molstar
Version:
A comprehensive macromolecular library.
97 lines (96 loc) • 4.23 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.HydrophobicityColorThemeProvider = exports.HydrophobicityColorThemeParams = void 0;
exports.getHydrophobicityColorThemeParams = getHydrophobicityColorThemeParams;
exports.hydrophobicity = hydrophobicity;
exports.HydrophobicityColorTheme = HydrophobicityColorTheme;
const color_1 = require("../../mol-util/color");
const structure_1 = require("../../mol-model/structure");
const param_definition_1 = require("../../mol-util/param-definition");
const types_1 = require("../../mol-model/structure/model/types");
const categories_1 = require("./categories");
const Description = 'Assigns a color to every amino acid according to the "Experimentally determined hydrophobicity scale for proteins at membrane interfaces" by Wimely and White (doi:10.1038/nsb1096-842).';
exports.HydrophobicityColorThemeParams = {
list: param_definition_1.ParamDefinition.ColorList('red-yellow-green', { presetKind: 'scale' }),
scale: param_definition_1.ParamDefinition.Select('DGwif', [['DGwif', 'DG water-membrane'], ['DGwoct', 'DG water-octanol'], ['Oct-IF', 'DG difference']])
};
function getHydrophobicityColorThemeParams(ctx) {
return exports.HydrophobicityColorThemeParams; // TODO return copy
}
const scaleIndexMap = { 'DGwif': 0, 'DGwoct': 1, 'Oct-IF': 2 };
function hydrophobicity(compId, scaleIndex) {
const c = types_1.ResidueHydrophobicity[compId];
return c === undefined ? 0 : c[scaleIndex];
}
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
}
}
function HydrophobicityColorTheme(ctx, props) {
const scaleIndex = scaleIndexMap[props.scale];
// get domain
let min = Infinity;
let max = -Infinity;
for (const name in types_1.ResidueHydrophobicity) {
const val = types_1.ResidueHydrophobicity[name][scaleIndex];
min = Math.min(min, val);
max = Math.max(max, val);
}
const scale = color_1.ColorScale.create({
listOrName: props.list.colors,
domain: [max, min],
minLabel: 'Hydrophilic',
maxLabel: 'Hydrophobic'
});
function color(location) {
let compId;
if (structure_1.StructureElement.Location.is(location)) {
if (structure_1.Unit.isAtomic(location.unit)) {
compId = getAtomicCompId(location.unit, location.element);
}
else {
compId = getCoarseCompId(location.unit, location.element);
}
}
else if (structure_1.Bond.isLocation(location)) {
if (structure_1.Unit.isAtomic(location.aUnit)) {
compId = getAtomicCompId(location.aUnit, location.aUnit.elements[location.aIndex]);
}
else {
compId = getCoarseCompId(location.aUnit, location.aUnit.elements[location.aIndex]);
}
}
return scale.color(compId ? hydrophobicity(compId, scaleIndex) : 0);
}
return {
factory: HydrophobicityColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
description: Description,
legend: scale ? scale.legend : undefined
};
}
exports.HydrophobicityColorThemeProvider = {
name: 'hydrophobicity',
label: 'Hydrophobicity',
category: categories_1.ColorThemeCategory.Residue,
factory: HydrophobicityColorTheme,
getParams: getHydrophobicityColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.HydrophobicityColorThemeParams),
isApplicable: (ctx) => !!ctx.structure
};