drugflow-molstar 0.3.44 → 0.3.47

package/build/drugflow-molstar-plugin-0.3.47.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-0.3.46.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.3.46.js.LICENSE.txt */
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package/lib/drugflow-molstar-component-build-0.3.46.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-0.3.47.js

@@ -0,0 +1,2 @@
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package/lib/drugflow-molstar-component-build-0.3.47.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/helpers.d.ts

@@ -15,6 +15,7 @@ export declare type LoadParams = {
     render_id?: string;
     ligand_name?: string;
     modelIndex?: number;
+    ligand_site?: string;
 };
 export declare namespace PDBeVolumes {
     function mapParams(defaultParams: any, mapParams: any, ref?: string | number): any;

package/lib/index.js

@@ -410,7 +410,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                         case 11:
                             _b.sent();
                             this.selected_info.all = { "polymer": [], "ligand": [], "other": [] };
-                            return [4 /*yield*/, this.create_structure_and_component(undefined, 'default', '0', need_recreate.polymer, need_recreate.ligand, need_recreate.water, false)];
+                            return [4 /*yield*/, this.create_structure_and_component(undefined, 'default', '0', need_recreate.polymer, need_recreate.ligand, need_recreate.water, false, '', '')];
                         case 12:
                             update_tree = _b.sent();
                             return [4 /*yield*/, this.applyState(update_tree)];
@@ -468,7 +468,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
                         case 10:
                             _b.sent();
                             this.selected_info.prev = { "polymer": [], "ligand": [], "other": [] };
-                            return [4 /*yield*/, this.create_structure_and_component(undefined, 'default', '0', need_recreate.polymer, need_recreate.ligand, need_recreate.water, false)];
+                            return [4 /*yield*/, this.create_structure_and_component(undefined, 'default', '0', need_recreate.polymer, need_recreate.ligand, need_recreate.water, false, '', '')];
                         case 11:
                             update_tree = _b.sent();
                             return [4 /*yield*/, this.applyState(update_tree)];
@@ -745,7 +745,7 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
-                        update_tree = this.create_structure_and_component(undefined, 'default', '0', recreate_params.polymer, recreate_params.ligand, recreate_params.water, false);
+                        update_tree = this.create_structure_and_component(undefined, 'default', '0', recreate_params.polymer, recreate_params.ligand, recreate_params.water, false, '', '');
                         return [4 /*yield*/, this.applyState(update_tree)];
                     case 1:
                         _b.sent();
@@ -917,13 +917,18 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             });
         });
     };
-    DrugflowMolstarPlugin.prototype.create_structure_and_component = function (model, type, ligand_id, add_polymer, add_ligand, add_water, no_structure, ligand_name) {
+    DrugflowMolstarPlugin.prototype.create_structure_and_component = function (model, type, ligand_id, add_polymer, add_ligand, add_water, no_structure, ligand_name, ligand_site) {
         if (add_polymer === void 0) { add_polymer = true; }
         if (add_ligand === void 0) { add_ligand = true; }
         if (add_water === void 0) { add_water = true; }
         if (no_structure === void 0) { no_structure = true; }
         if (ligand_name === void 0) { ligand_name = ''; }
+        if (ligand_site === void 0) { ligand_site = ''; }
         var s;
+        var ligand_chain = 'A';
+        if (ligand_site) {
+            ligand_chain = ligand_site.split(':')[0];
+        }
         if (no_structure) {
             s = this.plugin.state.data.build().to(model).apply(transforms_1.StateTransforms.Model.StructureFromModel, { type: { name: 'model', params: {} } }, { ref: 'Structure_' + ligand_id });
         }
@@ -961,46 +966,73 @@ var DrugflowMolstarPlugin = /** @class */ (function () {
             return s;
         }
         else if (type === 'ligand_view') {
-            this.create_ligand_view(s, ligand_id, true, 'A', 0, ligand_name);
+            this.create_ligand_view(s, ligand_id, true, ligand_chain, 0, ligand_name);
+            return s;
+        }
+        else if (type === 'peptide') {
+            // Polymer - 除了短肽链（p）以外的蛋白链
+            var polymer_query = (0, structure_selection_query_1.StructureSelectionQuery)('Polymer', builder_1.MolScriptBuilder.struct.modifier.union([
+                builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                    'entity-test': builder_1.MolScriptBuilder.core.logic.and([
+                        builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
+                    ])
+                })
+            ]), {
+                description: 'Polymer (excluding peptide-like)',
