diff --git a/src/examples/proteopedia-wrapper/annotation.ts b/src/examples/proteopedia-wrapper/annotation.ts
index 54c89117c7f78c5209364fab76dcd1d35f3f7599..54596826bb42f17e08f7bf6d8aca972f8c24474b 100644
--- a/src/examples/proteopedia-wrapper/annotation.ts
+++ b/src/examples/proteopedia-wrapper/annotation.ts
@@ -5,26 +5,84 @@
*/
import { CustomElementProperty } from 'mol-model-props/common/custom-element-property';
-import { Model, ElementIndex } from 'mol-model/structure';
+import { Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
import { Color } from 'mol-util/color';
-export const StripedResidues = CustomElementProperty.create<number>({
+// 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],
+ [240, 125, 171],
+ [250, 201, 222],
+ [252, 237, 244],
+ [255, 255, 255],
+ [234, 255, 255],
+ [215, 255, 255],
+ [140, 255, 255],
+ [16, 200, 209] // 1
+].reverse().map(([r, g, b]) => Color.fromRgb(r, g, b));
+
+export const EvolutionaryConservation = CustomElementProperty.create<number>({
isStatic: true,
- name: 'basic-wrapper-residue-striping',
- display: 'Residue Stripes',
- getData(model: Model) {
+ name: 'proteopedia-wrapper-evolutionary-conservation',
+ display: 'Evolutionary Conservation',
+ async getData(model: Model) {
+ const id = model.label.toLowerCase();
+ const req = await fetch(`https://proteopedia.org/cgi-bin/cnsrf?${id}`);
+ const json = await req.json();
+ const annotations = (json && json.residueAnnotations) || [];
+
+ const conservationMap = new Map<string, number>();
+
+ for (const e of annotations) {
+ for (const r of e.ids) {
+ conservationMap.set(r, e.annotation);
+ }
+ }
+
const map = new Map<ElementIndex, number>();
- const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
- for (let i = 0, _i = model.atomicHierarchy.atoms._rowCount; i < _i; i++) {
- map.set(i as ElementIndex, residueIndex[i] % 2);
+
+ const { _rowCount: residueCount } = model.atomicHierarchy.residues;
+ const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
+ const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
+
+ for (let rI = 0 as ResidueIndex; rI < residueCount; rI++) {
+ const cI = chainIndex[residueOffsets[rI]];
+ const key = `${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++) {
+ map.set(aI, ann);
+ }
}
+
return map;
},
coloring: {
- getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff) },
- defaultColor: Color(0x777777)
+ getColor(e) { return EvolutionaryConservationPalette[(e - 1) || 0]; },
+ defaultColor: Color(0x999999)
},
format(e) {
- return e === 0 ? 'Odd stripe' : 'Even stripe'
+ return e ? `Evolutionary Conservation ${e}` : void 0;
}
-})
\ No newline at end of file
+});
\ No newline at end of file
diff --git a/src/examples/proteopedia-wrapper/index.html b/src/examples/proteopedia-wrapper/index.html
index 59b5a762d6d7dc89cb42d34f862df3c5bc70f86f..c85de9b2d7ab92c941dcd6940c1bc2861f9c8bc1 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 = '3usb', assemblyId= 'preferred';
+ var pdbId = '2c1z', assemblyId= 'preferred';
var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
var format = 'cif';
@@ -107,9 +107,11 @@
addControl('Play Loop', () => MolStarProteopediaWrapper.animate.modelIndex.loop());
addControl('Stop', () => MolStarProteopediaWrapper.animate.modelIndex.stop());
+ addSeparator();
addHeader('Misc');
- addControl('Apply Stripes', () => MolStarProteopediaWrapper.coloring.applyStripes());
+ addControl('Apply Evo Cons', () => MolStarProteopediaWrapper.coloring.evolutionaryConservation());
+ addControl('Default Visuals', () => MolStarProteopediaWrapper.updateStyle());
////////////////////////////////////////////////////////
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index 3868ddf08a495c14e553e41fe969087b7f7ff298..56f3452510fed74120bcdb43e99ae99eff9f9628 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -14,7 +14,7 @@ import { Color } from 'mol-util/color';
import { PluginStateObject as PSO, PluginStateObject } from 'mol-plugin/state/objects';
import { AnimateModelIndex } from 'mol-plugin/state/animation/built-in';
import { StateBuilder, StateObject } from 'mol-state';
-import { StripedResidues } from './annotation';
+import { EvolutionaryConservation } from './annotation';
import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo } from './helpers';
