molstar
Version:
A comprehensive macromolecular library.
99 lines (98 loc) • 4.84 kB
JavaScript
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Mat4 } from '../../mol-math/linear-algebra';
import { QueryContext, StructureSelection } from '../../mol-model/structure';
import { superpose } from '../../mol-model/structure/structure/util/superposition';
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { compile } from '../../mol-script/runtime/query/compiler';
import { StateTransforms } from '../../mol-plugin-state/transforms';
import { Asset } from '../../mol-util/assets';
export function buildStaticSuperposition(plugin, src) {
return plugin.dataTransaction(async () => {
for (const s of src) {
const { structure } = await loadStructure(plugin, `https://www.ebi.ac.uk/pdbe/static/entry/${s.pdbId}_updated.cif`, 'mmcif');
await transform(plugin, structure, s.matrix);
const chain = await plugin.builders.structure.tryCreateComponentFromExpression(structure, chainSelection(s.auth_asym_id), `Chain ${s.auth_asym_id}`);
if (chain)
await plugin.builders.structure.representation.addRepresentation(chain, { type: 'cartoon' });
}
});
}
export const StaticSuperpositionTestData = [
{
pdbId: '1aj5', auth_asym_id: 'A', matrix: Mat4.identity()
},
{
pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows([
[0.406, 0.879, 0.248, -200.633],
[0.693, -0.473, 0.544, 73.403],
[0.596, -0.049, -0.802, -14.209],
[0, 0, 0, 1]
])
},
{
pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows([
[-0.053, -0.077, 0.996, -45.633],
[-0.312, 0.949, 0.057, -12.255],
[-0.949, -0.307, -0.074, 53.562],
[0, 0, 0, 1]
])
}
];
export function dynamicSuperpositionTest(plugin, src, comp_id) {
return plugin.dataTransaction(async () => {
for (const s of src) {
await loadStructure(plugin, `https://www.ebi.ac.uk/pdbe/static/entry/${s}_updated.cif`, 'mmcif');
}
const pivot = MS.struct.filter.first([
MS.struct.generator.atomGroups({
'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), comp_id]),
'group-by': MS.struct.atomProperty.macromolecular.residueKey()
})
]);
const rest = MS.struct.modifier.exceptBy({
0: MS.struct.modifier.includeSurroundings({
0: pivot,
radius: 5
}),
by: pivot
});
const query = compile(pivot);
const xs = plugin.managers.structure.hierarchy.current.structures;
const selections = xs.map(s => StructureSelection.toLociWithCurrentUnits(query(new QueryContext(s.cell.obj.data))));
const transforms = superpose(selections);
await siteVisual(plugin, xs[0].cell, pivot, rest);
for (let i = 1; i < selections.length; i++) {
await transform(plugin, xs[i].cell, transforms[i - 1].bTransform);
await siteVisual(plugin, xs[i].cell, pivot, rest);
}
});
}
async function siteVisual(plugin, s, pivot, rest) {
const center = await plugin.builders.structure.tryCreateComponentFromExpression(s, pivot, 'pivot');
if (center)
await plugin.builders.structure.representation.addRepresentation(center, { type: 'ball-and-stick', color: 'residue-name' });
const surr = await plugin.builders.structure.tryCreateComponentFromExpression(s, rest, 'rest');
if (surr)
await plugin.builders.structure.representation.addRepresentation(surr, { type: 'ball-and-stick', color: 'uniform', size: 'uniform', sizeParams: { value: 0.33 } });
}
async function loadStructure(plugin, url, format, assemblyId) {
const data = await plugin.builders.data.download({ url: Asset.Url(url) });
const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
const model = await plugin.builders.structure.createModel(trajectory);
const structure = await plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : void 0);
return { data, trajectory, model, structure };
}
function chainSelection(auth_asym_id) {
return MS.struct.generator.atomGroups({
'chain-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.auth_asym_id(), auth_asym_id])
});
}
function transform(plugin, s, matrix) {
const b = plugin.state.data.build().to(s)
.insert(StateTransforms.Model.TransformStructureConformation, { transform: { name: 'matrix', params: { data: matrix, transpose: false } } });
return plugin.runTask(plugin.state.data.updateTree(b));
}