molstar
Version:
A comprehensive macromolecular library.
78 lines (77 loc) • 4.07 kB
JavaScript
/**
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
*
* Example command-line application generating images of PDB structures
* Build: npm install --no-save gl jpeg-js pngjs // these packages are not listed in dependencies for performance reasons
* npm run build
* Run: node lib/commonjs/examples/image-renderer 1cbs ../outputs_1cbs/
*/
import { ArgumentParser } from 'argparse';
import fs from 'fs';
import path from 'path';
import gl from 'gl';
import pngjs from 'pngjs';
import jpegjs from 'jpeg-js';
import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
import { ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif } from '../../mol-plugin-state/transforms/model';
import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
import { HeadlessPluginContext } from '../../mol-plugin/headless-plugin-context';
import { DefaultPluginSpec } from '../../mol-plugin/spec';
import { STYLIZED_POSTPROCESSING } from '../../mol-plugin/util/headless-screenshot';
import { setFSModule } from '../../mol-util/data-source';
setFSModule(fs);
function parseArguments() {
const parser = new ArgumentParser({ description: 'Example command-line application generating images of PDB structures' });
parser.add_argument('pdbId', { help: 'PDB identifier' });
parser.add_argument('outDirectory', { help: 'Directory for outputs' });
const args = parser.parse_args();
return { ...args };
}
async function main() {
const args = parseArguments();
const url = `https://www.ebi.ac.uk/pdbe/entry-files/download/${args.pdbId}.bcif`;
console.log('PDB ID:', args.pdbId);
console.log('Source URL:', url);
console.log('Outputs:', args.outDirectory);
// Create a headless plugin
const externalModules = { gl, pngjs, 'jpeg-js': jpegjs };
const plugin = new HeadlessPluginContext(externalModules, DefaultPluginSpec(), { width: 800, height: 800 });
await plugin.init();
// Download and visualize data in the plugin
const update = plugin.build();
const structure = update.toRoot()
.apply(Download, { url, isBinary: true })
.apply(ParseCif)
.apply(TrajectoryFromMmCif)
.apply(ModelFromTrajectory)
.apply(StructureFromModel);
const polymer = structure.apply(StructureComponent, { type: { name: 'static', params: 'polymer' } });
const ligand = structure.apply(StructureComponent, { type: { name: 'static', params: 'ligand' } });
polymer.apply(StructureRepresentation3D, {
type: { name: 'cartoon', params: { alpha: 1 } },
colorTheme: { name: 'sequence-id', params: {} },
});
ligand.apply(StructureRepresentation3D, {
type: { name: 'ball-and-stick', params: { sizeFactor: 1 } },
colorTheme: { name: 'element-symbol', params: { carbonColor: { name: 'element-symbol', params: {} } } },
sizeTheme: { name: 'physical', params: {} },
});
await update.commit();
// Export images
fs.mkdirSync(args.outDirectory, { recursive: true });
await plugin.saveImage(path.join(args.outDirectory, 'basic.png'));
await plugin.saveImage(path.join(args.outDirectory, 'basic.jpg'));
await plugin.saveImage(path.join(args.outDirectory, 'large.png'), { width: 1600, height: 1200 });
await plugin.saveImage(path.join(args.outDirectory, 'large.jpg'), { width: 1600, height: 1200 });
await plugin.saveImage(path.join(args.outDirectory, 'stylized.png'), undefined, STYLIZED_POSTPROCESSING);
await plugin.saveImage(path.join(args.outDirectory, 'stylized.jpg'), undefined, STYLIZED_POSTPROCESSING);
await plugin.saveImage(path.join(args.outDirectory, 'stylized-compressed-jpg.jpg'), undefined, STYLIZED_POSTPROCESSING, undefined, 10);
// Export state loadable in Mol* Viewer
await plugin.saveStateSnapshot(path.join(args.outDirectory, 'molstar-state.molj'));
// Cleanup
await plugin.clear();
plugin.dispose();
}
main();