src/openbabel/kekulize.cpp

/**********************************************************************
kekulize.cpp - Alternate algorithm to kekulize a molecule.

Copyright (C) 2004-2005 by Fabien Fontaine
Some portions Copyright (C) 2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#include "mol.hpp"
#include "oberror.hpp"

#ifdef HAVE_SSTREAM
#include <sstream>
#else
#include <strstream>
#endif

#define SINGLE 1
#define DOUBLE 2

using namespace std;

namespace OpenBabel {

///////////////////////////////////////////////////////////////////////////////
//! \brief Kekulize aromatic rings without using implicit valence

//! This new perceive kekule bonds function has been especifically designed to 
//! handle molecule files without explicit hydrogens such as pdb or xyz.
//! The function does not rely on GetImplicitValence function
//! The function looks for groups of aromatic cycle 
//! For each group it tries to guess the number of electrons given by each atom
//! in order to satisfy the huckel (4n+2) rule
//! If the huckel rule cannot be satisfied the algorithm try with its best alternative guess
//! Then it recursively walk on the atoms of the cycle and assign single and double bonds
void OBMol::NewPerceiveKekuleBonds() 
{

  if (HasKekulePerceived())  return;
  SetKekulePerceived();

  OBAtom *atom;
  int n, de, minde;
  std::vector<OBAtom*> cycle;
  OBBitVec avisit,cvisit;
  avisit.Resize(NumAtoms()+1);
  cvisit.Resize(NumAtoms()+1);
  OBBond *bond;
  std::vector<OBEdgeBase*>::iterator bi;
  std::vector<int> electron;
  int BO;
  int sume, orden, bestorden, bestatom;
  // Init the kekulized bonds
  unsigned i;
        for(i=0; i< NumBonds(); i++ ) {
    bond = GetBond(i);
    BO = bond->GetBO();
    switch (BO)
    {
    case 1: bond->SetKSingle(); break;
    case 2: bond->SetKDouble(); break;
    case 3: bond->SetKTriple(); break;
    }
  }

  // Find all the groups of aromatic cycle
  for(i=1; i<= NumAtoms(); i++ ) {
    atom = GetAtom(i);
    if (atom->HasAromaticBond() && !cvisit[i]) { // is new aromatic atom of an aromatic cycle ?

      avisit.Clear();
      electron.clear();
      cycle.clear();
      
      avisit.SetBitOn(i);
      expandcycle (atom, avisit);
      //store the atoms of the cycle(s)
      unsigned int j;
      for(j=1; j<= NumAtoms(); j++) {
        if ( avisit[j] ) {
          atom = GetAtom(j);
          cycle.push_back(atom);
        }
      }
      // At the begining each atom give one electron to the cycle
      for(j=0; j< cycle.size(); j++) {
        electron.push_back(1);
      }
      
      // remove one electron if the atom make a double bond out of the cycle
      sume =0;
      for(j=0; j< cycle.size(); j++) {
        atom = cycle[j];
        for(bond = atom->BeginBond(bi); bond; bond = atom->NextBond(bi)) {
          if ( bond->IsDouble() ) {
            OBAtom *atom2 = bond->GetNbrAtom(atom);
            int fcharge = atom->GetFormalCharge();
            int fcharge2 = atom2->GetFormalCharge();
            if(atom->IsNitrogen() && atom2->IsOxygen() 
               && fcharge == 0 && fcharge2 == 0) { //n=O to [n+][O-]
              atom->SetFormalCharge(1);
              atom2->SetFormalCharge(-1);
              bond->SetKSingle();
              bond->SetBO(1);
            }
            else {
              electron[j] = 0;
            }
          }
        }
        // count the number of electrons
        sume += electron[j];
      }


      // Save the electron state in case huckel rule is not satisfied
      vector<int> previousElectron = electron;

      // find the ideal number of electrons according to the huckel 4n+2 rule
      minde=99;
      for (i=1; 1; i++) {
        n = 4 *i +2;
        de = n - sume;
        if (  de < minde )
          minde=de;
        else if ( minde < 0 )
          minde=de;
        else
          break;
      }
      
#ifdef HAVE_SSTREAM
    stringstream errorMsg;
#else
    strstream errorMsg;
#endif

