model.ts

/**
 * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @author David Sehnal <david.sehnal@gmail.com>
 */

import * as argparse from 'argparse'
require('util.promisify').shim();

import { CifFrame } from '../../mol-io/reader/cif'
import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from '../../mol-model/structure'
// import { Run, Progress } from '../../mol-task'
import { OrderedSet } from '../../mol-data/int';
import { openCif, downloadCif } from './helpers';
import { Vec3 } from '../../mol-math/linear-algebra';
import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';


async function downloadFromPdb(pdb: string) {
    // `https://files.rcsb.org/download/${pdb}.cif`
    const parsed = await downloadCif(`http://www.ebi.ac.uk/pdbe/static/entry/${pdb}_updated.cif`, false);
    return parsed.blocks[0];
}

export async function readCifFile(path: string) {
    const parsed = await openCif(path);
    return parsed.blocks[0];
}

export function atomLabel(model: Model, aI: number) {
    const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
    const { label_atom_id } = atoms
    const { label_comp_id, label_seq_id } = residues
    const { label_asym_id } = chains
    const rI = residueAtomSegments.index[aI]
    const cI = chainAtomSegments.index[aI]
    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`
}

export function residueLabel(model: Model, rI: number) {
    const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
    const { label_comp_id, label_seq_id } = residues
    const { label_asym_id } = chains
    const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]]
    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`
}

export function printSecStructure(model: Model) {
    console.log('\nSecondary Structure\n=============');
    const { residues } = model.atomicHierarchy;
    const { key, elements } = model.properties.secondaryStructure;

    const count = residues._rowCount;
    let rI = 0;
    while (rI < count) {
        let start = rI;
        while (rI < count && key[start] === key[rI]) rI++;
        rI--;

        const e = elements[key[start]];
        if (e.kind !== 'none') console.log(`${e.kind}: ${residueLabel(model, start)} - ${residueLabel(model, rI)}`);
        rI++;
    }
}

export function printLinks(structure: Structure, showIntra: boolean, showInter: boolean) {
    if (showIntra) {
        console.log('\nIntra Unit Links\n=============');
        for (const unit of structure.units) {