_parseSTRUCTURE()

in packages/miew/src/io/parsers/PDBParser.js [312:382]

• 64 lines of code
• 7 McCabe index (conditional complexity)

  _parseSTRUCTURE(stream, pars, adder) {
    const startId = 0;
    const startIndex = 1;
    const endId = 2;
    const endIndex = 3;

    // identify fields: debugging and stuff
    /* eslint-disable no-magic-numbers */
    const codeOfS = 0x53;
    const serialNumber = stream.readInt(8, 10);
    const structureName = stream.readString(12, 14).trim(); // FIXME: LString(3) forbids trim()
    const comment = stream.readString(41, 70).trim();
    const helLength = stream.readInt(72, 76);
    const helixClass = stream.readInt(39, 40);
    const shWidth = stream.readInt(15, 16);
    const shCur = stream.readInt(42, 45);
    const shPrev = stream.readInt(57, 60);
    /* eslint-enable no-magic-numbers */
    // file fields
    const startChainID = stream.readString(pars[startId], pars[endId] + 1).charCodeAt(0);
    const endChainID = stream.readString(pars[endId], pars[endId] + 1).charCodeAt(0);
    const startSequenceNumber = stream.readInt(pars[startIndex], pars[startIndex] + 3);
    let iCodeStr = stream.readString(pars[startIndex] + 4, pars[startIndex] + 4);
    let startICode = 0;

    if (iCodeStr.length > 0) {
      startICode = iCodeStr.charCodeAt(0);
    }
    const endSequenceNumber = stream.readInt(pars[endIndex], pars[endIndex] + 3);
    iCodeStr = stream.readString(pars[endIndex] + 4, pars[endIndex] + 4);
    let endICode = 0;
    if (iCodeStr.length > 0) {
      endICode = iCodeStr.charCodeAt(0);
    }

    let obj;
    let cs = this._sheet;
    if (stream.readCharCode(1) === codeOfS) {
      if (cs !== null && cs.getName() !== structureName) {
        cs = null;
        this._sheet = null;
      }
      if (cs === null) {
        this._sheet = obj = new Sheet(structureName, shWidth);
        adder(obj);
      } else {
        obj = cs;
      }
      const strand = new Strand(
        obj,
        this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),
        this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),
        helixClass,
        shCur,
        shPrev,
      );
      obj.addStrand(strand);
      this._complex.structures.push(strand);
    } else {
      obj = new Helix(
        helixClass,
        this._complex.getUnifiedSerial(startChainID, startSequenceNumber, startICode),
        this._complex.getUnifiedSerial(endChainID, endSequenceNumber, endICode),
        serialNumber,
        structureName,
        comment,
        helLength,
      );
      adder(obj);
    }
  }