      //cout << "minde before:" << minde << endl;
      // if huckel rule not satisfied some atoms must give more electrons
      //cout << "minde " << minde << endl;
      while ( minde != 0 ) {
        bestorden=99;
        for(j=0; j< cycle.size(); j++) {
          if (electron[j] == 1) {
            orden = getorden(cycle[j]);
            if (orden < bestorden) {
              bestorden = orden;
              bestatom = j;
            }
          }
        }
        if (bestorden==99) {  // no electron giving atom found
          errorMsg << "Kekulize: Huckel rule not satisfied for molecule " << GetTitle() << endl;
          obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
          break;             // Huckel rule cannot be satisfied
        }                    // try to kekulize anyway
        else {
          electron[bestatom] += 1;
          minde--;
        }
      }

      if (bestorden == 99) { // Huckel rule not satisfied, just try to get an even number of electron before kekulizing
        
        electron = previousElectron; // restore electon's state
        
        int odd = sume % 2; 
        //cout << "odd:" << odd << endl;
        if(odd) { // odd number of electrons try to add an electron to the best possible atom
          for(j=0; j< cycle.size(); j++) {
            if (electron[j] == 1) {
              orden = getorden(cycle[j]);
              if (orden < bestorden) {
                bestorden = orden;
                bestatom = j;
              }
            }
          }
          if (bestorden==99) {  // no electron giving atom found
            errorMsg << "Kekulize: Cannot get an even number of electron for molecule " << GetTitle() << "\n";
          obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
            break;             // impossible to choose an atom to obtain an even number of electron
          }                    // try to kekulize anyway
          else {
            electron[bestatom] += 1;
          }
        }
      }
      
      //cout << "minde after:" << minde <<endl;
      //for(j=0; j < cycle.size(); j++) {
      //OBAtom *cycleAtom = cycle[j];
      //cout << "\t" << cycleAtom->GetIdx();
      //}
      //cout << endl;

      //for(j=0; j < electron.size(); j++) {
      //cout << "\t" << electron[j];
      //}
      //cout << endl;

      // kekulize the cycle(s)
      start_kekulize(cycle,electron);

      // Set the kekulized cycle(s) as visited
      for(j=1; j<= NumAtoms(); j++) {
        if (avisit[j])
          cvisit.SetBitOn(j);
      }

    }
  }
  // Double bond have been assigned, set the remaining aromatic bonds to single
  //std::cout << "Set not assigned single bonds\n"; 
  for(i=0;i <NumBonds(); i++) {
    bond = GetBond(i);     
    //std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " ";   
    if (bond->GetBO()==5 ) {
      bond->SetKSingle();
      bond->SetBO(1);
      //std::cout << "single\n";
    }
    //else
    //  std::cout << "double\n";
  }

  return;
}

///////////////////////////////////////////////////////////////////////////////////////
//! \brief Start kekulizing one or a fused set of aromatic ring(s)

//! The initial electronic state indicates if an atoms must make a double bond or not
//! Kekulizing is attempted recursively for all the atoms bonded to the first atom
//! of the cycle. 
void OBMol::start_kekulize( std::vector <OBAtom*> &cycle, std::vector<int> &electron) {
  
  std::vector<int> initState;
  std::vector<int> currentState;
  std::vector<int> binitState;
  std::vector<int> bcurrentState;
  std::vector<bool> mark;
  unsigned int Idx;
  OBAtom *atom, *atom2;
  OBBond *bond;

  //init the atom arrays
  unsigned i;
        for(i=0;i <NumAtoms()+1; i++) {
    initState.push_back(-1);
    currentState.push_back(-1);
    mark.push_back(false);
  }
  
  //init the bond arrays with single bonds
  for(i=0;i <NumBonds(); i++) {
    binitState.push_back(SINGLE);
    bcurrentState.push_back(SINGLE);
  }
  
  //set the electron number
  for(i=0; i< cycle.size(); i++) {
    atom = cycle[i];
    Idx =  atom->GetIdx();
    if ( electron[i] == 1)
      initState[Idx] = 1; // make 1 double bond
    else
      initState[Idx] = 2; // make 2 single bonds

    currentState[Idx] = initState[Idx];
  }

  std::vector<OBEdgeBase*>::iterator b;
  OBAtom *nbr;
  
  bool second_pass=false;
  // for( i=1; i<= NumAtoms(); i++) {
//     if(currentState[i] == 1) { // the atom can make a double bond
//       atom = GetAtom(i);
//       //find a neighbour that can make a double bond
//       // and start kekulize
//       for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) {
//      if(currentState[nbr->GetIdx()]==1){
//        if(!expand_kekulize(atom,nbr,currentState,initState, bcurrentState,binitState, mark)) {
//          second_pass=true;
//        }
            
