_parseATOM()

in packages/miew/src/io/parsers/PDBParser.js [159:213]

• 39 lines of code
• 14 McCabe index (conditional complexity)

  _parseATOM(stream) {
    if (this._modelId !== 1) {
      return;
    }

    /* eslint-disable no-magic-numbers */
    const het = stream.readCharCode(1) === 0x48;

    // field names according to wwPDB Format
    // NOTE: Chimera allows (nonstandard) use of columns 6-11 for the integer atom serial number in ATOM records.
    const serial = het ? stream.readInt(7, 11) : stream.readInt(6, 11);
    let name = stream.readString(13, 16);
    const altLoc = stream.readChar(17);
    const resName = stream.readString(18, 20).trim();
    const chainID = stream.readChar(22);
    const resSeq = stream.readInt(23, 26);
    const iCode = stream.readChar(27);
    const x = stream.readFloat(31, 38);
    const y = stream.readFloat(39, 46);
    const z = stream.readFloat(47, 54);
    const occupancy = stream.readFloat(55, 60);
    const tempFactor = stream.readFloat(61, 66);
    const element = stream.readString(77, 78).trim() || nameToElement(name);
    const charge = stream.readInt(79, 80) || 0;
    /* eslint-enable no-magic-numbers */
    // skip waters (there may be lots of them)
    if (this.settings.now.nowater) {
      if (resName === 'HOH' || resName === 'WAT') {
        return;
      }
    }

    // PDB uses positional system for atom names. It helps derive element type from the name
    // but names may include extra spaces. From this point on we don't need those spaces anymore.
    name = name.trim();

    const type = Element.getByName(element);
    const role = Element.Role[name]; // FIXME: Maybe should use type as additional index (" CA " vs. "CA  ")

    // NOTE: Residues of a particular chain are not required to be listed next to each other.
    // https://github.com/biasmv/pv/commit/7319b898b7473ba380c26699e3b028b2b1a7e1a1
    let chain = this._chain;
    if (!chain || chain.getName() !== chainID) {
      this._chain = chain = this._complex.getChain(chainID) || this._complex.addChain(chainID);
      this._residue = null;
    }

    let residue = this._residue;
    if (!residue || residue.getSequence() !== resSeq || residue.getICode() !== iCode) {
      this._residue = residue = chain.addResidue(resName, resSeq, iCode);
    }

    const xyz = new THREE.Vector3(x, y, z);
    residue.addAtom(name, type, xyz, role, het, serial, altLoc, occupancy, tempFactor, charge);
  }