molstar
Version:
A comprehensive macromolecular library.
75 lines • 3.85 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';
var DefaultColor = Color(0xCCCCCC);
export function DensityFitColorTheme(ctx, props) {
var _a;
var color = function () { return DefaultColor; };
var scaleRsrz = ColorScale.create({
minLabel: 'Poor',
maxLabel: 'Better',
domain: [2, 0],
listOrName: 'red-yellow-blue',
});
var scaleRscc = ColorScale.create({
minLabel: 'Poor',
maxLabel: 'Better',
domain: [0.678, 1.0],
listOrName: 'red-yellow-blue',
});
var validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
var contextHash = validationReport === null || validationReport === void 0 ? void 0 : validationReport.version;
var model = (_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models[0];
if ((validationReport === null || validationReport === void 0 ? void 0 : validationReport.value) && model) {
var _b = validationReport.value, rsrz_1 = _b.rsrz, rscc_1 = _b.rscc;
var residueIndex_1 = model.atomicHierarchy.residueAtomSegments.index;
var getColor_1 = function (element) {
var rsrzValue = rsrz_1.get(residueIndex_1[element]);
if (rsrzValue !== undefined)
return scaleRsrz.color(rsrzValue);
var rsccValue = rscc_1.get(residueIndex_1[element]);
if (rsccValue !== undefined)
return scaleRscc.color(rsccValue);
return DefaultColor;
};
color = function (location) {
if (StructureElement.Location.is(location) && location.unit.model === model) {
return getColor_1(location.element);
}
else if (Bond.isLocation(location) && location.aUnit.model === model) {
return getColor_1(location.aUnit.elements[location.aIndex]);
}
return DefaultColor;
};
}
return {
factory: DensityFitColorTheme,
granularity: 'group',
preferSmoothing: true,
color: color,
props: props,
contextHash: contextHash,
description: 'Assigns residue colors according to the density fit using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from poor (RSRZ = 2 or RSCC = 0.678) - to better (RSRZ = 0 or RSCC = 1.0). Data from wwPDB Validation Report, obtained via RCSB PDB.',
legend: scaleRsrz.legend
};
}
export var DensityFitColorThemeProvider = {
name: ValidationReport.Tag.DensityFit,
label: 'Density Fit',
category: "Validation" /* Validation */,
factory: DensityFitColorTheme,
getParams: function () { return ({}); },
defaultValues: PD.getDefaultValues({}),
isApplicable: function (ctx) { return !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromXray(ctx.structure.models[0]) && Model.probablyHasDensityMap(ctx.structure.models[0]); },
ensureCustomProperties: {
attach: function (ctx, data) { return data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(); },
detach: function (data) { return data.structure && ValidationReportProvider.ref(data.structure.models[0], false); }
}
};
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