Proteopedia wrapper fixes

src/examples/proteopedia-wrapper/annotation.ts

@@ -8,27 +8,6 @@ import { CustomElementProperty } from 'mol-model-props/common/custom-element-pro
 import { Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
 import { Color } from 'mol-util/color';
 
-// export const StripedResidues = CustomElementProperty.create<number>({
-//     isStatic: true,
-//     name: 'basic-wrapper-residue-striping',
-//     display: 'Residue Stripes',
-//     getData(model: Model) {
-//         const map = new Map<ElementIndex, number>();
-//         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
-//         for (let i = 0, _i = model.atomicHierarchy.atoms._rowCount; i < _i; i++) {
-//             map.set(i as ElementIndex, residueIndex[i] % 2);
-//         }
-//         return map;
-//     },
-//     coloring: {
-//         getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff) },
-//         defaultColor: Color(0x777777)
-//     },
-//     format(e) {
-//         return e === 0 ? 'Odd stripe' : 'Even stripe'
-//     }
-// });
-
 const EvolutionaryConservationPalette: Color[] = [
     [255, 255, 150], // 9
     [160, 37, 96],
@@ -41,6 +20,8 @@ const EvolutionaryConservationPalette: Color[] = [
     [140, 255, 255],
     [16, 200, 209] // 1
 ].reverse().map(([r, g, b]) => Color.fromRgb(r, g, b));
+// const EvolutionaryConservationInsufficientColor = Color(0xcccc00);
+const EvolutionaryConservationDefaultColor = Color(0x999999);
 
 export const EvolutionaryConservation = CustomElementProperty.create<number>({
     isStatic: true,
@@ -71,7 +52,7 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
             const key = `${model.atomicHierarchy.chains.auth_asym_id.value(cI)} ${model.atomicHierarchy.residues.auth_seq_id.value(rI)}`;
             if (!conservationMap.has(key)) continue;
             const ann = conservationMap.get(key)!;
-            for (let aI = residueOffsets[rI]; aI < residueOffsets[aI + 1]; aI++) {
+            for (let aI = residueOffsets[rI]; aI < residueOffsets[rI + 1]; aI++) {
                 map.set(aI, ann);
             }
         }
@@ -79,10 +60,16 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
         return map;
     },
     coloring: {
-        getColor(e) { return EvolutionaryConservationPalette[(e - 1) || 0]; },
-        defaultColor: Color(0x999999)
+        getColor(e: number) {
+            // TODO
+            // if (e === 10) return EvolutionaryConservationInsufficientColor;
+            if (e < 0 || e > 9) return EvolutionaryConservationDefaultColor;
+            return EvolutionaryConservationPalette[e];
+        },
+        defaultColor: EvolutionaryConservationDefaultColor
     },
     format(e) {
-        return e ? `Evolutionary Conservation ${e}` : void 0;
+        if (e === 0) return `Evolutionary Conservation: InsufficientData`;
+        return e ? `Evolutionary Conservation: ${e}` : void 0;
     }
 });

src/examples/proteopedia-wrapper/index.html

@@ -61,7 +61,7 @@
 
             function $(id) { return document.getElementById(id); }
         
-            var pdbId = '2c1z', assemblyId= 'preferred';
+            var pdbId = '1eve', assemblyId= 'preferred';
             var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
             var format = 'cif';
             

src/examples/proteopedia-wrapper/index.ts

@@ -178,17 +178,17 @@ class MolStarProteopediaWrapper {
 
     coloring = {
         evolutionaryConservation: async () => {
-            await this.updateStyle({ sequence: { kind: 'molecular-surface' } });
+            await this.updateStyle({ sequence: { kind: 'spacefill' } });
 
             const state = this.state;
 
-            //const visuals = state.selectQ(q => q.ofType(PluginStateObject.Molecule.Representation3D).filter(c => c.transform.transformer === StateTransforms.Representation.StructureRepresentation3D));
+            // const visuals = state.selectQ(q => q.ofType(PluginStateObject.Molecule.Representation3D).filter(c => c.transform.transformer === StateTransforms.Representation.StructureRepresentation3D));
             const tree = state.build();
             const colorTheme = { name: EvolutionaryConservation.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(EvolutionaryConservation.Descriptor.name).defaultValues };
 
             tree.to('sequence-visual').update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
-            //for (const v of visuals) {
-            //}
+            // for (const v of visuals) {
+            // }
 
             await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
         }