_extractAtoms()

in packages/miew/src/io/parsers/PubChemParser.js [37:76]

• 35 lines of code
• 27 McCabe index (conditional complexity)

  _extractAtoms(complex, complexData) {
    let aids = complexData.atoms && complexData.atoms.aid;
    let elements = aids && complexData.atoms.element;
    if (!elements || aids.length !== elements.length) {
      throw new Error('Unable to parse atom elements');
    }
    elements = _.fromPairs(_.zip(aids, elements));
    const atoms = {};

    const coords = complexData.coords && complexData.coords[0];
    const model = coords && coords.conformers && coords.conformers[0];
    const xs = model && model.x;
    const ys = model && model.y;
    const zs = (model && model.z) || [];
    aids = coords && coords.aid;
    if (!aids || !xs || !ys) {
      throw new Error('Coordinates are not found in the file');
    }

    const chain = complex.addChain(' ');
    const residue = chain.addResidue('UNK', 1, ' ');

    for (let i = 0, n = aids.length; i < n; ++i) {
      const aid = aids[i];
      const element = Element.ByAtomicNumber[elements[aid]];
      const xyz = new THREE.Vector3(xs[i], ys[i], zs[i] || 0.0);
      atoms[aid] = residue.addAtom(element.name, element, xyz, undefined, true, aid, ' ', 1.0, 0.0, 0);
    }

    const aids1 = complexData.bonds && complexData.bonds.aid1;
    const aids2 = complexData.bonds && complexData.bonds.aid2;
    const orders = (complexData.bonds && complexData.bonds.order) || [];
    if (!aids1 || !aids2 || aids1.length !== aids2.length) {
      return;
    }

    for (let j = 0, m = aids1.length; j < m; ++j) {
      complex.addBond(atoms[aids1[j]], atoms[aids2[j]], orders[j] || 1, 0, true);
    }
  }