molstar
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A comprehensive macromolecular library.
161 lines (160 loc) • 5.56 kB
JavaScript
/**
* Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Lukáš Polák <admin@lukaspolak.cz>
*/
import { Color, ColorMap } from '../../mol-util/color/index.js';
import { StructureElement, Unit, Bond } from '../../mol-model/structure.js';
import { ParamDefinition as PD } from '../../mol-util/param-definition.js';
import { TableLegend } from '../../mol-util/legend.js';
import { getAdjustedColorMap } from '../../mol-util/color/color.js';
import { getColorMapParams } from '../../mol-util/color/params.js';
import { ColorThemeCategory } from './categories.js';
// Colors for charged residues (by-name)
export const ChargedResidueColors = ColorMap({
// standard amino acids (charged)
'ARG': 0x0000FF,
'ASP': 0xFF0000,
'GLU': 0xFF0000,
'HIS': 0x33C3F9,
'LYS': 0x0000FF,
// standard amino acids (uncharged)
'ALA': 0xFFFFFF,
'ASN': 0xFFFFFF,
'CYS': 0xFFFFFF,
'GLN': 0xFFFFFF,
'GLY': 0xFFFFFF,
'ILE': 0xFFFFFF,
'LEU': 0xFFFFFF,
'MET': 0xFFFFFF,
'PHE': 0xFFFFFF,
'PRO': 0xFFFFFF,
'SER': 0xFFFFFF,
'THR': 0xFFFFFF,
'TRP': 0xFFFFFF,
'TYR': 0xFFFFFF,
'VAL': 0xFFFFFF,
// common from CCD
'MSE': 0xFFFFFF,
'SEP': 0xFFFFFF,
'TPO': 0xFFFFFF,
'PTR': 0xFFFFFF,
'PCA': 0xFFFFFF,
'HYP': 0xFFFFFF,
// charmm ff
'HSD': 0xFFFFFF,
'HSE': 0xFFFFFF,
'HSP': 0x0000FF,
'LSN': 0xFFFFFF,
'ASPP': 0xFFFFFF,
'GLUP': 0xFFFFFF,
// amber ff
'HID': 0xFFFFFF,
'HIE': 0xFFFFFF,
'HIP': 0x0000FF,
'LYN': 0xFFFFFF,
'ASH': 0xFFFFFF,
'GLH': 0xFFFFFF,
// rna bases
'A': 0xFFFFFF,
'G': 0xFFFFFF,
'I': 0xFFFFFF,
'C': 0xFFFFFF,
'T': 0xFFFFFF,
'U': 0xFFFFFF,
// dna bases
'DA': 0xFFFFFF,
'DG': 0xFFFFFF,
'DI': 0xFFFFFF,
'DC': 0xFFFFFF,
'DT': 0xFFFFFF,
'DU': 0xFFFFFF,
// peptide bases
'APN': 0xFFFFFF,
'GPN': 0xFFFFFF,
'CPN': 0xFFFFFF,
'TPN': 0xFFFFFF,
});
const DefaultResidueChargeColor = Color(0xFF00FF);
const Description = 'Assigns a color to every residue based on its charge state.';
export const ResidueChargeColorThemeParams = {
method: PD.MappedStatic('by-name', {
'by-name': PD.Group({
saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
colors: PD.MappedStatic('default', {
'default': PD.EmptyGroup(),
'custom': PD.Group(getColorMapParams(ChargedResidueColors)),
})
}, { isFlat: true })
})
};
export function getResidueChargeColorThemeParams(ctx) {
return PD.clone(ResidueChargeColorThemeParams);
}
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 residueChargeColor(colorMap, residueName) {
const c = colorMap[residueName];
return c === undefined ? DefaultResidueChargeColor : c;
}
export function ResidueChargeColorTheme(ctx, props) {
const { saturation, lightness, colors } = props.method.params;
const colorMap = getAdjustedColorMap(props.method.params.colors.name === 'default' ? ChargedResidueColors : colors.params, saturation, lightness);
function color(location) {
if (StructureElement.Location.is(location)) {
if (Unit.isAtomic(location.unit)) {
const compId = getAtomicCompId(location.unit, location.element);
return residueChargeColor(colorMap, compId);
}
else {
const compId = getCoarseCompId(location.unit, location.element);
if (compId)
return residueChargeColor(colorMap, compId);
}
}
else if (Bond.isLocation(location)) {
if (Unit.isAtomic(location.aUnit)) {
const compId = getAtomicCompId(location.aUnit, location.aUnit.elements[location.aIndex]);
return residueChargeColor(colorMap, compId);
}
else {
const compId = getCoarseCompId(location.aUnit, location.aUnit.elements[location.aIndex]);
if (compId)
return residueChargeColor(colorMap, compId);
}
}
return DefaultResidueChargeColor;
}
return {
factory: ResidueChargeColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
description: Description,
legend: TableLegend(Object.keys(colorMap).map(name => {
return [name, colorMap[name]];
}).concat([['Unknown', DefaultResidueChargeColor]]))
};
}
export const ResidueChargeColorThemeProvider = {
name: 'residue-charge',
label: 'Residue Charge',
category: ColorThemeCategory.Residue,
factory: ResidueChargeColorTheme,
getParams: getResidueChargeColorThemeParams,
defaultValues: PD.getDefaultValues(ResidueChargeColorThemeParams),
isApplicable: (ctx) => !!ctx.structure
};