From 1acdfdf2afee883ef01321755307698f8239f532 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 25 Feb 2019 21:54:04 +0100
Subject: [PATCH] Proteopedia wrapper fixes
---
.../proteopedia-wrapper/annotation.ts | 37 ++++++-------------
src/examples/proteopedia-wrapper/index.html | 2 +-
src/examples/proteopedia-wrapper/index.ts | 8 ++--
3 files changed, 17 insertions(+), 30 deletions(-)
diff --git a/src/examples/proteopedia-wrapper/annotation.ts b/src/examples/proteopedia-wrapper/annotation.ts
index 54596826b..e161d2ef8 100644
--- a/src/examples/proteopedia-wrapper/annotation.ts
+++ b/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;
}
});
\ No newline at end of file
diff --git a/src/examples/proteopedia-wrapper/index.html b/src/examples/proteopedia-wrapper/index.html
index c85de9b2d..1b9ba9903 100644
--- a/src/examples/proteopedia-wrapper/index.html
+++ b/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';
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index 56f345251..962e5642f 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/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 });
}
--
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