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BasicWrapper PDB support, PDB parser fix

David Sehnal 6 years ago
parent
1d22600c22
commit
79ba2fb2bc
3 changed files with 55 additions and 21 deletions
Split View Show Diff Stats
  1. 8 4
      src/apps/basic-wrapper/index.html
  2. 41 15
      src/apps/basic-wrapper/index.ts
  3. 6 2
      src/mol-model-formats/structure/pdb/assembly.ts

+ 8 - 4
src/apps/basic-wrapper/index.html
View File 

@@ -3,7 +3,7 @@
 
     <head>
 
         <meta charset="utf-8" />
 
         <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
 
-        <title>Mol* Viewer</title>
 
+        <title>Mol* Plugin Wrapper</title>
 
         <style>
 
             * {
 
                 margin: 0;
 
@@ -30,15 +30,19 @@
 
         <script>            
             var pdbId = '5ire', assemblyId= '1';
 
             var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
 
+            var format = 'cif';
 
+
 
+            // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
 
+            // var format = 'pdb';
 
 
             BasicMolStarWrapper.init('app' /** or document.getElementById('app') */);
 
             BasicMolStarWrapper.setBackground(0xffffff);
 
-            BasicMolStarWrapper.loadCif(url, assemblyId);
 
+            BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId });
 
             BasicMolStarWrapper.toggleSpin();
 
 
             document.getElementById('spin').onclick = () => BasicMolStarWrapper.toggleSpin();
 
-            document.getElementById('asym').onclick = () => BasicMolStarWrapper.loadCif(url);
 
-            document.getElementById('asm').onclick = () => BasicMolStarWrapper.loadCif(url, assemblyId);
 
+            document.getElementById('asym').onclick = () => BasicMolStarWrapper.load({ url: url, format: format });
 
+            document.getElementById('asm').onclick = () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId });
 
         </script>
 
     </body>
 
 </html>

+ 41 - 15
src/apps/basic-wrapper/index.ts
View File 

@@ -10,13 +10,16 @@ import { PluginContext } from 'mol-plugin/context';
 
 import { PluginCommands } from 'mol-plugin/command';
 
 import { StateTransforms } from 'mol-plugin/state/transforms';
 
 import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
 
-import { StateTree } from 'mol-state';
 
 import { Color } from 'mol-util/color';
 
+import { StateTreeBuilder } from 'mol-state/tree/builder';
 
+import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
 
 require('mol-plugin/skin/light.scss')
 
 
+type SupportedFormats = 'cif' | 'pdb'
 
+type LoadParams = { url: string, format?: SupportedFormats, assemblyId?: string }
 
+
 
 class BasicWrapper {
 
     plugin: PluginContext;
 
-    stateTemplate: StateTree;
 
 
     init(target: string | HTMLElement) {
 
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
 
@@ -26,15 +29,23 @@ class BasicWrapper {
 
                 showControls: false
 
             }
 
         });
 
+    }
 
+
 
+    private download(b: StateTreeBuilder.To<PSO.Root>, url: string) {
 
+        return b.apply(StateTransforms.Data.Download, { url, isBinary: false })
 
+    }
 
 
-        const state = this.plugin.state.dataState.build();
 
-        const visualRoot = state.toRoot()
 
-            .apply(StateTransforms.Data.Download, { url: '', isBinary: false }, { ref: 'url' })
 
-            .apply(StateTransforms.Data.ParseCif)
 
-            .apply(StateTransforms.Model.TrajectoryFromMmCif)
 
+    private parse(b: StateTreeBuilder.To<PSO.Data.Binary | PSO.Data.String>, format: SupportedFormats, assemblyId: string) {
 
+        const parsed = format === 'cif'
 
+            ? b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.TrajectoryFromMmCif)
 
+            : b.apply(StateTransforms.Model.TrajectoryFromPDB);
 
+
 
+        return parsed
 
             .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
 
-            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: '' }, { ref: 'asm' })
 
+            .apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
 
+    }
 
 
+    private visual(visualRoot: StateTreeBuilder.To<PSO.Molecule.Structure>) {
 
         visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
 
             .apply(StateTransforms.Representation.StructureRepresentation3D,
 
                 StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'cartoon'));
 
@@ -47,18 +58,33 @@ class BasicWrapper {
 
         visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'spheres' })
 
             .apply(StateTransforms.Representation.StructureRepresentation3D,
 
                 StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'spacefill'));
 
-
 
-        this.stateTemplate = state.getTree();
 
+        return visualRoot;
 
     }
 
 
-    async loadCif(url: string, assemblyId?: string) {
 
-        const state = this.stateTemplate.build();
 
+    private loadedParams: LoadParams = { url: '', format: 'cif', assemblyId: '' };
 
+    async load({ url, format = 'cif', assemblyId = '' }: LoadParams) {
 
+        let loadType: 'full' | 'update' = 'full';
 
+
 
+        const state = this.plugin.state.dataState;
 
 
-        state.to('url').update(StateTransforms.Data.Download, p => ({ ...p, url }));
 
-        state.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
 
+        if (this.loadedParams.url !== url || this.loadedParams.format !== format) {
 
+            loadType = 'full';
 
+        } else if (this.loadedParams.url === url) {
 
+            if (state.select('asm').length > 0) loadType = 'update';
 
+        }
 
 
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree: state });
 
+        let tree: StateTreeBuilder.Root;
 
+        if (loadType === 'full') {
 
+            await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref });
 
+            tree = state.build();
 
+            this.visual(this.parse(this.download(tree.toRoot(), url), format, assemblyId));
 
+        } else {
 
+            tree = state.build();
 
+            tree.to('asm').update(StateTransforms.Model.StructureAssemblyFromModel, p => ({ ...p, id: assemblyId || 'deposited' }));
 
+        }
 
 
+        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
 
+        this.loadedParams = { url, format, assemblyId };
 
         PluginCommands.Camera.Reset.dispatch(this.plugin, { });
 
     }

+ 6 - 2
src/mol-model-formats/structure/pdb/assembly.ts
View File 

@@ -65,8 +65,12 @@ export function parseRemark350(lines: Tokens, lineStart: number, lineEnd: number
 
         let line = getLine(i);
 
         if (line.substr(11, 12) === 'BIOMOLECULE:') {
 
             const id = line.substr(23).trim();
 
-            line = getLine(++i);
 
-            const details = line.substr(11).trim();
 
+            let details: string = `Biomolecule ` + id;
 
+            line = getLine(i + 1);
 
+            if (line.substr(11, 30) !== 'APPLY THE FOLLOWING TO CHAINS:') {
 
+                i++;
 
+                details = line.substr(11).trim();
 
+            }
 
             current = PdbAssembly(id, details);
 
             assemblies.push(current);
 
         } else if (line.substr(13, 5) === 'BIOMT') {