//      }
//       }
//     }
//   }
  bool expand_successful;
  atom = cycle[0];
  for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) {
    if(initState[nbr->GetIdx()] == -1) //neighbor atom not in the cycle, try next one
      continue; 
    //std::cout << "Expand kekulize\n";
    expand_kekulize(atom,nbr,currentState,initState, bcurrentState,binitState, mark) ; 
    //Control that all the electron have been given to the cycle(s)
    expand_successful = true;
    for(unsigned i=0; i< cycle.size(); i++) {
      atom2 = cycle[i];
      Idx =  atom2->GetIdx();
      //cout << "\t" << currentState[Idx];
      if (currentState[Idx] == 1)
        expand_successful=false;
    }
    //cout << endl;
    if (expand_successful)
      break;
    else {
                        unsigned i;
      for(i=0;i <NumAtoms()+1; i++) {
        currentState[i]=initState[i];
        mark[i]=false;
      }
      for(i=0;i <NumBonds(); i++) {
        bcurrentState[i]=binitState[i];
      }   
    }
  }
  if (!expand_successful)
    {
#ifdef HAVE_SSTREAM
    stringstream errorMsg;
#else
    strstream errorMsg;
#endif
    errorMsg << "Kekulize Error for molecule " << GetTitle() << endl;
    obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
    }

  // Set the double bonds
  // std::cout << "Set double bonds\n";
  for(i=0;i <NumBonds(); i++) {
    bond = GetBond(i);    
    // std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " ";
    if (bond->GetBO()==5 && bcurrentState[i] == DOUBLE) {
      bond->SetKDouble();
      bond->SetBO(2);
      //std::cout << "double\n";
    }
    //else
      //std::cout << "single\n";
    //else if (bond->IsAromatic() && bond->GetBO() != 2)
    //  bond->SetBO(1);
  }

  return;
}


/////////////////////////////////////////////////////////////////////////////////////////
//! \brief recursively assign single and double bonds according to the electronical state
//! of the atoms of the current bond 
int OBMol::expand_kekulize(OBAtom *atom1, OBAtom *atom2, std::vector<int> &currentState, std::vector<int> &initState, std::vector<int> &bcurrentState, std::vector<int> &binitState, std::vector<bool> &mark)
{
  int done;
  int Idx1=atom1->GetIdx(), Idx2=atom2->GetIdx();
  OBBond *bond;
  std::vector<OBEdgeBase*>::iterator i;
  OBAtom *nbr;
  int natom;

  mark[Idx1]= true;
  bond = atom1->GetBond(atom2);
  int bIdx = bond->GetIdx();
  
  //cout << "assign bond state for atoms " << Idx1 << " and " << Idx2 << endl;
  if (currentState[Idx1] == 1 && currentState[Idx2] == 1) {
    currentState[Idx1]=0;
    currentState[Idx2]=0;
    // set bond to double
    //std::cout << "bond " << Idx1 << " " << Idx2 << " double\n";
    bcurrentState[bIdx]=DOUBLE;
  }
  else if (currentState[Idx1] == 0 && currentState[Idx2] == 1 ||
           currentState[Idx1] == 2 && currentState[Idx2] == 1 ||
           currentState[Idx1] == 2 && currentState[Idx2] == 2) {
    //std::cout << "bond " << Idx1 << " " << Idx2 << " single\n";
    // leave bond to single
  }  
  else if (currentState[Idx1] == 1 && currentState[Idx2] == 0 ||
      currentState[Idx1] == 1 && currentState[Idx2] == 2) {
    mark[Idx1]=false;
    //std::cout << "bond " << Idx1 << " " << Idx2 << " error\n";
    return (0); // error
  }
  else if (currentState[Idx1] == 0 && currentState[Idx2] == 0
      || currentState[Idx1] == 2 && currentState[Idx2] == 0) { 
    //std::cout << "bond " << Idx1 << " " << Idx2 << " done\n";
    mark[Idx2]=true;
    return (1); //done
  }
  else if (currentState[Idx1] == 0 && currentState[Idx2] == 2) {
    currentState[Idx2]=0;
    //std::cout << "bond " << Idx1 << " " << Idx2 << " leave single\n";
    // leave bond to single
  }
  else {

