drugflow-molstar 0.1.0 → 0.1.2

package/lib/helpers.d.ts

@@ -9,6 +9,7 @@ export declare type LoadParams = {
     assemblyId?: string;
     isHetView?: boolean;
     isBinary?: boolean;
+    pdb_string?: string;
 };
 export declare namespace PDBeVolumes {
     function mapParams(defaultParams: any, mapParams: any, ref?: string | number): any;

package/lib/index.js

@@ -18,7 +18,7 @@ var subscribe_events_1 = require("./subscribe-events");
 var pdbe_left_panel_1 = require("./ui/pdbe-left-panel");
 var superposition_1 = require("./superposition");
 var custom_events_1 = require("./custom-events");
-var assets_1 = require("Molstar/mol-util/assets");
+// import { Asset } from 'Molstar/mol-util/assets';
 var config_1 = require("Molstar/mol-plugin/config");
 var color_1 = require("Molstar/mol-util/color/color");
 var component_1 = require("Molstar/mol-plugin-state/manager/structure/component");
@@ -610,7 +610,7 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                             this.plugin.behaviors.layout.leftPanelTabName.next('none');
                             dataSource = this.getMoleculeSrcUrl();
                             if (dataSource) {
-                                this.load({ url: dataSource.url, format: dataSource.format, assemblyId: this.initParams.assemblyId, isBinary: dataSource.isBinary });
+                                this.load({ url: dataSource.url, format: dataSource.format, assemblyId: this.initParams.assemblyId, isBinary: dataSource.isBinary, pdb_string: dataSource.pdb_string });
                             }
                             // Binding to other PDB Component events
                             if (this.initParams.subscribeEvents) {
@@ -650,8 +650,13 @@ var PDBeMolstarPlugin = /** @class */ (function () {
         var url = "".concat(this.initParams.pdbeUrl, "model-server/v1/").concat(id, "/").concat(query).concat(sep, "encoding=").concat(this.initParams.encoding).concat(this.initParams.lowPrecisionCoords ? '&lowPrecisionCoords=1' : '');
         var isBinary = this.initParams.encoding === 'bcif' ? true : false;
         var format = 'mmcif';
+        var pdb_string = undefined;
+        console.log('drugflow_test');
         if (this.initParams.customData) {
-            if (!this.initParams.customData.url || !this.initParams.customData.format) {
+            if (!this.initParams.customData.url && !this.initParams.customData.pdb_string) {
+                throw new Error("Provide all custom data parameters");
+            }
+            if (!this.initParams.customData.format) {
                 throw new Error("Provide all custom data parameters");
             }
             url = this.initParams.customData.url;
@@ -662,12 +667,14 @@ var PDBeMolstarPlugin = /** @class */ (function () {
             if (supportedFormats.indexOf(format) === -1) {
                 throw new Error("".concat(format, " not supported."));
             }
+            pdb_string = this.initParams.customData.pdb_string;
             isBinary = this.initParams.customData.binary ? this.initParams.customData.binary : false;
         }
         return {
             url: url,
             format: format,
-            isBinary: isBinary
+            isBinary: isBinary,
+            pdb_string: pdb_string
         };
     };
     Object.defineProperty(PDBeMolstarPlugin.prototype, "state", {
@@ -765,48 +772,54 @@ var PDBeMolstarPlugin = /** @class */ (function () {
         });
     };
     PDBeMolstarPlugin.prototype.load = function (_a, fullLoad) {
-        var url = _a.url, _b = _a.format, format = _b === void 0 ? 'mmcif' : _b, _c = _a.isBinary, isBinary = _c === void 0 ? false : _c, _d = _a.assemblyId, assemblyId = _d === void 0 ? '' : _d;
+        var url = _a.url, _b = _a.format, format = _b === void 0 ? 'mmcif' : _b, _c = _a.isBinary, isBinary = _c === void 0 ? false : _c, _d = _a.assemblyId, assemblyId = _d === void 0 ? '' : _d, _e = _a.pdb_string, pdb_string = _e === void 0 ? '' : _e;
         if (fullLoad === void 0) { fullLoad = true; }
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var isHetView, downloadOptions, isBranchedView, data, trajectory, model, pivotIndex, pivot, asm, defaultMapParams, pdbeMapParams;
-            return tslib_1.__generator(this, function (_e) {
-                switch (_e.label) {
+            var isHetView, isBranchedView, data, trajectory, model, pivotIndex, pivot, asm, defaultMapParams, pdbeMapParams;
+            return tslib_1.__generator(this, function (_f) {
+                switch (_f.label) {
                     case 0:
                         if (fullLoad)
                             this.clear();
                         isHetView = this.initParams.ligandView ? true : false;
-                        downloadOptions = void 0;
                         isBranchedView = false;
                         if (this.initParams.ligandView && this.initParams.ligandView.label_comp_id_list) {
                             isBranchedView = true;
-                            downloadOptions = { body: JSON.stringify(this.initParams.ligandView.label_comp_id_list), headers: [['Content-type', 'application/json']] };
+                            // downloadOptions = { body: JSON.stringify(this.initParams.ligandView!.label_comp_id_list), headers: [['Content-type', 'application/json']]};
                         }
-                        return [4 /*yield*/, this.plugin.builders.data.download({ url: assets_1.Asset.Url(url, downloadOptions), isBinary: isBinary }, { state: { isGhost: true } })];
+                        data = null;
+                        if (!pdb_string) return [3 /*break*/, 2];
