AlphaFold coloring behavior

src/viewer/helpers/af-confidence/behavior.ts

@@ -0,0 +1,70 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Mandar Deshpande <mandar@ebi.ac.uk>
+ */
+
+import { OrderedSet } from 'molstar/lib/mol-data/int';
+import { AlphaFoldConfidence, AlphaFoldConfidenceProvider } from './prop';
+import { AlphaFoldConfidenceColorThemeProvider } from './color';
+import { Loci } from 'molstar/lib/mol-model/loci';
+import { StructureElement } from 'molstar/lib/mol-model/structure';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior/behavior';
+
+export const AlphaFoldConfidenceScore = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'af-confidence-prop',
+    category: 'custom-props',
+    display: {
+        name: 'AlphaFold Confidence Score',
+        description: 'AlphaFold Confidence Score.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+        private provider = AlphaFoldConfidenceProvider
+
+        private labelProvider = {
+            label: (loci: Loci): string | undefined => {
+                if (!this.params.showTooltip) return;
+
+                switch (loci.kind) {
+                    case 'element-loci':
+                        if (loci.elements.length === 0) return;
+                        const e = loci.elements[0];
+                        const u = e.unit;
+                        if (!u.model.customProperties.hasReference(AlphaFoldConfidenceProvider.descriptor)) return;
+
+                        const se = StructureElement.Location.create(loci.structure, u, u.elements[OrderedSet.getAt(e.indices, 0)]);
+                        const confidenceScore = AlphaFoldConfidence.getConfidenceScore(se);
+                        return confidenceScore ? `Confidence score: ${confidenceScore[0]} <small>( ${confidenceScore[1]} )</small>` : `No confidence score`;
+
+                    default: return;
+                }
+            }
+        }
+
+        register(): void {
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.managers.lociLabels.addProvider(this.labelProvider);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(AlphaFoldConfidenceColorThemeProvider);
+        }
+
+        update(p: { autoAttach: boolean, showTooltip: boolean }) {
+            let updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showTooltip = p.showTooltip;
+            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            this.ctx.customModelProperties.unregister(AlphaFoldConfidenceProvider.descriptor.name);
+            this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(AlphaFoldConfidenceColorThemeProvider);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false),
+        showTooltip: PD.Boolean(true)
+    })
+});

src/viewer/index.html

@@ -62,7 +62,6 @@
                 layoutShowLog: !pdbId,
                 layoutShowControls: !isEmbedded,
                 showMembraneOrientationPreset: true,
-                showAlphaFoldConfidenceColorTheme: true,
                 detachedFromSierra: true // needed when running without sierra
             })
 

src/viewer/index.ts

@@ -3,6 +3,8 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Joan Segura <joan.segura@rcsb.org>
+ * @author Yana Rose <yana.rose@rcsb.org>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 
 import { BehaviorSubject } from 'rxjs';
@@ -38,7 +40,7 @@ import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
 import { ANVILMembraneOrientation, MembraneOrientationPreset } from 'molstar/lib/extensions/anvil/behavior';
 import { MembraneOrientationRepresentationProvider } from 'molstar/lib/extensions/anvil/representation';
 import { MotifAlignmentRequest, alignMotifs } from './helpers/superpose/pecos-integration';
-import { AlphaFoldConfidenceColorThemeProvider } from './helpers/af-confidence/color';
+import { AlphaFoldConfidenceScore } from './helpers/af-confidence/behavior';
 
 /** package version, filled in at bundle build time */
 declare const __RCSB_MOLSTAR_VERSION__: string;
@@ -53,7 +55,8 @@ const Extensions = {
     'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
     'mp4-export': PluginSpec.Behavior(Mp4Export),
-    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation)
+    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
+    'af-confidence': PluginSpec.Behavior(AlphaFoldConfidenceScore)
 };
 
 const DefaultViewerProps = {
@@ -63,7 +66,6 @@ const DefaultViewerProps = {
     showStructureSourceControls: true,
     showSuperpositionControls: true,
     showMembraneOrientationPreset: false,
-    showAlphaFoldConfidenceColorTheme: false,
     /**
      * Needed when running outside of sierra. If set to true, the strucmotif UI will use an absolute URL to sierra-prod.
      * Otherwise, the link will be relative on the current host.
@@ -186,10 +188,7 @@ export class Viewer {
                 const renderer = this.plugin.canvas3d!.props.renderer;
                 await PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: o.backgroundColor } } });
                 this.plugin.representation.structure.themes.colorThemeRegistry.add(SuperposeColorThemeProvider);
-                // conditionally load PDBe's AlphaFold preset
-                if (o.showAlphaFoldConfidenceColorTheme) {
-                    this.plugin.representation.structure.themes.colorThemeRegistry.add(AlphaFoldConfidenceColorThemeProvider);
-                }
+                // this.plugin.representation.structure.themes.colorThemeRegistry.add(AlphaFoldConfidenceColorThemeProvider);
 
                 if (o.showWelcomeToast) {
                     await PluginCommands.Toast.Show(this.plugin, {