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+/**
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+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ *
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+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
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+ */
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+
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+import * as argparse from 'argparse'
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+import createContext = require('gl')
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+import fs = require('fs')
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+import { PNG } from 'pngjs'
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+import { Canvas3D, Canvas3DParams } from 'mol-canvas3d/canvas3d';
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+import InputObserver from 'mol-util/input/input-observer';
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+import { ColorTheme } from 'mol-theme/color';
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+import { SizeTheme } from 'mol-theme/size';
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+import { CartoonRepresentationProvider } from 'mol-repr/structure/representation/cartoon';
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+import CIF, { CifFrame } from 'mol-io/reader/cif'
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+import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
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+import { Model, Structure } from 'mol-model/structure';
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+import { ajaxGet } from 'mol-util/data-source';
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+import { ColorNames } from 'mol-util/color/tables';
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+
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+const width = 1024
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+const height = 768
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+const gl = createContext(width, height, {
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+ alpha: false,
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+ antialias: true,
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+ depth: true,
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+ preserveDrawingBuffer: true
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+})
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+
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+const input = InputObserver.create()
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+const canvas3d = Canvas3D.create(gl, input, {
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+ multiSample: 'on',
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+ sampleLevel: 3,
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+ renderer: {
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+ ...Canvas3DParams.renderer.defaultValue,
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+ lightIntensity: 0,
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+ ambientIntensity: 1,
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+ backgroundColor: ColorNames.white
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+ },
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+ postprocessing: {
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+ ...Canvas3DParams.postprocessing.defaultValue,
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+ occlusionEnable: true,
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+ outlineEnable: true
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+ }
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+})
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+canvas3d.animate()
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+
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+const reprCtx = {
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+ wegbl: canvas3d.webgl,
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+ colorThemeRegistry: ColorTheme.createRegistry(),
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+ sizeThemeRegistry: SizeTheme.createRegistry()
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+}
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+function getCartoonRepr() {
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+ return CartoonRepresentationProvider.factory(reprCtx, CartoonRepresentationProvider.getParams)
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+}
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+
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+async function parseCif(data: string|Uint8Array) {
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+ const comp = CIF.parse(data);
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+ const parsed = await comp.run();
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+ if (parsed.isError) throw parsed;
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+ return parsed.result;
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+}
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+
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+async function downloadCif(url: string, isBinary: boolean) {
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+ const data = await ajaxGet({ url, type: isBinary ? 'binary' : 'string' }).run();
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+ return parseCif(data);
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+}
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+
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+async function downloadFromPdb(pdb: string) {
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+ const parsed = await downloadCif(`https://files.rcsb.org/download/${pdb}.cif`, false);
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+ // const parsed = await downloadCif(`https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${pdb}`, true);
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+ return parsed.blocks[0];
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+}
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+
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+async function getModels(frame: CifFrame) {
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+ return await trajectoryFromMmCIF(frame).run();
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+}
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+
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+async function getStructure(model: Model) {
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+ return Structure.ofModel(model);
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+}
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+
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+async function run(id: string, out: string) {
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+ try {
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+ const cif = await downloadFromPdb(id)
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+ const models = await getModels(cif)
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+ const structure = await getStructure(models[0])
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+
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+ const cartoonRepr = getCartoonRepr()
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+ cartoonRepr.setTheme({
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+ color: reprCtx.colorThemeRegistry.create('sequence-id', { structure }),
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+ size: reprCtx.sizeThemeRegistry.create('uniform', { structure })
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+ })
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+ await cartoonRepr.createOrUpdate({ ...CartoonRepresentationProvider.defaultValues, quality: 'auto' }, structure).run()
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+
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+ canvas3d.add(cartoonRepr)
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+ canvas3d.resetCamera()
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+ } catch (e) {
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+ console.log(e)
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+ process.exit(1)
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+ }
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+
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+ setTimeout(() => {
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+ const pixelData = canvas3d.getPixelData('draw')
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+ const png = new PNG({ width, height })
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+ png.data = Buffer.from(pixelData.array)
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+ png.pack().pipe(fs.createWriteStream(out)).on('finish', () => {
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+ process.exit()
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+ })
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+ }, 2000)
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+}
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+
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+//
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+
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+const parser = new argparse.ArgumentParser({
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+ addHelp: true,
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+ description: 'render image as PNG (work in progress)'
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+});
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+parser.addArgument([ '--id', '-i' ], {
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+ required: true,
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+ help: 'PDB ID'
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+});
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+parser.addArgument([ '--out', '-o' ], {
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+ required: true,
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+ help: 'image output path'
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+});
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+
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+interface Args {
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+ id: string
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+ out: string
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+}
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+const args: Args = parser.parseArgs();
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+
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+run(args.id, args.out)
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Alexander Rose