Smiles.prototype.writeAtom = function()

in packages/ketcher-core/src/domain/serializers/smi/smiles.js [420:572]

• 87 lines of code
• 53 McCabe index (conditional complexity)

Smiles.prototype.writeAtom = function (
  mol,
  idx,
  aromatic,
  lowercase,
  chirality,
) {
  // eslint-disable-line max-params, max-statements
  const atom = mol.atoms.get(idx);
  let needBrackets = false;
  let hydro = -1;
  let aam = 0;

  /*
	if (mol.haveQueryAtoms())
	{
	  query_atom = &mol.getQueryAtom(idx);

	  if (query_atom->type == QUERY_ATOM_RGROUP)
	  {
		 if (mol.getRGroups()->isRGroupAtom(idx))
		 {
			const Array<int> &rg = mol.getRGroups()->getSiteRGroups(idx);

			if (rg.length != 1)
			   throw Error("rgroup count %d", rg.length);

			_output.printf("[&%d]", rg[0] + 1);
		 }
		 else
			_output.printf("[&%d]", 1);

		 return;
	  }
	}
	*/

  if (atom.label === 'A') {
    this.smiles += '*';
    return;
  }

  if (atom.label === 'R' || atom.label === 'R#') {
    this.smiles += '[*]';
    return;
  }

  // KETCHER-598 (Ketcher does not save AAM into reaction SMILES)
  // BEGIN
  //    if (this.atom_atom_mapping)
  //        aam = atom_atom_mapping[idx];
  aam = atom.aam;
  // END

  if (
    atom.label !== 'C' &&
    atom.label !== 'P' &&
    atom.label !== 'N' &&
    atom.label !== 'S' &&
    atom.label !== 'O' &&
    atom.label !== 'Cl' &&
    atom.label !== 'F' &&
    atom.label !== 'Br' &&
    atom.label !== 'B' &&
    atom.label !== 'I'
  ) {
    needBrackets = true;
  }

  if (
    atom.explicitValence >= 0 ||
    atom.radical !== 0 ||
    chirality > 0 ||
    (aromatic && atom.label !== 'C' && atom.label !== 'O') ||
    (aromatic &&
      atom.label === 'C' &&
      this.atoms[idx].neighbours.length < 3 &&
      this.atoms[idx].h_count === 0)
  ) {
    hydro = this.atoms[idx].h_count;
  }

  let label = atom.label;
  if (atom.atomList && !atom.atomList.notList) {
    label = atom.atomList.label();
    needBrackets = false; // atom list label already has brackets
  } else if (atom.isPseudo() || (atom.atomList && atom.atomList.notList)) {
    label = '*';
    needBrackets = false;
  } else if (
    chirality ||
    (atom.charge !== 0 && atom.charge !== null) ||
    atom.isotope > 0 ||
    hydro >= 0 ||
    aam > 0
  ) {
    needBrackets = true;
  }

  if (needBrackets) {
    if (hydro === -1) hydro = this.atoms[idx].h_count;
    this.smiles += '[';
  }

  if (atom.isotope > 0) this.smiles += atom.isotope;

  if (lowercase) this.smiles += label.toLowerCase();
  else this.smiles += label;

  if (chirality > 0) {
    if (chirality === 1) this.smiles += '@';
    // chirality == 2
    else this.smiles += '@@';

    if (atom.implicitH > 1) {
      throw new Error(atom.implicitH + ' implicit H near stereocenter');
    }
  }

  if (atom.label !== 'H') {
    if (hydro > 1 || (hydro === 0 && !needBrackets)) this.smiles += 'H' + hydro;
    else if (hydro === 1) this.smiles += 'H';
  }

  if (atom.charge > 1) this.smiles += '+' + atom.charge;
  else if (atom.charge < -1) this.smiles += atom.charge;
  else if (atom.charge === 1) this.smiles += '+';
  else if (atom.charge === -1) this.smiles += '-';

  if (aam > 0) this.smiles += ':' + aam;

  if (needBrackets) this.smiles += ']';

  /*
	if (mol.getRGroupFragment() != 0)
	{
	  for (i = 0; i < 2; i++)
	  {
		 int j;

		 for (j = 0; mol.getRGroupFragment()->getAttachmentPoint(i, j) != -1; j++)
			if (idx == mol.getRGroupFragment()->getAttachmentPoint(i, j))
			{
			   _output.printf("([*])");
			   break;
			}

		 if (mol.getRGroupFragment()->getAttachmentPoint(i, j) != -1)
			break;
	  }
	}
	*/
};