molstar
Version:
A comprehensive macromolecular library.
56 lines (55 loc) • 2.23 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { StructureElement, Unit, Bond } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
const Description = `Assigns a size reflecting 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 UncertaintySizeThemeParams = {
bfactorFactor: PD.Numeric(0.1, { min: 0, max: 1, step: 0.01 }),
rmsfFactor: PD.Numeric(0.05, { min: 0, max: 1, step: 0.01 }),
baseSize: PD.Numeric(0.2, { min: 0, max: 2, step: 0.1 }),
};
export function getUncertaintySizeThemeParams(ctx) {
return UncertaintySizeThemeParams; // TODO return copy
}
export function getUncertainty(unit, element, props) {
if (Unit.isAtomic(unit)) {
return unit.model.atomicConformation.B_iso_or_equiv.value(element) * props.bfactorFactor;
}
else if (Unit.isSpheres(unit)) {
return unit.model.coarseConformation.spheres.rmsf[element] * props.rmsfFactor;
}
else {
return 0;
}
}
export function UncertaintySizeTheme(ctx, props) {
function size(location) {
let size = props.baseSize;
if (StructureElement.Location.is(location)) {
size += getUncertainty(location.unit, location.element, props);
}
else if (Bond.isLocation(location)) {
size += getUncertainty(location.aUnit, location.aUnit.elements[location.aIndex], props);
}
return size;
}
return {
factory: UncertaintySizeTheme,
granularity: 'group',
size,
props,
description: Description
};
}
export const UncertaintySizeThemeProvider = {
name: 'uncertainty',
label: 'Uncertainty/Disorder',
category: '',
factory: UncertaintySizeTheme,
getParams: getUncertaintySizeThemeParams,
defaultValues: PD.getDefaultValues(UncertaintySizeThemeParams),
isApplicable: (ctx) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined)
};