#ifdef HAVE_SSTREAM
    stringstream errorMsg;
#else
    strstream errorMsg;
#endif

    errorMsg << "unexpected state:" << "atom " << Idx1 << " " << currentState[Idx1] 
         << " atom " << Idx2 << " " << currentState[Idx2] << endl;
    obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug);
    return(false);
  }

  //int c;
  //for(c=1; c < currentState.size(); c++) {
  //cout << c << "\t";
  //}
  //cout << endl;
  //for(c=1; c < currentState.size(); c++) { 
  //cout << currentState[c] << "\t";
  //}   
  //cout << endl;

  vector<int> previousState = currentState;   // Backup the atom
  vector<int> bpreviousState = bcurrentState; // and the bond states before expanding again

  bool return_false=false;
  // for each neighbor of atom 2 not already kekulized
  for (nbr = atom2->BeginNbrAtom(i);nbr;nbr = atom2->NextNbrAtom(i))
   {
     natom = nbr->GetIdx();
     if(initState[natom] == -1) //neighbor atom not in the cycle, try next one
       continue;            
     if ( !mark[natom] ) {
       done = expand_kekulize(atom2, nbr, currentState, initState, bcurrentState, binitState, mark);
       if ( !done )  // kekulize failed
         return_false =true;
       else 
         return_false =false;
     }
    
   }
  if (return_false) { // no good solution found 
    //cout << "return_false:no good solution\n" << endl;
    //cout << "reset state of " << Idx1 << " and " << Idx2 << " from "  << currentState[Idx1]
    //<< " " << currentState[Idx2] << " to ";
    
    // retrieve the states that might have been changed during kekulize expansion
    currentState = previousState;
    
    
    bcurrentState = bpreviousState;
    
    
    // reset the bond and the atom states
    if (bcurrentState[bIdx] == DOUBLE)
      currentState[Idx1]=initState[Idx1];
    
    currentState[Idx2]=initState[Idx2];
    bcurrentState[bIdx]=binitState[bIdx]; // should be always single
    mark[Idx2]=false;

    //cout << currentState[Idx1] << " " << currentState[Idx2] << endl;
    return (false);
  }
  // atom 2 cannot make any bond, should not have 1 electron 
  if (currentState[Idx2] == 1) {
    // currentState[Idx1]=initState[Idx1];
    //cout << "return true but " << Idx2 << " state = 1\n";
    mark[Idx1]=false;
    return (false);
  }
  else {
    // if we found a good solution, then the state of Idx2 may have shifted from 1 to 0 during the kekulization
    // If it is the case, we should check if there is a remaining unmarked neighbor because it is possible
    // that kekulizing from this neigbor failed just because Idx2 was equal to 1

    if(previousState[Idx2] == 1) {
      // Since now Idx2 is equal to 0 because it kekulized well the kekulizing of the failed neigbor could be successfull
      // If there is still an unmarked neigbor try to kekulize it again
      //mark[Idx2]=true;        
      return_false=false;
      //cout << "retry kekulizing from " << Idx2 << endl;
  
      for (nbr = atom2->BeginNbrAtom(i);nbr;nbr = atom2->NextNbrAtom(i))
        {
          natom = nbr->GetIdx();
          if(initState[natom] == -1) //neighbor atom not in the cycle, try next one
            continue;            
          if ( !mark[natom] ) {
            //cout << "atom " << natom << " not marked, expand again" << endl;
            done = expand_kekulize(atom2, nbr, currentState, initState, bcurrentState, binitState, mark);
            if ( !done )  // kekulize failed
              return_false =true;
            else 
              return_false =false;
          }
    
        }
  
      // if we cannot kekulize the remaining neigbor again then we have to return false
      // we do not have to reset the states because the kekulize will fail anyway
      if(return_false) {
        //cout << "rekekulize failed" << endl;
        return(false);
      }
      else {
        //cout << "rekekulized successfull" << endl;
        return (true);
      }
          
