molstar
Version:
A comprehensive macromolecular library.
64 lines (63 loc) • 3.06 kB
JavaScript
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { Color, ColorScale } from '../../../../mol-util/color';
import { StructureElement, Model, Bond } from '../../../../mol-model/structure';
import { ValidationReportProvider, ValidationReport } from '../prop';
import { ColorThemeCategory } from '../../../../mol-theme/color/categories';
const DefaultColor = Color(0xCCCCCC);
export function RandomCoilIndexColorTheme(ctx, props) {
var _a, _b;
let color = () => DefaultColor;
const scale = ColorScale.create({
reverse: true,
domain: [0, 0.6],
listOrName: 'red-yellow-blue',
});
const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
const contextHash = validationReport === null || validationReport === void 0 ? void 0 : validationReport.version;
const rci = (_a = validationReport === null || validationReport === void 0 ? void 0 : validationReport.value) === null || _a === void 0 ? void 0 : _a.rci;
const model = (_b = ctx.structure) === null || _b === void 0 ? void 0 : _b.models[0];
if (rci && model) {
const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
const getColor = (element) => {
const value = rci.get(residueIndex[element]);
return value === undefined ? DefaultColor : scale.color(value);
};
color = (location) => {
if (StructureElement.Location.is(location) && location.unit.model === model) {
return getColor(location.element);
}
else if (Bond.isLocation(location) && location.aUnit.model === model) {
return getColor(location.aUnit.elements[location.aIndex]);
}
return DefaultColor;
};
}
return {
factory: RandomCoilIndexColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
contextHash,
description: 'Assigns residue colors according to the Random Coil Index value. Data from wwPDB Validation Report, obtained via RCSB PDB.',
legend: scale.legend
};
}
export const RandomCoilIndexColorThemeProvider = {
name: ValidationReport.Tag.RandomCoilIndex,
label: 'Random Coil Index',
category: ColorThemeCategory.Validation,
factory: RandomCoilIndexColorTheme,
getParams: () => ({}),
defaultValues: PD.getDefaultValues({}),
isApplicable: (ctx) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromNmr(ctx.structure.models[0]),
ensureCustomProperties: {
attach: (ctx, data) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
}
};