rdkit/Code/GraphMol/FileParsers/SmilesWriter.cpp

// $Id$
//
//  Copyright (C) 2003-2008  Greg Landrum and 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/BadFileException.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include "MolWriters.h"
#include "FileParsers.h"

#include <fstream>
#include <iostream>
#include <sstream>
#include <string>

namespace RDKit {
  
  SmilesWriter::SmilesWriter(const std::string &fileName, 
			     const std::string &delimiter,
			     const std::string &nameHeader,
			     bool includeHeader,
                             bool isomericSmiles,
                             bool kekuleSmiles) {
    if(fileName!= "-"){
      std::ofstream *tmpStream = new std::ofstream(fileName.c_str());
      if (!tmpStream || !(*tmpStream) || (tmpStream->bad()) ) {
        std::ostringstream errout;
        errout << "Bad output file " << fileName;
        throw BadFileException(errout.str());
      }
      dp_ostream = static_cast<std::ostream *>(tmpStream);
      df_owner = true;
    } else {
      dp_ostream = static_cast<std::ostream *>(&std::cout);
      df_owner=false;
    }
    this->init(delimiter,nameHeader,includeHeader,isomericSmiles,kekuleSmiles);
  }

  SmilesWriter::SmilesWriter(std::ostream *outStream, 
			     std::string delimiter,
			     std::string nameHeader,
			     bool includeHeader,
			     bool takeOwnership,
                             bool isomericSmiles,
                             bool kekuleSmiles) {
    PRECONDITION(outStream,"null stream");
    if (outStream->bad()){
      throw FileParseException("Bad output stream.");
    }

    dp_ostream = outStream;
    df_owner = takeOwnership;
    this->init(delimiter,nameHeader,includeHeader,isomericSmiles,kekuleSmiles);
  }
  void SmilesWriter::init(const std::string &delimiter,
			  const std::string &nameHeader,
			  bool includeHeader,
                          bool isomericSmiles,
                          bool kekuleSmiles){

    d_molid = 0;
    d_delim = delimiter;
    d_nameHeader=nameHeader;
    df_includeHeader=includeHeader;
    df_isomericSmiles=isomericSmiles;
    df_kekuleSmiles=kekuleSmiles;
    //these are set by the setProps function as required
    d_props.clear();
  }

  void SmilesWriter::setProps(const STR_VECT &propNames) {
    if (d_molid > 0) {
      BOOST_LOG(rdErrorLog) << "ERROR: Atleast one molecule has already been written\n";
      BOOST_LOG(rdErrorLog) << "ERROR: Cannot set properties now - ignoring setProps\n";
      return;
    }
    d_props = propNames;
  }

  void SmilesWriter::dumpHeader() const {
    CHECK_INVARIANT(dp_ostream,"no output stream");
    if(df_includeHeader){
      (*dp_ostream) << "SMILES" << d_delim;
      if(d_nameHeader!="") (*dp_ostream) << d_nameHeader << d_delim;

      if (d_props.size() > 0) {
	STR_VECT_CI pi = d_props.begin();
	(*dp_ostream) << (*pi);
	pi++;
	while (pi != d_props.end()) {
	  (*dp_ostream) << d_delim << (*pi);
	  pi++;
	}
      }
      (*dp_ostream) << "\n";
    }
  }

  SmilesWriter::~SmilesWriter() {
    
    if (df_owner) {
      // this has to be froma ofstream
      // cast it back to fstream and clsoe it
      //std::ofstream *tmpStream = static_cast<std::ofstream *>(dp_ostream);
      //tmpStream->close();
      delete dp_ostream;
    }
  }

  void SmilesWriter::write(const ROMol &mol,int confId) {
    RDUNUSED_PARAM(confId);
    CHECK_INVARIANT(dp_ostream,"no output stream");
    if(d_molid<=0 && df_includeHeader){
      dumpHeader();
    }
    
    std::string name = "";
    std::string smi = MolToSmiles(mol,df_isomericSmiles,df_kekuleSmiles);
    (*dp_ostream) << smi;
    if(d_nameHeader!=""){
      if (!mol.getPropIfPresent(common_properties::_Name, name) ||
          name.size()==0 ) {
        std::stringstream tstream;
        tstream << d_molid;
        name = tstream.str();
      }
    
      (*dp_ostream) << d_delim << name;
    }

    STR_VECT_CI pi;
    for (pi = d_props.begin(); pi != d_props.end(); pi++) {
      std::string pval;
      // FIX: we will assume that any property that the user requests is castable to
      // a std::string 
      if(mol.getPropIfPresent(*pi, pval)) {
        (*dp_ostream) << d_delim << pval;
      } else {
         (*dp_ostream) << d_delim << "";
      }
    }
    (*dp_ostream) << "\n";
    d_molid++;
  }

}