rdkit/Code/GraphMol/FileParsers/TplFileWriter.cpp

// $Id$
//
//  Copyright (C) 2007-2008 Greg Landrum
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//

#include "FileParsers.h"
#include <RDGeneral/RDLog.h>
#include <sstream>
#include <fstream>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>

namespace RDKit {
namespace TPLWriter {
void writeAtom(const ROMol &mol, unsigned int atomId,
               ROMol::ConstConformerIterator confIt, std::ostringstream &dest,
               std::string partialChargeProp) {
  const Atom *atom = mol.getAtomWithIdx(atomId);
  dest << atomId + 1;
  dest << " " << atom->getSymbol();
  dest << " " << atom->getFormalCharge();
  std::string propVal;
  if (atom->hasProp(partialChargeProp)) {
    atom->getProp(partialChargeProp, propVal);
  } else {
    propVal = "0.0";
  }
  dest << " " << propVal;

  const RDGeom::Point3D &pos = (*confIt)->getAtomPos(atomId);
  dest << " " << 100. * pos.x << " " << 100. * pos.y << " " << 100. * pos.z;

  ROMol::ADJ_ITER nbrIdx, endNbrs;
  boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(atom);
  dest << " " << (endNbrs - nbrIdx);
  while (nbrIdx != endNbrs) {
    dest << " " << (*nbrIdx + 1);
    ++nbrIdx;
  }

  // FIX: get this right:
  dest << " "
       << "U";

  dest << std::endl;
}

void writeBond(const ROMol &mol, unsigned int bondId,
               ROMol::ConstConformerIterator confIt, std::ostringstream &dest) {
  RDUNUSED_PARAM(confIt);
  const Bond *bond = mol.getBondWithIdx(bondId);
  dest << bondId + 1;
  std::string bondLabel;

  switch (bond->getBondType()) {
    case Bond::SINGLE:
      if (bond->getIsAromatic()) {
        bondLabel = "1.5";
      } else {
        bondLabel = "1.0";
      }
      break;
    case Bond::DOUBLE:
      if (bond->getIsAromatic()) {
        bondLabel = "1.5";
      } else {
        bondLabel = "2.0";
      }
      break;
    case Bond::AROMATIC:
      bondLabel = "1.5";
      break;
    case Bond::TRIPLE:
      bondLabel = "3.0";
      break;
    default:
      BOOST_LOG(rdWarningLog) << "TPL files only support single, double, "
                                 "aromatic, and triple bonds."
                              << std::endl;
      BOOST_LOG(rdWarningLog) << "Bond of with type " << bond->getBondType()
                              << " written as single in output." << std::endl;
      bondLabel = "1.0";
  }
  dest << " " << bondLabel;

  dest << " " << bond->getBeginAtomIdx() + 1 << " "
       << bond->getEndAtomIdx() + 1;

  // FIX: add these
  dest << " "
       << "0"
       << " "
       << "0";

  dest << std::endl;
}
}  // namespace TPLWriter

std::string MolToTPLText(const ROMol &mol, const std::string &partialChargeProp,
                         bool writeFirstConfTwice) {
  if (!mol.getNumConformers()) {
    BOOST_LOG(rdErrorLog)
        << "Cannot write molecules with no conformers to TPL files\n";
    return "";
  }
  std::ostringstream res;
  std::string tempStr;
  res << "BioCAD format, all rights reserved" << std::endl;
  res << "Output from RDKit" << std::endl;
  if (!mol.hasProp(common_properties::_Name)) {
    BOOST_LOG(rdWarningLog)
        << "Molecule has no name; arbitrary name assigned.\n";
    tempStr = "Unnamed molecule";
  } else {
    mol.getProp(common_properties::_Name, tempStr);
  }
  res << "NAME " << tempStr << std::endl;
  res << "PROP 7 1" << std::endl;
  res << mol.getNumAtoms() << " " << mol.getNumBonds() << std::endl;

  auto confIt = mol.beginConformers();
  // write the atoms:
  for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
    TPLWriter::writeAtom(mol, i, confIt, res, partialChargeProp);
  }

  // write the bonds:
  for (unsigned int i = 0; i < mol.getNumBonds(); ++i) {
    TPLWriter::writeBond(mol, i, confIt, res);
  }

  // write the additional conformations:
  res << "CONFS " << mol.getNumConformers() - 1 << std::endl;
  if (!writeFirstConfTwice) {
    ++confIt;
  }
  while (confIt != mol.endConformers()) {
    std::stringstream tmpStrm;
    std::string confName;

    tmpStrm << "conformer_" << (*confIt)->getId();
    confName = tmpStrm.str();
    res << "NAME " << confName << std::endl;

    for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
      const RDGeom::Point3D &pos = (*confIt)->getAtomPos(i);
      res << " " << 100. * pos.x << " " << 100. * pos.y << " " << 100. * pos.z
          << std::endl;
    }
    ++confIt;
    if (confIt != mol.endConformers()) {
      res << std::endl;
    }
  }

  return res.str();
}

void MolToTPLFile(const ROMol &mol, const std::string &fName,
                  const std::string &partialChargeProp,
                  bool writeFirstConfTwice) {
  auto *outStream = new std::ofstream(fName.c_str());
  if (!(*outStream) || outStream->bad()) {
    delete outStream;
    std::ostringstream errout;
    errout << "Bad output file " << fName;
    throw BadFileException(errout.str());
  }

  std::string outString =
      MolToTPLText(mol, partialChargeProp, writeFirstConfTwice);
  *outStream << outString;
  delete outStream;
}
}  // namespace RDKit