molstar
Version:
A comprehensive macromolecular library.
93 lines • 6.72 kB
JavaScript
;
/**
* Copyright (c) 2018-2020 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.ElementSymbolColorThemeProvider = exports.ElementSymbolColorTheme = exports.elementSymbolColor = exports.getElementSymbolColorThemeParams = exports.ElementSymbolColorThemeParams = exports.ElementSymbolColors = void 0;
var tslib_1 = require("tslib");
var color_1 = require("../../mol-util/color");
var structure_1 = require("../../mol-model/structure");
var param_definition_1 = require("../../mol-util/param-definition");
var legend_1 = require("../../mol-util/legend");
var color_2 = require("../../mol-util/color/color");
var chain_id_1 = require("./chain-id");
var operator_name_1 = require("./operator-name");
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
exports.ElementSymbolColors = (0, color_1.ColorMap)({
'H': 0xFFFFFF, 'D': 0xFFFFC0, 'T': 0xFFFFA0, 'HE': 0xD9FFFF, 'LI': 0xCC80FF, 'BE': 0xC2FF00, 'B': 0xFFB5B5, 'C': 0x909090, 'N': 0x3050F8, 'O': 0xFF0D0D, 'F': 0x90E050, 'NE': 0xB3E3F5, 'NA': 0xAB5CF2, 'MG': 0x8AFF00, 'AL': 0xBFA6A6, 'SI': 0xF0C8A0, 'P': 0xFF8000, 'S': 0xFFFF30, 'CL': 0x1FF01F, 'AR': 0x80D1E3, 'K': 0x8F40D4, 'CA': 0x3DFF00, 'SC': 0xE6E6E6, 'TI': 0xBFC2C7, 'V': 0xA6A6AB, 'CR': 0x8A99C7, 'MN': 0x9C7AC7, 'FE': 0xE06633, 'CO': 0xF090A0, 'NI': 0x50D050, 'CU': 0xC88033, 'ZN': 0x7D80B0, 'GA': 0xC28F8F, 'GE': 0x668F8F, 'AS': 0xBD80E3, 'SE': 0xFFA100, 'BR': 0xA62929, 'KR': 0x5CB8D1, 'RB': 0x702EB0, 'SR': 0x00FF00, 'Y': 0x94FFFF, 'ZR': 0x94E0E0, 'NB': 0x73C2C9, 'MO': 0x54B5B5, 'TC': 0x3B9E9E, 'RU': 0x248F8F, 'RH': 0x0A7D8C, 'PD': 0x006985, 'AG': 0xC0C0C0, 'CD': 0xFFD98F, 'IN': 0xA67573, 'SN': 0x668080, 'SB': 0x9E63B5, 'TE': 0xD47A00, 'I': 0x940094, 'XE': 0x940094, 'CS': 0x57178F, 'BA': 0x00C900, 'LA': 0x70D4FF, 'CE': 0xFFFFC7, 'PR': 0xD9FFC7, 'ND': 0xC7FFC7, 'PM': 0xA3FFC7, 'SM': 0x8FFFC7, 'EU': 0x61FFC7, 'GD': 0x45FFC7, 'TB': 0x30FFC7, 'DY': 0x1FFFC7, 'HO': 0x00FF9C, 'ER': 0x00E675, 'TM': 0x00D452, 'YB': 0x00BF38, 'LU': 0x00AB24, 'HF': 0x4DC2FF, 'TA': 0x4DA6FF, 'W': 0x2194D6, 'RE': 0x267DAB, 'OS': 0x266696, 'IR': 0x175487, 'PT': 0xD0D0E0, 'AU': 0xFFD123, 'HG': 0xB8B8D0, 'TL': 0xA6544D, 'PB': 0x575961, 'BI': 0x9E4FB5, 'PO': 0xAB5C00, 'AT': 0x754F45, 'RN': 0x428296, 'FR': 0x420066, 'RA': 0x007D00, 'AC': 0x70ABFA, 'TH': 0x00BAFF, 'PA': 0x00A1FF, 'U': 0x008FFF, 'NP': 0x0080FF, 'PU': 0x006BFF, 'AM': 0x545CF2, 'CM': 0x785CE3, 'BK': 0x8A4FE3, 'CF': 0xA136D4, 'ES': 0xB31FD4, 'FM': 0xB31FBA, 'MD': 0xB30DA6, 'NO': 0xBD0D87, 'LR': 0xC70066, 'RF': 0xCC0059, 'DB': 0xD1004F, 'SG': 0xD90045, 'BH': 0xE00038, 'HS': 0xE6002E, 'MT': 0xEB0026, 'DS': 0xFFFFFF, 'RG': 0xFFFFFF, 'CN': 0xFFFFFF, 'UUT': 0xFFFFFF, 'FL': 0xFFFFFF, 'UUP': 0xFFFFFF, 'LV': 0xFFFFFF, 'UUH': 0xFFFFFF
});
var DefaultElementSymbolColor = (0, color_1.Color)(0xFFFFFF);
var Description = 'Assigns a color to every atom according to its chemical element.';
// TODO generalise `carbonColor` param to all themes?
