molstar
Version:
A comprehensive macromolecular library.
131 lines (130 loc) • 6.75 kB
JavaScript
;
/**
* Copyright (c) 2018-2022 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.SecondaryStructureColorThemeProvider = exports.SecondaryStructureColorThemeParams = void 0;
exports.getSecondaryStructureColorThemeParams = getSecondaryStructureColorThemeParams;
exports.secondaryStructureColor = secondaryStructureColor;
exports.SecondaryStructureColorTheme = SecondaryStructureColorTheme;
const color_1 = require("../../mol-util/color");
const structure_1 = require("../../mol-model/structure");
const types_1 = require("../../mol-model/structure/model/types");
const util_1 = require("../../mol-model/structure/util");
const param_definition_1 = require("../../mol-util/param-definition");
const legend_1 = require("../../mol-util/legend");
const secondary_structure_1 = require("../../mol-model-props/computed/secondary-structure");
const color_2 = require("../../mol-util/color/color");
const params_1 = require("../../mol-util/color/params");
const util_2 = require("../../mol-data/util");
const categories_1 = require("./categories");
// from Jmol http://jmol.sourceforge.net/jscolors/ (shapely)
const SecondaryStructureColors = (0, color_1.ColorMap)({
'alphaHelix': 0xFF0080,
'threeTenHelix': 0xA00080,
'piHelix': 0x600080,
'betaTurn': 0x6080FF,
'betaStrand': 0xFFC800,
'coil': 0xFFFFFF,
'bend': 0x66D8C9 /* biting original color used 0x00FF00 */,
'turn': 0x00B266,
'dna': 0xAE00FE,
'rna': 0xFD0162,
'carbohydrate': 0xA6A6FA
});
const DefaultSecondaryStructureColor = (0, color_1.Color)(0x808080);
const Description = 'Assigns a color based on the type of secondary structure and basic molecule type.';
exports.SecondaryStructureColorThemeParams = {
saturation: param_definition_1.ParamDefinition.Numeric(-1, { min: -6, max: 6, step: 0.1 }),
lightness: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
colors: param_definition_1.ParamDefinition.MappedStatic('default', {
'default': param_definition_1.ParamDefinition.EmptyGroup(),
'custom': param_definition_1.ParamDefinition.Group((0, params_1.getColorMapParams)(SecondaryStructureColors))
})
};
function getSecondaryStructureColorThemeParams(ctx) {
return exports.SecondaryStructureColorThemeParams; // TODO return copy
}
function secondaryStructureColor(colorMap, unit, element, computedSecondaryStructure) {
let secStrucType = types_1.SecondaryStructureType.create(0 /* SecondaryStructureType.Flag.None */);
if (computedSecondaryStructure && structure_1.Unit.isAtomic(unit)) {
const secondaryStructure = computedSecondaryStructure.get(unit.invariantId);
if (secondaryStructure)
secStrucType = secondaryStructure.type[secondaryStructure.getIndex(unit.residueIndex[element])];
}
if (types_1.SecondaryStructureType.is(secStrucType, 2 /* SecondaryStructureType.Flag.Helix */)) {
if (types_1.SecondaryStructureType.is(secStrucType, 2048 /* SecondaryStructureType.Flag.Helix3Ten */)) {
return colorMap.threeTenHelix;
}
else if (types_1.SecondaryStructureType.is(secStrucType, 32768 /* SecondaryStructureType.Flag.HelixPi */)) {
return colorMap.piHelix;
}
return colorMap.alphaHelix;
}
else if (types_1.SecondaryStructureType.is(secStrucType, 4 /* SecondaryStructureType.Flag.Beta */)) {
return colorMap.betaStrand;
}
else if (types_1.SecondaryStructureType.is(secStrucType, 8 /* SecondaryStructureType.Flag.Bend */)) {
return colorMap.bend;
}
else if (types_1.SecondaryStructureType.is(secStrucType, 16 /* SecondaryStructureType.Flag.Turn */)) {
return colorMap.turn;
}
else {
const moleculeType = (0, util_1.getElementMoleculeType)(unit, element);
if (moleculeType === 7 /* MoleculeType.DNA */) {
return colorMap.dna;
}
else if (moleculeType === 6 /* MoleculeType.RNA */) {
return colorMap.rna;
}
else if (moleculeType === 9 /* MoleculeType.Saccharide */) {
return colorMap.carbohydrate;
}
else if (moleculeType === 5 /* MoleculeType.Protein */) {
return colorMap.coil;
}
}
return DefaultSecondaryStructureColor;
}
function SecondaryStructureColorTheme(ctx, props) {
const computedSecondaryStructure = ctx.structure && secondary_structure_1.SecondaryStructureProvider.get(ctx.structure);
const contextHash = computedSecondaryStructure ? (0, util_2.hash2)(computedSecondaryStructure.id, computedSecondaryStructure.version) : -1;
const colorMap = (0, color_2.getAdjustedColorMap)(props.colors.name === 'default' ? SecondaryStructureColors : props.colors.params, props.saturation, props.lightness);
function color(location) {
if (structure_1.StructureElement.Location.is(location)) {
return secondaryStructureColor(colorMap, location.unit, location.element, computedSecondaryStructure === null || computedSecondaryStructure === void 0 ? void 0 : computedSecondaryStructure.value);
}
else if (structure_1.Bond.isLocation(location)) {
return secondaryStructureColor(colorMap, location.aUnit, location.aUnit.elements[location.aIndex], computedSecondaryStructure === null || computedSecondaryStructure === void 0 ? void 0 : computedSecondaryStructure.value);
}
return DefaultSecondaryStructureColor;
}
return {
factory: SecondaryStructureColorTheme,
granularity: 'group',
preferSmoothing: true,
color,
props,
contextHash,
description: Description,
legend: (0, legend_1.TableLegend)(Object.keys(colorMap).map(name => {
return [name, colorMap[name]];
}).concat([['Other', DefaultSecondaryStructureColor]]))
};
}
exports.SecondaryStructureColorThemeProvider = {
name: 'secondary-structure',
label: 'Secondary Structure',
category: categories_1.ColorThemeCategory.Residue,
factory: SecondaryStructureColorTheme,
getParams: getSecondaryStructureColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.SecondaryStructureColorThemeParams),
isApplicable: (ctx) => !!ctx.structure,
ensureCustomProperties: {
attach: (ctx, data) => data.structure ? secondary_structure_1.SecondaryStructureProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
detach: (data) => data.structure && secondary_structure_1.SecondaryStructureProvider.ref(data.structure, false)
}
};