molstar
Version:
A comprehensive macromolecular library.
62 lines • 2.94 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.UncertaintySizeThemeProvider = exports.UncertaintySizeTheme = exports.getUncertainty = exports.getUncertaintySizeThemeParams = exports.UncertaintySizeThemeParams = void 0;
var structure_1 = require("../../mol-model/structure");
var param_definition_1 = require("../../mol-util/param-definition");
var 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.";
exports.UncertaintySizeThemeParams = {
bfactorFactor: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0, max: 1, step: 0.01 }),
rmsfFactor: param_definition_1.ParamDefinition.Numeric(0.05, { min: 0, max: 1, step: 0.01 }),
baseSize: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 2, step: 0.1 }),
};
function getUncertaintySizeThemeParams(ctx) {
return exports.UncertaintySizeThemeParams; // TODO return copy
}
exports.getUncertaintySizeThemeParams = getUncertaintySizeThemeParams;
function getUncertainty(unit, element, props) {
if (structure_1.Unit.isAtomic(unit)) {
return unit.model.atomicConformation.B_iso_or_equiv.value(element) * props.bfactorFactor;
}
else if (structure_1.Unit.isSpheres(unit)) {
return unit.model.coarseConformation.spheres.rmsf[element] * props.rmsfFactor;
}
else {
return 0;
}
}
exports.getUncertainty = getUncertainty;
function UncertaintySizeTheme(ctx, props) {
function size(location) {
var size = props.baseSize;
if (structure_1.StructureElement.Location.is(location)) {
size += getUncertainty(location.unit, location.element, props);
}
else if (structure_1.Bond.isLocation(location)) {
size += getUncertainty(location.aUnit, location.aUnit.elements[location.aIndex], props);
}
return size;
}
return {
factory: UncertaintySizeTheme,
granularity: 'group',
size: size,
props: props,
description: Description
};
}
exports.UncertaintySizeTheme = UncertaintySizeTheme;
exports.UncertaintySizeThemeProvider = {
name: 'uncertainty',
label: 'Uncertainty/Disorder',
category: '',
factory: UncertaintySizeTheme,
getParams: getUncertaintySizeThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.UncertaintySizeThemeParams),
isApplicable: function (ctx) { return !!ctx.structure && ctx.structure.models.some(function (m) { return m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined; }); }
};
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