molstar
Version:
A comprehensive macromolecular library.
70 lines • 3.25 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.UncertaintyColorThemeProvider = exports.UncertaintyColorTheme = exports.getUncertainty = exports.getUncertaintyColorThemeParams = exports.UncertaintyColorThemeParams = void 0;
var color_1 = require("../../mol-util/color");
var structure_1 = require("../../mol-model/structure");
var param_definition_1 = require("../../mol-util/param-definition");
var DefaultUncertaintyColor = (0, color_1.Color)(0xffff99);
var 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.";
exports.UncertaintyColorThemeParams = {
domain: param_definition_1.ParamDefinition.Interval([0, 100]),
list: param_definition_1.ParamDefinition.ColorList('red-white-blue', { presetKind: 'scale' }),
};
function getUncertaintyColorThemeParams(ctx) {
return exports.UncertaintyColorThemeParams; // TODO return copy
}
exports.getUncertaintyColorThemeParams = getUncertaintyColorThemeParams;
function getUncertainty(unit, element) {
if (structure_1.Unit.isAtomic(unit)) {
return unit.model.atomicConformation.B_iso_or_equiv.value(element);
}
else if (structure_1.Unit.isSpheres(unit)) {
return unit.model.coarseConformation.spheres.rmsf[element];
}
else {
return 0;
}
}
exports.getUncertainty = getUncertainty;
function UncertaintyColorTheme(ctx, props) {
var scale = color_1.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 (structure_1.StructureElement.Location.is(location)) {
return scale.color(getUncertainty(location.unit, location.element));
}
else if (structure_1.Bond.isLocation(location)) {
return scale.color(getUncertainty(location.aUnit, location.aUnit.elements[location.aIndex]));
}
return DefaultUncertaintyColor;
}
return {
factory: UncertaintyColorTheme,
granularity: 'group',
preferSmoothing: true,
color: color,
props: props,
description: Description,
legend: scale ? scale.legend : undefined
};
}
exports.UncertaintyColorTheme = UncertaintyColorTheme;
exports.UncertaintyColorThemeProvider = {
name: 'uncertainty',
label: 'Uncertainty/Disorder',
category: "Atom Property" /* Atom */,
factory: UncertaintyColorTheme,
getParams: getUncertaintyColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.UncertaintyColorThemeParams),
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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