exports.ElementSymbolColorThemeParams = {
carbonColor: param_definition_1.ParamDefinition.MappedStatic('chain-id', {
'chain-id': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({}, chain_id_1.ChainIdColorThemeParams)),
'operator-name': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({}, operator_name_1.OperatorNameColorThemeParams)),
'element-symbol': param_definition_1.ParamDefinition.Group({})
}, { description: 'Use chain-id coloring for carbon atoms.' }),
saturation: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
lightness: param_definition_1.ParamDefinition.Numeric(0.2, { min: -6, max: 6, step: 0.1 })
};
function getElementSymbolColorThemeParams(ctx) {
return exports.ElementSymbolColorThemeParams; // TODO return copy
}
exports.getElementSymbolColorThemeParams = getElementSymbolColorThemeParams;
function elementSymbolColor(colorMap, element) {
var c = colorMap[element];
return c === undefined ? DefaultElementSymbolColor : c;
}
exports.elementSymbolColor = elementSymbolColor;
function ElementSymbolColorTheme(ctx, props) {
var colorMap = (0, color_2.getAdjustedColorMap)(exports.ElementSymbolColors, props.saturation, props.lightness);
var carbonColor = props.carbonColor.name === 'chain-id'
? (0, chain_id_1.ChainIdColorTheme)(ctx, props.carbonColor.params).color
: props.carbonColor.name === 'operator-name'
? (0, operator_name_1.OperatorNameColorTheme)(ctx, props.carbonColor.params).color
: undefined;
function elementColor(element, location) {
return (carbonColor && element === 'C')
? carbonColor(location, false)
: elementSymbolColor(colorMap, element);
}
function color(location) {
if (structure_1.StructureElement.Location.is(location)) {
if (structure_1.Unit.isAtomic(location.unit)) {
var type_symbol = location.unit.model.atomicHierarchy.atoms.type_symbol;
return elementColor(type_symbol.value(location.element), location);
}
}
else if (structure_1.Bond.isLocation(location)) {
if (structure_1.Unit.isAtomic(location.aUnit)) {
var type_symbol = location.aUnit.model.atomicHierarchy.atoms.type_symbol;
var element = type_symbol.value(location.aUnit.elements[location.aIndex]);
return elementColor(element, location);
}
}
return DefaultElementSymbolColor;
}
var granularity = props.carbonColor.name === 'operator-name' ? 'groupInstance' : 'group';
return {
factory: ElementSymbolColorTheme,
granularity: granularity,
preferSmoothing: true,
color: color,
props: props,
description: Description,
legend: (0, legend_1.TableLegend)(Object.keys(exports.ElementSymbolColors).map(function (name) {
return [name, exports.ElementSymbolColors[name]];
}))
};
}
exports.ElementSymbolColorTheme = ElementSymbolColorTheme;
exports.ElementSymbolColorThemeProvider = {
name: 'element-symbol',
label: 'Element Symbol',
category: "Atom Property" /* Atom */,
factory: ElementSymbolColorTheme,
getParams: getElementSymbolColorThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ElementSymbolColorThemeParams),
isApplicable: function (ctx) { return !!ctx.structure; }
};
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