molstar
Version:
A comprehensive macromolecular library.
76 lines (75 loc) • 2.9 kB
JavaScript
/**
* Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Lukáš Polák <admin@lukaspolak.cz>
*/
import { Color, ColorScale } from '../../mol-util/color';
import { StructureElement, Unit, Bond } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ColorThemeCategory } from './categories';
const DefaultUncertaintyColor = Color(0xffff99);
const Description = `Assigns a color based on the uncertainty or disorder of an element's position, e.g. B-factor or RMSF, depending on the data availability and experimental technique.`;
export const UncertaintyColorThemeParams = {
domain: PD.Interval([0, 100]),
list: PD.ColorList('red-white-blue', { presetKind: 'scale' }),
};
export function getUncertaintyColorThemeParams(ctx) {
return UncertaintyColorThemeParams; // TODO return copy
}
export function getUncertainty(unit, element) {
if (Unit.isAtomic(unit)) {
return unit.model.atomicConformation.B_iso_or_equiv.value(element);
}
else if (Unit.isSpheres(unit)) {
return unit.model.coarseConformation.spheres.rmsf[element];
}
else {
return 0;
}
}
export function UncertaintyColorTheme(ctx, props) {
let scale;
if (props.list.kind === 'set') {
scale = ColorScale.createDiscrete({
reverse: true,
domain: props.domain,
listOrName: props.list.colors
});
}
else {
scale = ColorScale.create({
reverse: true,
domain: props.domain,
listOrName: props.list.colors
});
}
// TODO calc domain based on data, set min/max as 10/90 percentile to be robust against outliers
function color(location) {
if (StructureElement.Location.is(location)) {
return scale.color(getUncertainty(location.unit, location.element));
}
else if (Bond.isLocation(location)) {
return scale.color(getUncertainty(location.aUnit, location.aUnit.elements[location.aIndex]));
}
return DefaultUncertaintyColor;
}
return {
factory: UncertaintyColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
description: Description,
legend: scale ? scale.legend : undefined
};
}
export const UncertaintyColorThemeProvider = {
name: 'uncertainty',
label: 'Uncertainty/Disorder',
category: ColorThemeCategory.Atom,
factory: UncertaintyColorTheme,
getParams: getUncertaintyColorThemeParams,
defaultValues: PD.getDefaultValues(UncertaintyColorThemeParams),
isApplicable: (ctx) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined)
};