    }

    
    //cout << "return_true: good solution" << endl;
    return (true);
  }
}

//! Give the priority to give two electrons instead of 1
int OBMol::getorden( OBAtom *atom) 
{
  if ( atom->IsSulfur() ) return 1;
  if ( atom->IsOxygen() ) return 2;
  if ( atom->GetAtomicNum() == 34 ) return 3;
  if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->GetValence() == 3) return 5;
  if ( atom->IsAmideNitrogen() ) return 4;
  if ( atom->IsNitrogen() && atom->GetFormalCharge() == -1) return 6;
  if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->IsInRingSize(5) ) return 7;
  if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 ) return 8;
  if ( atom->IsCarbon() && atom->GetFormalCharge() == -1) return 9;
  //if ( atom->IsCarbon() ) return 9;
  
  return (100); //no atom found
}

//! Recursively find the aromatic atoms with an aromatic bond to the current atom
void OBMol::expandcycle (OBAtom *atom, OBBitVec &avisit)
{
  OBAtom *nbr;
//  OBBond *bond;
  std::vector<OBEdgeBase*>::iterator i;
  int natom;
  //for each neighbour atom test if it is in the aromatic ring
  for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
   {
     natom = nbr->GetIdx();
     // if (!avisit[natom] && nbr->IsAromatic() && ((OBBond*) *i)->IsAromatic()) {
     if (!avisit[natom] && ((OBBond*) *i)->GetBO()==5) {
       avisit.SetBitOn(natom);
       expandcycle(nbr, avisit);
     }
   }
}

