molstar
Version:
A comprehensive macromolecular library.
70 lines (69 loc) • 2.66 kB
JavaScript
;
/**
* Copyright (c) 2018 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.PhysicalSizeThemeProvider = exports.PhysicalSizeThemeParams = void 0;
exports.getPhysicalSizeThemeParams = getPhysicalSizeThemeParams;
exports.getPhysicalRadius = getPhysicalRadius;
exports.PhysicalSizeTheme = PhysicalSizeTheme;
const structure_1 = require("../../mol-model/structure");
const atomic_1 = require("../../mol-model/structure/model/properties/atomic");
const param_definition_1 = require("../../mol-util/param-definition");
const DefaultSize = 1;
const Description = 'Assigns a physical size, i.e. vdW radius for atoms or given radius for coarse spheres.';
exports.PhysicalSizeThemeParams = {
scale: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 5, step: 0.1 })
};
function getPhysicalSizeThemeParams(ctx) {
return exports.PhysicalSizeThemeParams; // TODO return copy
}
function getPhysicalRadius(unit, element) {
if (structure_1.Unit.isAtomic(unit)) {
return (0, atomic_1.VdwRadius)(unit.model.atomicHierarchy.atoms.type_symbol.value(element));
}
else if (structure_1.Unit.isSpheres(unit)) {
return unit.model.coarseConformation.spheres.radius[element];
}
else {
return 0;
}
}
/**
* Create attribute data with the physical size of an element,
* i.e. vdw for atoms and radius for coarse spheres
*/
function PhysicalSizeTheme(ctx, props) {
const scale = props.scale === void 0 ? 1 : props.scale;
function size(location) {
let size;
if (structure_1.StructureElement.Location.is(location)) {
size = scale * getPhysicalRadius(location.unit, location.element);
}
else if (structure_1.Bond.isLocation(location)) {
size = scale * Math.min(getPhysicalRadius(location.aUnit, location.aUnit.elements[location.aIndex]), getPhysicalRadius(location.bUnit, location.bUnit.elements[location.bIndex]));
}
else {
size = scale * DefaultSize;
}
return size;
}
return {
factory: PhysicalSizeTheme,
granularity: 'group',
size,
props,
description: Description
};
}
exports.PhysicalSizeThemeProvider = {
name: 'physical',
label: 'Physical',
category: '',
factory: PhysicalSizeTheme,
getParams: getPhysicalSizeThemeParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.PhysicalSizeThemeParams),
isApplicable: (ctx) => !!ctx.structure
};