molstar
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A comprehensive macromolecular library.
133 lines (132 loc) • 4.85 kB
JavaScript
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Color, ColorMap } from '../../mol-util/color';
import { StructureElement, Unit, Bond } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { TableLegend } from '../../mol-util/legend';
import { getAdjustedColorMap } from '../../mol-util/color/color';
import { getColorMapParams } from '../../mol-util/color/params';
import { ColorThemeCategory } from './categories';
// protein colors from Jmol http://jmol.sourceforge.net/jscolors/
export const ResidueNameColors = ColorMap({
// standard amino acids
'ALA': 0x8CFF8C,
'ARG': 0x00007C,
'ASN': 0xFF7C70,
'ASP': 0xA00042,
'CYS': 0xFFFF70,
'GLN': 0xFF4C4C,
'GLU': 0x660000,
'GLY': 0xEEEEEE,
'HIS': 0x7070FF,
'ILE': 0x004C00,
'LEU': 0x455E45,
'LYS': 0x4747B8,
'MET': 0xB8A042,
'PHE': 0x534C52,
'PRO': 0x525252,
'SER': 0xFF7042,
'THR': 0xB84C00,
'TRP': 0x4F4600,
'TYR': 0x8C704C,
'VAL': 0xFF8CFF,
// rna bases
'A': 0xDC143C, // Crimson Red
'G': 0x32CD32, // Lime Green
'I': 0x9ACD32, // Yellow Green
'C': 0xFFD700, // Gold Yellow
'T': 0x4169E1, // Royal Blue
'U': 0x40E0D0, // Turquoise Cyan
// dna bases
'DA': 0xDC143C,
'DG': 0x32CD32,
'DI': 0x9ACD32,
'DC': 0xFFD700,
'DT': 0x4169E1,
'DU': 0x40E0D0,
// peptide bases
'APN': 0xDC143C,
'GPN': 0x32CD32,
'CPN': 0xFFD700,
'TPN': 0x4169E1,
});
const DefaultResidueNameColor = Color(0xFF00FF);
const Description = 'Assigns a color to every residue according to its name.';
export const ResidueNameColorThemeParams = {
saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 }),
colors: PD.MappedStatic('default', {
'default': PD.EmptyGroup(),
'custom': PD.Group(getColorMapParams(ResidueNameColors))
})
};
export function getResidueNameColorThemeParams(ctx) {
return ResidueNameColorThemeParams; // TODO return copy
}
function getAtomicCompId(unit, element) {
return unit.model.atomicHierarchy.atoms.label_comp_id.value(element);
}
function getCoarseCompId(unit, element) {
const seqIdBegin = unit.coarseElements.seq_id_begin.value(element);
const seqIdEnd = unit.coarseElements.seq_id_end.value(element);
if (seqIdBegin === seqIdEnd) {
const entityKey = unit.coarseElements.entityKey[element];
const seq = unit.model.sequence.byEntityKey[entityKey].sequence;
return seq.compId.value(seqIdBegin - 1); // 1-indexed
}
}
export function residueNameColor(colorMap, residueName) {
const c = colorMap[residueName];
return c === undefined ? DefaultResidueNameColor : c;
}
export function ResidueNameColorTheme(ctx, props) {
const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ResidueNameColors : props.colors.params, props.saturation, props.lightness);
function color(location) {
if (StructureElement.Location.is(location)) {
if (Unit.isAtomic(location.unit)) {
const compId = getAtomicCompId(location.unit, location.element);
return residueNameColor(colorMap, compId);
}
else {
const compId = getCoarseCompId(location.unit, location.element);
if (compId)
return residueNameColor(colorMap, compId);
}
}
else if (Bond.isLocation(location)) {
if (Unit.isAtomic(location.aUnit)) {
const compId = getAtomicCompId(location.aUnit, location.aUnit.elements[location.aIndex]);
return residueNameColor(colorMap, compId);
}
else {
const compId = getCoarseCompId(location.aUnit, location.aUnit.elements[location.aIndex]);
if (compId)
return residueNameColor(colorMap, compId);
}
}
return DefaultResidueNameColor;
}
return {
factory: ResidueNameColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
description: Description,
legend: TableLegend(Object.keys(colorMap).map(name => {
return [name, colorMap[name]];
}).concat([['Unknown', DefaultResidueNameColor]]))
};
}
export const ResidueNameColorThemeProvider = {
name: 'residue-name',
label: 'Residue Name',
category: ColorThemeCategory.Residue,
factory: ResidueNameColorTheme,
getParams: getResidueNameColorThemeParams,
defaultValues: PD.getDefaultValues(ResidueNameColorThemeParams),
isApplicable: (ctx) => !!ctx.structure
};