} // end namespace OpenBabel

//! \file kekulize.cpp
//! \brief Alternate algorithm to kekulize a molecule (OBMol::NewPerceiveKekuleBonds()).
Revision:	819
Committed:	Fri Dec 16 21:52:50 2005 UTC (19 years, 10 months ago) by tim
File size:	17801 byte(s)
Log Message:	changed __FUNCTION__ to __func__ to match C99 standard, and then added an autoconf test to check for __func__ usability. Changed some default compile flags for the Sun architecture
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			kekulize.cpp - Alternate algorithm to kekulize a molecule.
3
4			Copyright (C) 2004-2005 by Fabien Fontaine
5			Some portions Copyright (C) 2005 by Geoffrey R. Hutchison
6
7			This file is part of the Open Babel project.
8			For more information, see <http://openbabel.sourceforge.net/>
9
10			This program is free software; you can redistribute it and/or modify
11			it under the terms of the GNU General Public License as published by
12			the Free Software Foundation version 2 of the License.
13
14			This program is distributed in the hope that it will be useful,
15			but WITHOUT ANY WARRANTY; without even the implied warranty of
16			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17			GNU General Public License for more details.
18			***********************************************************************/
19
20			#include "mol.hpp"
21			#include "oberror.hpp"
22
23			#ifdef HAVE_SSTREAM
24			#include <sstream>
25			#else
26			#include <strstream>
27			#endif
28
29			#define SINGLE 1
30			#define DOUBLE 2
31
32			using namespace std;
33
34			namespace OpenBabel {
35
36			///////////////////////////////////////////////////////////////////////////////
37			//! \brief Kekulize aromatic rings without using implicit valence
38
39			//! This new perceive kekule bonds function has been especifically designed to
40			//! handle molecule files without explicit hydrogens such as pdb or xyz.
41			//! The function does not rely on GetImplicitValence function
42			//! The function looks for groups of aromatic cycle
43			//! For each group it tries to guess the number of electrons given by each atom
44			//! in order to satisfy the huckel (4n+2) rule
45			//! If the huckel rule cannot be satisfied the algorithm try with its best alternative guess
46			//! Then it recursively walk on the atoms of the cycle and assign single and double bonds
47			void OBMol::NewPerceiveKekuleBonds()
48			{
49
50			if (HasKekulePerceived()) return;
51			SetKekulePerceived();
52
53			OBAtom *atom;
54			int n, de, minde;
55			std::vector<OBAtom*> cycle;
56			OBBitVec avisit,cvisit;
57			avisit.Resize(NumAtoms()+1);
58			cvisit.Resize(NumAtoms()+1);
59			OBBond *bond;
60			std::vector<OBEdgeBase*>::iterator bi;
61			std::vector<int> electron;
62			int BO;
63			int sume, orden, bestorden, bestatom;
64			// Init the kekulized bonds
65			unsigned i;
66			for(i=0; i< NumBonds(); i++ ) {
67			bond = GetBond(i);
68			BO = bond->GetBO();
69			switch (BO)
70			{
71			case 1: bond->SetKSingle(); break;
72			case 2: bond->SetKDouble(); break;
73			case 3: bond->SetKTriple(); break;
74			}
75			}
76
77			// Find all the groups of aromatic cycle
78			for(i=1; i<= NumAtoms(); i++ ) {
79			atom = GetAtom(i);
80			if (atom->HasAromaticBond() && !cvisit[i]) { // is new aromatic atom of an aromatic cycle ?
81
82			avisit.Clear();
83			electron.clear();
84			cycle.clear();
85
86			avisit.SetBitOn(i);
87			expandcycle (atom, avisit);
88			//store the atoms of the cycle(s)
89			unsigned int j;
90			for(j=1; j<= NumAtoms(); j++) {
91			if ( avisit[j] ) {
92			atom = GetAtom(j);
93			cycle.push_back(atom);
94			}
95			}
96			// At the begining each atom give one electron to the cycle
97			for(j=0; j< cycle.size(); j++) {
98			electron.push_back(1);
99			}
100
101			// remove one electron if the atom make a double bond out of the cycle
102			sume =0;
103			for(j=0; j< cycle.size(); j++) {
104			atom = cycle[j];
105			for(bond = atom->BeginBond(bi); bond; bond = atom->NextBond(bi)) {
106			if ( bond->IsDouble() ) {
107			OBAtom *atom2 = bond->GetNbrAtom(atom);
108			int fcharge = atom->GetFormalCharge();
109			int fcharge2 = atom2->GetFormalCharge();
110			if(atom->IsNitrogen() && atom2->IsOxygen()
111			&& fcharge == 0 && fcharge2 == 0) { //n=O to [n+][O-]
112			atom->SetFormalCharge(1);
113			atom2->SetFormalCharge(-1);
114			bond->SetKSingle();
115			bond->SetBO(1);
116			}
117			else {
118			electron[j] = 0;
119			}
120			}
121			}
122			// count the number of electrons
123			sume += electron[j];
124			}
125
126
127			// Save the electron state in case huckel rule is not satisfied
128			vector<int> previousElectron = electron;
129
130			// find the ideal number of electrons according to the huckel 4n+2 rule
131			minde=99;
132			for (i=1; 1; i++) {
133			n = 4 *i +2;
134			de = n - sume;
135			if ( de < minde )
136			minde=de;
137			else if ( minde < 0 )
138			minde=de;
139			else
140			break;
141			}
142
143			#ifdef HAVE_SSTREAM
144			stringstream errorMsg;
145			#else
146			strstream errorMsg;
147			#endif
148
149			//cout << "minde before:" << minde << endl;
150			// if huckel rule not satisfied some atoms must give more electrons
151			//cout << "minde " << minde << endl;
152			while ( minde != 0 ) {
153			bestorden=99;
154			for(j=0; j< cycle.size(); j++) {
155			if (electron[j] == 1) {
156			orden = getorden(cycle[j]);