+                        return [4 /*yield*/, this.plugin.builders.data.rawData({ data: pdb_string }, { state: { isGhost: true } })];
                     case 1:
-                        data = _e.sent();
-                        return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(data, format)];
-                    case 2:
-                        trajectory = _e.sent();
-                        if (!!isHetView) return [3 /*break*/, 4];
+                        data = _f.sent();
+                        return [3 /*break*/, 4];
+                    case 2: return [4 /*yield*/, this.plugin.builders.data.download({ url: url }, { state: { isGhost: true } })];
+                    case 3:
+                        data = _f.sent();
+                        _f.label = 4;
+                    case 4: return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(data, format)];
+                    case 5:
+                        trajectory = _f.sent();
+                        if (!!isHetView) return [3 /*break*/, 7];
                         return [4 /*yield*/, this.plugin.builders.structure.hierarchy.applyPreset(trajectory, this.initParams.defaultPreset, {
                                 structure: assemblyId ? (assemblyId === 'preferred') ? void 0 : { name: 'assembly', params: { id: assemblyId } } : { name: 'model', params: {} },
                                 showUnitcell: false,
                                 representationPreset: 'auto'
                             })];
-                    case 3:
-                        _e.sent();
+                    case 6:
+                        _f.sent();
                         if (this.initParams.hideStructure || this.initParams.visualStyle) {
                             this.applyVisualParams();
                         }
-                        return [3 /*break*/, 7];
-                    case 4: return [4 /*yield*/, this.plugin.builders.structure.createModel(trajectory)];
-                    case 5:
-                        model = _e.sent();
+                        return [3 /*break*/, 10];
+                    case 7: return [4 /*yield*/, this.plugin.builders.structure.createModel(trajectory)];
+                    case 8:
+                        model = _f.sent();
                         return [4 /*yield*/, this.plugin.builders.structure.createStructure(model, { name: 'model', params: {} })];
-                    case 6:
-                        _e.sent();
-                        _e.label = 7;
-                    case 7:
+                    case 9:
+                        _f.sent();
+                        _f.label = 10;
+                    case 10:
                         // show selection if param is set
                         if (this.initParams.selection) {
                             this.visual.select(this.initParams.selection);
@@ -815,26 +828,26 @@ var PDBeMolstarPlugin = /** @class */ (function () {
                         pivot = this.plugin.managers.structure.hierarchy.selection.structures[pivotIndex];
                         if (pivot && pivot.cell.parent)
                             this.assemblyRef = pivot.cell.transform.ref;
-                        if (!this.initParams.loadMaps) return [3 /*break*/, 9];
+                        if (!this.initParams.loadMaps) return [3 /*break*/, 12];
                         if (this.assemblyRef === '')
                             return [2 /*return*/];
                         asm = this.state.select(this.assemblyRef)[0].obj;
                         defaultMapParams = transformers_1.InitVolumeStreaming.createDefaultParams(asm, this.plugin);
                         pdbeMapParams = helpers_1.PDBeVolumes.mapParams(defaultMapParams, this.initParams.mapSettings, '');
-                        if (!pdbeMapParams) return [3 /*break*/, 9];
+                        if (!pdbeMapParams) return [3 /*break*/, 12];
                         return [4 /*yield*/, this.plugin.runTask(this.state.applyAction(transformers_1.InitVolumeStreaming, pdbeMapParams, this.assemblyRef))];
-                    case 8:
-                        _e.sent();
+                    case 11:
+                        _f.sent();
                         if (pdbeMapParams.method !== 'em' && !this.initParams.ligandView)
                             helpers_1.PDBeVolumes.displayUsibilityMessage(this.plugin);
-                        _e.label = 9;
-                    case 9:
-                        if (!isHetView) return [3 /*break*/, 11];
+                        _f.label = 12;
+                    case 12:
+                        if (!isHetView) return [3 /*break*/, 14];
                         return [4 /*yield*/, this.createLigandStructure(isBranchedView)];
-                    case 10:
-                        _e.sent();
-                        _e.label = 11;
-                    case 11:
+                    case 13:
+                        _f.sent();
+                        _f.label = 14;
+                    case 14:
                         this.events.loadComplete.next(true);
                         return [2 /*return*/];
                 }

package/lib/spec.d.ts

@@ -37,6 +37,7 @@ export declare type InitParams = {
         url: string;
         format: string;
         binary: boolean;
+        pdb_string: string;
     };
     loadCartoonsOnly?: boolean;
     alphafoldView?: boolean;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "drugflow-molstar",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "description": "Molstar implementation for DrugFlow",
   "main": "index.js",
   "scripts": {