rdkit/Code/GraphMol/Depictor/Basement/DepictorDLL.cpp

//
//  Copyright (C) 2003-2006 Rational Discovery LLC
//
//   @@ 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 <RDGeneral/Invariant.h>

#include "Depictor.h"
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/RDLog.h>
#include <cstdlib>
namespace RDKit {
#ifdef WIN32_DLLBUILD
//*************************************************************************************
//
//  Uses the Depict DLL to generate a Mol file (on disk) for a
//  SMILES.
//
//  ARGUMENTS:
//    smi:     the SMILES string to be converted
//    fName:   the name of the output file
//    dllName: (OPTIONAL) the name of the actual DLL to be opened.  The path
//             to the DLL is taken from the environment (see below).
//
//  RETURNS:
//   1 on success, 0 otherwise
//
//  NOTES:
//   - To use the DLL, it's essential that the COMBICHEM_ROOT and
//   COMBICHEM_RELEASE
//     environment variables be set.  If this isn't done, this whole process
//     will fail.
//   - The Depict DLL is not re-entrant, which means it can't be used from
//   multiple
//     threads at the same time.  We're going to try and minimize this problem
//     by
//     leaving it open for as short a period of time as possible.
//     Still, opening the DLL may fail, in which case we'll return 0 for
//     failure.
//     You can always try again.
//
//*************************************************************************************
int SmilesToMolFileDLL(std::string smi, std::string fName,
                       std::string dllName) {
  // std::string dllName="c:/glandrum/dgen/combi/bin/depict32-0.dll";
  const char *root = getenv("COMBICHEM_ROOT");
  const char *release = getenv("COMBICHEM_RELEASE");
  if (!root || !release) {
    BOOST_LOG(rdErrorLog) << "ERROR: COMBICHEM_ROOT and COMBICHEM_RELEASE must "
                             "be set to use depictor\n";
    return 0;
  }
  std::string fullName = root;
  fullName += std::string("/") + release;
  fullName += std::string("/bin/") + dllName;

  Depictor_TwoArgFunc func1;
  HINSTANCE hDLL;
  hDLL = LoadLibrary(fullName.c_str());
  if (!hDLL) {
    BOOST_LOG(rdErrorLog) << "ERROR: could not load depict32.dll\n"
                          << std::endl;
    return 0;
  }
  func1 = (Depictor_TwoArgFunc)GetProcAddress(hDLL, "SMILESSTRINGTOMOLFILE");
  if (!func1) {
    FreeLibrary(hDLL);
    BOOST_LOG(rdErrorLog)
        << "ERROR: could not find SmilesToMolFile function in DLL\n"
        << std::endl;
    return 0;
  }
  func1(smi.c_str(), fName.c_str());

  FreeLibrary(hDLL);
  return 1;
}

//*************************************************************************************
//
//  Adds 2D coordinates to a molecule using the Depict.dll
//
//  ARGUMENTS:
//    mol:          the molecule to be altered
//    tempFilename: (OPTIONAL) the name of the temporary file
//
//  RETURNS:
//   1 on success, 0 otherwise
//
//  Here's the process by which this works (it's kind of contorted):
//   1) convert the mol to SMILES
//   2) use the DLL to convert the SMILES to a mol file (on disk)
//   3) parse the mol file into a temporary molecule
//   4) do a substructure match from the old molecule to the
//      temp one (which may have a different atom numbering or additional
//      atoms added).
//   5) Update the positions of the atoms on the old molecule.
//   6) Free the temp molecule.
//
//  NOTES:
//   - *FIX:* at the moment we're not doing anything to clear up the
//     temp file created in this process.  It'll always have the same
//     name unless the user explicitly asks that we do something different.
//   - To use the DLL, it's essential that the COMBICHEM_ROOT and
//   COMBICHEM_RELEASE
//     environment variables be set.  If this isn't done, this whole process
//     will fail.
//   - See the notes above about failures when opening the DLL.
//
//*************************************************************************************
int Add2DCoordsToMolDLL(ROMol &mol, std::string tempFilename) {
  std::string smi = MolToSmiles(mol, true);
  int tmp = SmilesToMolFileDLL(smi, tempFilename);
  int res = -1;
  if (tmp) {
    // build another mol from that mol file:
    RWMol *tmpMol = MolFileToMol(tempFilename, false);
    // match it up with the starting mol:
    //  (We need to do this because the depict.dll conversion
    //   to a mol file may have added Hs)
    MatchVectType matchVect;
    bool hasMatch = SubstructMatch(tmpMol, &mol, matchVect);
    if (hasMatch) {
      const Conformer &conf = tmpMol->getCoformer(0);
      Coformer *nconf = new Coformer(mol.getNumAtoms());
      for (MatchVectType::const_iterator mvi = matchVect.begin();
           mvi != matchVect.end(); mvi++) {
        nconf->setAtomPos(conf.getAtomPos(mvi->first));
      }
      confId = (int)mol.addConformer(nconf, true);
    }
    delete tmpMol;
  }
  return res;
}

#endif
}