds);
+                }
+                else {
+                    await this.visual.hideResidues(chainId, residueIds);
+                }
+            },
             /**
              * 使用透明度隐藏指定的配体
              * @param chainId 链ID
@@ -482,6 +562,7 @@ class DrugflowMolstarPlugin {
                 // 清空隐藏状态
                 this.hiddenState.chains.clear();
                 this.hiddenState.ligands.clear();
+                this.hiddenState.residues.clear();
                 // 清除所有透明度
                 const structures = this.plugin.managers.structure.hierarchy.current.structures;
                 const components = [];
@@ -497,9 +578,19 @@ class DrugflowMolstarPlugin {
              * 获取当前隐藏状态
              */
             getHiddenState: () => {
+                // 解析残基状态，按链分组
+                const residuesByChain = {};
+                for (const residueKey of this.hiddenState.residues) {
+                    const [chainId, resIdStr] = residueKey.split(':');
+                    if (!residuesByChain[chainId]) {
+                        residuesByChain[chainId] = [];
+                    }
+                    residuesByChain[chainId].push(Number(resIdStr));
+                }
                 return {
                     chains: Array.from(this.hiddenState.chains),
-                    ligands: Array.from(this.hiddenState.ligands)
+                    ligands: Array.from(this.hiddenState.ligands),
+                    residues: residuesByChain
                 };
             }
         };
@@ -901,6 +992,16 @@ class DrugflowMolstarPlugin {
         });
         if (surroundingsRef)
             componentRefs.push(surroundingsRef);
+        // 5. 创建背景cartoon，如果ligand_id == ‘0’
+        if (ligandId === '0') {
+            const ref = await this.createComponent({
+                type: 'polymer',
+                structureId,
+                componentRef: 'Ligand_background'
+            });
+            if (ref)
+                componentRefs.push(ref);
+        }
         return componentRefs;
     }
     /**

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.4.5",
+  "version": "0.4.7",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {