molstar
Version:
A comprehensive macromolecular library.
69 lines (68 loc) • 4.05 kB
JavaScript
/**
* Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Representation } from '../../../mol-repr/representation';
import { Structure } from '../../../mol-model/structure';
import { UnitsRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
import { EllipsoidMeshParams, EllipsoidMeshVisual, StructureEllipsoidMeshVisual } from '../visual/ellipsoid-mesh';
import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property/anisotropic';
import { IntraUnitBondCylinderParams, IntraUnitBondCylinderVisual, StructureIntraUnitBondCylinderVisual } from '../visual/bond-intra-unit-cylinder';
import { InterUnitBondCylinderVisual, InterUnitBondCylinderParams } from '../visual/bond-inter-unit-cylinder';
import { getUnitKindsParam } from '../params';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
const EllipsoidVisuals = {
'ellipsoid-mesh': (ctx, getParams) => UnitsRepresentation('Ellipsoid Mesh', ctx, getParams, EllipsoidMeshVisual),
'intra-bond': (ctx, getParams) => UnitsRepresentation('Intra-unit bond cylinder', ctx, getParams, IntraUnitBondCylinderVisual),
'inter-bond': (ctx, getParams) => ComplexRepresentation('Inter-unit bond cylinder', ctx, getParams, InterUnitBondCylinderVisual),
'structure-ellipsoid-mesh': (ctx, getParams) => ComplexRepresentation('Structure Ellipsoid Mesh', ctx, getParams, StructureEllipsoidMeshVisual),
'structure-intra-bond': (ctx, getParams) => ComplexRepresentation('Structure intra-unit bond cylinder', ctx, getParams, StructureIntraUnitBondCylinderVisual),
};
export const EllipsoidParams = {
...EllipsoidMeshParams,
...IntraUnitBondCylinderParams,
...InterUnitBondCylinderParams,
includeParent: PD.Boolean(false),
adjustCylinderLength: PD.Boolean(false, { isHidden: true }), // not useful here
unitKinds: getUnitKindsParam(['atomic']),
sizeFactor: PD.Numeric(1, { min: 0.01, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }),
linkCap: PD.Boolean(true),
visuals: PD.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], PD.objectToOptions(EllipsoidVisuals)),
bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
};
export function getEllipsoidParams(ctx, structure) {
let params = EllipsoidParams;
const size = Structure.getSize(structure);
if (size >= Structure.Size.Huge) {
params = PD.clone(params);
params.visuals.defaultValue = ['ellipsoid-mesh', 'intra-bond'];
}
else if (structure.unitSymmetryGroups.length > 5000) {
params = PD.clone(params);
params.visuals.defaultValue = ['structure-ellipsoid-mesh', 'structure-intra-bond'];
}
return params;
}
export function EllipsoidRepresentation(ctx, getParams) {
return Representation.createMulti('Ellipsoid', ctx, getParams, StructureRepresentationStateBuilder, EllipsoidVisuals);
}
export const EllipsoidRepresentationProvider = StructureRepresentationProvider({
name: 'ellipsoid',
label: 'Ellipsoid',
description: 'Displays anisotropic displacement ellipsoids of atomic elements plus bonds as cylinders.',
factory: EllipsoidRepresentation,
getParams: getEllipsoidParams,
defaultValues: PD.getDefaultValues(EllipsoidParams),
defaultColorTheme: { name: 'element-symbol' },
defaultSizeTheme: { name: 'uniform' },
isApplicable: (structure) => structure.elementCount > 0 && structure.models.some(m => AtomSiteAnisotrop.Provider.isApplicable(m)),
getData: (structure, props) => {
return props.includeParent ? structure.asParent() : structure;
},
mustRecreate: (oldProps, newProps) => {
return oldProps.includeParent !== newProps.includeParent;
}
});