top.ts

/**
 * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

import { Column, Table } from '../../mol-data/db';
import { TopFile } from '../../mol-io/reader/top/parser';
import { getMoleculeType, MoleculeType } from '../../mol-model/structure/model/types';
import { Topology } from '../../mol-model/structure/topology/topology';
import { Task } from '../../mol-task';
import { ModelFormat } from '../format';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
import { getChainId } from './common/util';
import { guessElementSymbolString } from './util';

function getBasic(top: TopFile) {
    const { molecules, compounds } = top;

    const singleResidue: Record<string, boolean> = {};
    let atomCount = 0;

    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
        const mol = molecules.compound.value(i);
        const count = molecules.molCount.value(i);
        const { atoms } = compounds[mol];

        Column.asArrayColumn(atoms.atom);
        Column.asArrayColumn(atoms.resnr);
        Column.asArrayColumn(atoms.residu);

        atomCount += count * atoms._rowCount;

        let prevResnr = atoms.resnr.value(0);
        singleResidue[mol] = true;
        for (let j = 1, jl = atoms._rowCount; j < jl; ++j) {
            const resnr = atoms.resnr.value(j);
            if (resnr !== prevResnr) {
                singleResidue[mol] = false;
                break;
            }
            prevResnr = resnr;
        }
    }

    //

    const atomNames = new Array<string>(atomCount);
    const residueIds = new Uint32Array(atomCount);
    const residueNames = new Array<string>(atomCount);

    let k = 0;
    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
        const mol = molecules.compound.value(i);
        const count = molecules.molCount.value(i);
        const { atoms } = compounds[mol];
        const isSingleResidue = singleResidue[mol];
        for (let j = 0; j < count; ++j) {
            for (let l = 0, ll = atoms._rowCount; l < ll; ++l) {
                atomNames[k] = atoms.atom.value(l);
                residueIds[k] = atoms.resnr.value(l);
                residueNames[k] = atoms.residu.value(l);

                if (isSingleResidue) residueIds[k] += j;

                k += 1;
            }
        }