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Viewing changes to Code/GraphMol/SmilesParse/SmilesWrite.cpp

  • Committer: Package Import Robot
  • Author(s): Michael Banck
  • Date: 2012-05-18 15:09:10 UTC
  • mfrom: (2.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20120518150910-0wavbii0kr13pifa
Tags: 201203-1
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Code/GraphMol/SmilesParse/SmilesWrite.cpp
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// $Id: SmilesWrite.cpp 1775 2011-07-01 03:42:35Z glandrum $
 
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// $Id: SmilesWrite.cpp 2004 2012-03-26 03:12:37Z glandrum $
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//
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//  Copyright (C) 2002-2010 Greg Landrum and Rational Discovery LLC
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//
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      return res.str();
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    }
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    std::string GetBondSmiles(const Bond *bond,int atomToLeftIdx,bool doKekule){
 
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    std::string GetBondSmiles(const Bond *bond,int atomToLeftIdx,bool doKekule,bool allBondsExplicit){
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      PRECONDITION(bond,"bad bond");
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      if(atomToLeftIdx<0) atomToLeftIdx=bond->getBeginAtomIdx();
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          // FIX: we should be able to dump kekulized smiles
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          //   currently this is possible by removing all
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          //   isAromatic flags, but there should maybe be another way
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          if( aromatic && !bond->getIsAromatic() ) res << "-";
 
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          if(allBondsExplicit) res<<"-";
 
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          else if( aromatic && !bond->getIsAromatic() ) res << "-";
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        }
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        break;
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      case Bond::DOUBLE:
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            break;
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          }
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        }
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        if(!aromatic) res << ":";
 
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        if(allBondsExplicit) res << ":";
 
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        else if(!aromatic) res << ":";
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        break;
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      case Bond::DATIVE:
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        if(atomToLeftIdx>=0 &&
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    std::string FragmentSmilesConstruct(ROMol &mol,int atomIdx,
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                                        std::vector<Canon::AtomColors> &colors,
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                                        INT_VECT &ranks,bool doKekule){
 
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                                        INT_VECT &ranks,bool doKekule,bool canonical,
 
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                                        bool allBondsExplicit){
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      Canon::MolStack molStack;
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      // try to prevent excessive reallocation
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      std::map<int,int> ringClosureMap;
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      int ringIdx,closureVal;
 
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      if(!canonical) mol.setProp("_StereochemDone",1);
 
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      Canon::canonicalizeFragment(mol,atomIdx,colors,ranks,
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                                  molStack);
 
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                                    molStack);
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      Bond *bond=0;
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      BOOST_FOREACH(Canon::MolStackElem mSE,molStack){
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        switch(mSE.type){
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        case Canon::MOL_STACK_BOND:
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          bond = mSE.obj.bond;
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          //std::cout<<"\t\tBond: "<<bond->getIdx()<<std::endl;
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          res << GetBondSmiles(bond,mSE.number,doKekule);
 
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          res << GetBondSmiles(bond,mSE.number,doKekule,allBondsExplicit);
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          break;
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        case Canon::MOL_STACK_RING:
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          ringIdx = mSE.number;
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  // decisions and I'm gonna want to smack myself for doing this,
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  // but we'll try anyway.
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  std::string MolToSmiles(ROMol &mol,bool doIsomericSmiles,
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                          bool doKekule,int rootedAtAtom,bool canonical){
 
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                          bool doKekule,int rootedAtAtom,bool canonical,
 
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                          bool allBondsExplicit){
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    PRECONDITION(rootedAtAtom<0||static_cast<unsigned int>(rootedAtAtom)<mol.getNumAtoms(),
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                 "rootedAtomAtom must be less than the number of atoms");
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    if(!mol.getNumAtoms()) return "";
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    std::string res;
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    for(ROMol::AtomIterator atIt=tmol.beginAtoms();atIt!=tmol.endAtoms();atIt++){
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      (*atIt)->updatePropertyCache();
 
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      (*atIt)->updatePropertyCache(false);
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    }
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    unsigned int nAtoms=tmol.getNumAtoms();
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      CHECK_INVARIANT(nextAtomIdx>=0,"no start atom found");
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      subSmi = SmilesWrite::FragmentSmilesConstruct(tmol, nextAtomIdx, colors,
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                                                    ranks,doKekule);
 
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                                                    ranks,doKekule,canonical,allBondsExplicit);
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      res += subSmi;
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      colorIt = std::find(colors.begin(),colors.end(),Canon::WHITE_NODE);