// $Id$
//
//  Copyright (c) 2008, Novartis Institutes for BioMedical Research Inc.
//  All rights reserved.
// 
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// modification, are permitted provided that the following conditions are
// met: 
//
//     * Redistributions of source code must retain the above copyright 
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above
//       copyright notice, this list of conditions and the following 
//       disclaimer in the documentation and/or other materials provided 
//       with the distribution.
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//       nor the names of its contributors may be used to endorse or promote 
//       products derived from this software without specific prior
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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//  Created by Greg Landrum, Sept. 2006
//

#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SLNParse/SLNParse.h>
#include <GraphMol/SLNParse/SLNAttribs.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Invariant.h>
#include <boost/algorithm/string.hpp>
#include <boost/regex.hpp>


int yysln_parse (const char *,std::vector<RDKit::RWMol *>*,bool,void *);
int yysln_lex_init (void **);
void yysln_set_extra (void *,void *);
int yysln_lex_destroy (void *);
void setup_sln_string(const std::string &text,void *);
extern int yysln_debug; 

int sln_parse(const std::string &inp,
	      bool doQueries,
	      std::vector<RDKit::RWMol *> &molVect){
  void *scanner;
  TEST_ASSERT(!yysln_lex_init(&scanner));
  setup_sln_string(inp,scanner);
  yysln_set_extra((void *)doQueries,scanner);
  int res=yysln_parse(inp.c_str(),&molVect,doQueries,scanner);
  yysln_lex_destroy(scanner);
  return res;
}


namespace RDKit {
  namespace SLNParse {
    std::vector<RDKit::RWMol *> molList_g;

    void finalizeQueryMol(ROMol *mol,bool mergeHs){
      PRECONDITION(mol,"bad query molecule");

      // do we need to remove the Hs from the molecule?
      if(mergeHs){
        for(ROMol::AtomIterator atomIt=mol->beginAtoms();
            atomIt!=mol->endAtoms();++atomIt){
          // set a query for the H count:
          if((*atomIt)->getNumExplicitHs()){
            (*atomIt)->expandQuery(makeAtomHCountQuery((*atomIt)->getNumExplicitHs()));
          }
        }
      }

      // we don't want to sanitize, but we do need to get 
      // some ring info:
      VECT_INT_VECT sssr;
      MolOps::symmetrizeSSSR(*mol,sssr);
      int rootIdx=-1;
      for(ROMol::AtomIterator atomIt=mol->beginAtoms();
          atomIt!=mol->endAtoms();++atomIt){
        SLNParse::parseFinalAtomAttribs(*atomIt,true);
        if((*atomIt)->hasProp("_starred")){
          if(rootIdx>-1){
            BOOST_LOG(rdErrorLog)<<"SLN Error: mulitple starred atoms in a recursive query. Extra stars ignored" << std::endl;
          } else {
            rootIdx=(*atomIt)->getIdx();
          }
        }
      }
      if(rootIdx>-1){
        mol->setProp("_queryRootAtom",rootIdx);
      }
    }

    std::string replaceSLNMacroAtoms(std::string inp,int debugParse){
      const boost::regex defn("\\{(.+?):(.+?)\\}");
      const char *empty="";

      std::string res;
      // remove any macro definitions:
      res=boost::regex_replace(inp,defn,empty,boost::match_default|boost::format_all);

      if(res!=inp){
        // there are macro definitions, we're going to replace
        // the macro atoms in the input:
        std::string::const_iterator start, end;
        start=inp.begin();
        end=inp.end();
        boost::match_results<std::string::const_iterator> what; 
        boost::match_flag_type flags = boost::match_default; 
        while(regex_search(start, end, what, defn, flags)){
          std::string macroNm(what[1].first,what[1].second);
          std::string macroVal(what[2].first,what[2].second);
          res = boost::regex_replace(res,boost::regex(macroNm),macroVal.c_str(),
                                     boost::match_default|boost::format_all);
          // update search position: 
          start = what[0].second; 
          // update flags: 
          flags |= boost::match_prev_avail; 
          flags |= boost::match_not_bob;
        }
      }
      return res;
    }
    
    RWMol *toMol(std::string inp,bool doQueries,int debugParse){
      RWMol *res;
      inp = replaceSLNMacroAtoms(inp,debugParse);
      if(debugParse){
        std::cerr<<"****** PARSING SLN: ->"<<inp<<"<-"<<std::endl;
      }
      std::vector<RDKit::RWMol *> molVect;
      try {
        sln_parse(inp,doQueries,molVect);
        if(molVect.size()<=0){
          res = 0;
        } else {
          res = molVect[0];
	  molVect[0]=0;
          for(ROMol::BOND_BOOKMARK_MAP::const_iterator bmIt=res->getBondBookmarks()->begin();
              bmIt != res->getBondBookmarks()->end();++bmIt){
            if(bmIt->first>0 && bmIt->first<static_cast<int>(res->getNumAtoms())){
              std::stringstream err;
              err << "SLN Parser error: Ring closure " << bmIt->first << " does not have a corresponding opener.";
              throw SLNParseException(err.str());
            }
          }

        }
      } catch (SLNParseException &e) {
        BOOST_LOG(rdErrorLog) << e.message() << std::endl;
        res = 0;
      }
      if(res){
        // cleanup:
        res->clearAllAtomBookmarks();
        res->clearAllBondBookmarks();

        // set up the chirality flags as soon as the molecule is finished
        // since we'll be removing Hs later and that will break things:
        adjustAtomChiralities(res);
      }
      for(std::vector<RDKit::RWMol *>::iterator iter=molVect.begin();
	  iter!=molVect.end();++iter){
	if(*iter) delete *iter;
      }
      return res;
    };
  } // end of SLNParse namespace
  
  RWMol *SLNToMol(std::string sln,bool sanitize,int debugParse){
    // FIX: figure out how to reset lexer state
    yysln_debug = debugParse;
    // strip any leading/trailing whitespace:
    boost::trim_if(sln,boost::is_any_of(" \t\r\n"));

    RWMol *res = SLNParse::toMol(sln,false,debugParse);
    if(res){
      for(ROMol::AtomIterator atomIt=res->beginAtoms();
          atomIt!=res->endAtoms();++atomIt){
        SLNParse::parseFinalAtomAttribs(*atomIt,false);
      }
      if(sanitize){
        // we're going to remove explicit Hs from the graph,
        // this triggers a sanitization, so we do not need to
        // worry about doing one here:
        try{
          MolOps::removeHs(*res,false,false);
        } catch (...) {
          delete res;
          throw;
        }
      }
    }
    return res;
  };

  RWMol *SLNQueryToMol(std::string sln,bool mergeHs,int debugParse){
    yysln_debug = debugParse;
    // strip any leading/trailing whitespace:
    boost::trim_if(sln,boost::is_any_of(" \t\r\n"));
    RWMol *res = SLNParse::toMol(sln,true,debugParse);
    if(res){
      SLNParse::finalizeQueryMol(res,mergeHs);
    }
    return res;
  };
}