+                category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                referencesCurrent: true
+            });
+            s.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'expression', params: polymer_query.expression } }, { ref: 'Polymer' });
+            // Polymer p - 短肽链
+            var peptide_query = (0, structure_selection_query_1.StructureSelectionQuery)('Polymer p', builder_1.MolScriptBuilder.struct.modifier.union([
+                builder_1.MolScriptBuilder.struct.generator.atomGroups({
+                    'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'p'])
+                })
+            ]), {
+                description: 'Peptide-like polymer',
+                category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
+                referencesCurrent: true
+            });
+            s.apply(transforms_1.StateTransforms.Model.StructureComponent, { type: { name: 'expression', params: peptide_query.expression } }, { ref: 'Polymer_p' });
             return s;
         }
         return s;
     };
     DrugflowMolstarPlugin.prototype.load_tree = function (_b, fullLoad) {
-        var url = _b.url, _c = _b.format, format = _c === void 0 ? 'mmcif' : _c, _d = _b.isBinary, isBinary = _d === void 0 ? false : _d, _e = _b.assemblyId, assemblyId = _e === void 0 ? '' : _e, _f = _b.pdb_string, pdb_string = _f === void 0 ? '' : _f, _g = _b.if_render, if_render = _g === void 0 ? true : _g, _h = _b.render_type, render_type = _h === void 0 ? 'default' : _h, _k = _b.render_id, render_id = _k === void 0 ? '0' : _k, _l = _b.ligand_name, ligand_name = _l === void 0 ? '' : _l, _m = _b.modelIndex, modelIndex = _m === void 0 ? 0 : _m;
+        var url = _b.url, _c = _b.format, format = _c === void 0 ? 'mmcif' : _c, _d = _b.isBinary, isBinary = _d === void 0 ? false : _d, _e = _b.assemblyId, assemblyId = _e === void 0 ? '' : _e, _f = _b.pdb_string, pdb_string = _f === void 0 ? '' : _f, _g = _b.if_render, if_render = _g === void 0 ? true : _g, _h = _b.render_type, render_type = _h === void 0 ? 'default' : _h, _k = _b.render_id, render_id = _k === void 0 ? '0' : _k, _l = _b.ligand_name, ligand_name = _l === void 0 ? '' : _l, _m = _b.modelIndex, modelIndex = _m === void 0 ? 0 : _m, _o = _b.ligand_site, ligand_site = _o === void 0 ? '' : _o;
         if (fullLoad === void 0) { fullLoad = true; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, data, trajectory, model, updata_tree, pivotIndex, pivot;
-            return tslib_1.__generator(this, function (_o) {
-                switch (_o.label) {
+            return tslib_1.__generator(this, function (_p) {
+                switch (_p.label) {
                     case 0:
                         state = this.plugin.state.data;
                         if (!fullLoad) return [3 /*break*/, 2];
                         return [4 /*yield*/, commands_1.PluginCommands.State.RemoveObject(this.plugin, { state: state, ref: state.tree.root.ref })];
                     case 1:
-                        _o.sent();
-                        _o.label = 2;
+                        _p.sent();
+                        _p.label = 2;
                     case 2:
                         data = null;
                         if (!pdb_string) return [3 /*break*/, 4];
                         return [4 /*yield*/, this.plugin.builders.data.rawData({ data: pdb_string }, { state: { isGhost: true } })];
                     case 3:
-                        data = _o.sent();
+                        data = _p.sent();
                         return [3 /*break*/, 6];
                     case 4: return [4 /*yield*/, this.plugin.builders.data.download({ url: url, isBinary: isBinary }, { state: { isGhost: true } })];
                     case 5:
-                        data = _o.sent();
-                        _o.label = 6;
+                        data = _p.sent();
+                        _p.label = 6;
                     case 6: return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(data, format)];
                     case 7:
-                        trajectory = _o.sent();
+                        trajectory = _p.sent();
                         return [4 /*yield*/, this.plugin.builders.structure.createModel(trajectory, { modelIndex: modelIndex })];
                     case 8:
-                        model = _o.sent();
-                        updata_tree = this.create_structure_and_component(model, render_type, render_id, true, true, true, true, ligand_name);
+                        model = _p.sent();
+                        updata_tree = this.create_structure_and_component(model, render_type, render_id, true, true, true, true, ligand_name, ligand_site);
                         return [4 /*yield*/, this.applyState(updata_tree)];
                     case 9:
-                        _o.sent();
+                        _p.sent();
                         pivotIndex = this.plugin.managers.structure.hierarchy.selection.structures.length - 1;
                         pivot = this.plugin.managers.structure.hierarchy.selection.structures[pivotIndex];
                         if (pivot && pivot.cell.parent) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.3.44",
+  "version": "0.3.47",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {