molstar
Version:
A comprehensive macromolecular library.
55 lines (54 loc) • 2.64 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 { PolymerTubeVisual, PolymerTubeParams } from '../visual/polymer-tube-mesh';
import { PolymerGapVisual, PolymerGapParams } from '../visual/polymer-gap-cylinder';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsRepresentation } from '../units-representation';
import { StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
import { Representation } from '../../../mol-repr/representation';
import { Unit } from '../../../mol-model/structure';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
const PuttyVisuals = {
'polymer-tube': (ctx, getParams) => UnitsRepresentation('Polymer tube mesh', ctx, getParams, PolymerTubeVisual),
'polymer-gap': (ctx, getParams) => UnitsRepresentation('Polymer gap cylinder', ctx, getParams, PolymerGapVisual),
};
export const PuttyParams = {
...PolymerTubeParams,
...PolymerGapParams,
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
visuals: PD.MultiSelect(['polymer-tube', 'polymer-gap'], PD.objectToOptions(PuttyVisuals)),
bumpFrequency: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
density: PD.Numeric(0.1, { min: 0, max: 1, step: 0.01 }, BaseGeometry.ShadingCategory),
};
export function getPuttyParams(ctx, structure) {
const params = PD.clone(PuttyParams);
let hasNucleotides = false;
let hasGaps = false;
structure.units.forEach(u => {
if (!hasNucleotides && Unit.isAtomic(u) && u.nucleotideElements.length)
hasNucleotides = true;
if (!hasGaps && u.gapElements.length)
hasGaps = true;
});
params.visuals.defaultValue = ['polymer-tube'];
if (hasGaps)
params.visuals.defaultValue.push('polymer-gap');
return params;
}
export function PuttyRepresentation(ctx, getParams) {
return Representation.createMulti('Putty', ctx, getParams, StructureRepresentationStateBuilder, PuttyVisuals);
}
export const PuttyRepresentationProvider = StructureRepresentationProvider({
name: 'putty',
label: 'Putty',
description: 'Displays a tube smoothly following the trace atoms of polymers.',
factory: PuttyRepresentation,
getParams: getPuttyParams,
defaultValues: PD.getDefaultValues(PuttyParams),
defaultColorTheme: { name: 'chain-id' },
defaultSizeTheme: { name: 'uncertainty' },
isApplicable: (structure) => structure.polymerResidueCount > 0,
});