import { RxEventHelper } from 'mol-util/rx-event-helper';
require('mol-plugin/skin/light.scss')
@@ -39,9 +39,9 @@ class MolStarProteopediaWrapper {
}
});
- this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add(StripedResidues.Descriptor.name, StripedResidues.colorTheme!);
- this.plugin.lociLabels.addProvider(StripedResidues.labelProvider);
- this.plugin.customModelProperties.register(StripedResidues.propertyProvider);
+ this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add(EvolutionaryConservation.Descriptor.name, EvolutionaryConservation.colorTheme!);
+ this.plugin.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
+ this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider);
}
get state() {
@@ -65,7 +65,7 @@ class MolStarProteopediaWrapper {
const model = this.state.build().to('model');
return model
- .apply(StateTransforms.Model.CustomModelProperties, { properties: [StripedResidues.Descriptor.name] }, { ref: 'props', props: { isGhost: false } })
+ .apply(StateTransforms.Model.CustomModelProperties, { properties: [EvolutionaryConservation.Descriptor.name] }, { ref: 'props', props: { isGhost: false } })
.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
}
@@ -97,7 +97,7 @@ class MolStarProteopediaWrapper {
return root;
}
- private getObj<T extends StateObject>(ref: string) {
+ private getObj<T extends StateObject>(ref: string): T['data'] {
const state = this.state;
const cell = state.select(ref)[0];
if (!cell || !cell.obj) return void 0;
@@ -105,10 +105,10 @@ class MolStarProteopediaWrapper {
}
private async doInfo(checkPreferredAssembly: boolean) {
- const s = this.getObj<PluginStateObject.Molecule.Model>('model');
- if (!s) return;
+ const model = this.getObj<PluginStateObject.Molecule.Model>('model');
+ if (!model) return;
- const info = await ModelInfo.get(this.plugin, s, checkPreferredAssembly)
+ const info = await ModelInfo.get(this.plugin, model, checkPreferredAssembly)
this.events.modelInfo.next(info);
return info;
}
@@ -177,18 +177,18 @@ class MolStarProteopediaWrapper {
}
coloring = {
- applyStripes: async () => {
+ evolutionaryConservation: async () => {
await this.updateStyle({ sequence: { kind: 'molecular-surface' } });
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: StripedResidues.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(StripedResidues.Descriptor.name).defaultValues };
+ const colorTheme = { name: EvolutionaryConservation.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(EvolutionaryConservation.Descriptor.name).defaultValues };
- for (const v of visuals) {
- tree.to(v.transform.ref).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
- }
+ tree.to('sequence-visual').update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
+ //for (const v of visuals) {
+ //}
await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
}
diff --git a/src/mol-model-props/common/custom-element-property.ts b/src/mol-model-props/common/custom-element-property.ts
index 609674ae6f8b420e841e2033f366c1e91fa72969..85f9306753784f838dbc00dce60b168394c5b6be 100644
--- a/src/mol-model-props/common/custom-element-property.ts
+++ b/src/mol-model-props/common/custom-element-property.ts
@@ -26,7 +26,7 @@ namespace CustomElementProperty {
display: string,
attachableTo?: (model: Model) => boolean,
getData(model: Model): Map<ElementIndex, T> | Promise<Map<ElementIndex, T>>,
- format?(e: T): string,
+ format?(e: T): string | undefined,
coloring?: {
getColor: (e: T) => Color,
defaultColor: Color
@@ -43,17 +43,24 @@ namespace CustomElementProperty {
function attach(model: Model) {
return Task.create(`Attach ${params.display}`, async () => {
- const data = await params.getData(model);
+ try {
+ if (model.customProperties.has(Descriptor)) return true;
- if (params.isStatic) {
- model._staticPropertyData[name] = data;
- } else {
- model._dynamicPropertyData[name] = data;
- }
+ const data = await params.getData(model);
+
+ if (params.isStatic) {
+ model._staticPropertyData[name] = data;
+ } else {
+ model._dynamicPropertyData[name] = data;
+ }
- model.customProperties.add(Descriptor);
+ model.customProperties.add(Descriptor);
- return true;
+ return true;
+ } catch (e) {
+ console.warn('Attach Property', e);
+ return false;
+ }
})
}