157			if (orden < bestorden) {
158			bestorden = orden;
159			bestatom = j;
160			}
161			}
162			}
163			if (bestorden==99) { // no electron giving atom found
164			errorMsg << "Kekulize: Huckel rule not satisfied for molecule " << GetTitle() << endl;
165	tim	819	obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
166	tim	741	break; // Huckel rule cannot be satisfied
167			} // try to kekulize anyway
168			else {
169			electron[bestatom] += 1;
170			minde--;
171			}
172			}
173
174			if (bestorden == 99) { // Huckel rule not satisfied, just try to get an even number of electron before kekulizing
175
176			electron = previousElectron; // restore electon's state
177
178			int odd = sume % 2;
179			//cout << "odd:" << odd << endl;
180			if(odd) { // odd number of electrons try to add an electron to the best possible atom
181			for(j=0; j< cycle.size(); j++) {
182			if (electron[j] == 1) {
183			orden = getorden(cycle[j]);
184			if (orden < bestorden) {
185			bestorden = orden;
186			bestatom = j;
187			}
188			}
189			}
190			if (bestorden==99) { // no electron giving atom found
191			errorMsg << "Kekulize: Cannot get an even number of electron for molecule " << GetTitle() << "\n";
192	tim	819	obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
193	tim	741	break; // impossible to choose an atom to obtain an even number of electron
194			} // try to kekulize anyway
195			else {
196			electron[bestatom] += 1;
197			}
198			}
199			}
200
201			//cout << "minde after:" << minde <<endl;
202			//for(j=0; j < cycle.size(); j++) {
203			//OBAtom *cycleAtom = cycle[j];
204			//cout << "\t" << cycleAtom->GetIdx();
205			//}
206			//cout << endl;
207
208			//for(j=0; j < electron.size(); j++) {
209			//cout << "\t" << electron[j];
210			//}
211			//cout << endl;
212
213			// kekulize the cycle(s)
214			start_kekulize(cycle,electron);
215
216			// Set the kekulized cycle(s) as visited
217			for(j=1; j<= NumAtoms(); j++) {
218			if (avisit[j])
219			cvisit.SetBitOn(j);
220			}
221
222			}
223			}
224			// Double bond have been assigned, set the remaining aromatic bonds to single
225			//std::cout << "Set not assigned single bonds\n";
226			for(i=0;i <NumBonds(); i++) {
227			bond = GetBond(i);
228			//std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " ";
229			if (bond->GetBO()==5 ) {
230			bond->SetKSingle();
231			bond->SetBO(1);
232			//std::cout << "single\n";
233			}
234			//else
235			// std::cout << "double\n";
236			}
237
238			return;
239			}
240
241			///////////////////////////////////////////////////////////////////////////////////////
242			//! \brief Start kekulizing one or a fused set of aromatic ring(s)
243
244			//! The initial electronic state indicates if an atoms must make a double bond or not
245			//! Kekulizing is attempted recursively for all the atoms bonded to the first atom
246			//! of the cycle.
247			void OBMol::start_kekulize( std::vector <OBAtom*> &cycle, std::vector<int> &electron) {
248
249			std::vector<int> initState;
250			std::vector<int> currentState;
251			std::vector<int> binitState;
252			std::vector<int> bcurrentState;
253			std::vector<bool> mark;
254			unsigned int Idx;
255			OBAtom atom, atom2;
256			OBBond *bond;
257
258			//init the atom arrays
259			unsigned i;
260			for(i=0;i <NumAtoms()+1; i++) {
261			initState.push_back(-1);
262			currentState.push_back(-1);
263			mark.push_back(false);
264			}
265
266			//init the bond arrays with single bonds
267			for(i=0;i <NumBonds(); i++) {
268			binitState.push_back(SINGLE);
269			bcurrentState.push_back(SINGLE);
270			}
271
272			//set the electron number
273			for(i=0; i< cycle.size(); i++) {
274			atom = cycle[i];
275			Idx = atom->GetIdx();
276			if ( electron[i] == 1)
277			initState[Idx] = 1; // make 1 double bond
278			else
279			initState[Idx] = 2; // make 2 single bonds
280
281			currentState[Idx] = initState[Idx];
282			}
283
284			std::vector<OBEdgeBase*>::iterator b;
285			OBAtom *nbr;
286
287			bool second_pass=false;
288			// for( i=1; i<= NumAtoms(); i++) {
289			// if(currentState[i] == 1) { // the atom can make a double bond
290			// atom = GetAtom(i);
291			// //find a neighbour that can make a double bond
292			// // and start kekulize
293			// for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) {
294			// if(currentState[nbr->GetIdx()]==1){
295			// if(!expand_kekulize(atom,nbr,currentState,initState, bcurrentState,binitState, mark)) {
296			// second_pass=true;
297			// }
298
299			// }
300			// }
301			// }
302			// }
303			bool expand_successful;
304			atom = cycle[0];
305			for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) {
306			if(initState[nbr->GetIdx()] == -1) //neighbor atom not in the cycle, try next one
307			continue;
308			//std::cout << "Expand kekulize\n";
309			expand_kekulize(atom,nbr,currentState,initState, bcurrentState,binitState, mark) ;
310			//Control that all the electron have been given to the cycle(s)
311			expand_successful = true;
312			for(unsigned i=0; i< cycle.size(); i++) {
313			atom2 = cycle[i];
314			Idx = atom2->GetIdx();
315			//cout << "\t" << currentState[Idx];
316			if (currentState[Idx] == 1)
317			expand_successful=false;
318			}
319			//cout << endl;
320			if (expand_successful)
321			break;
322			else {
323			unsigned i;
324			for(i=0;i <NumAtoms()+1; i++) {
325			currentState[i]=initState[i];
326			mark[i]=false;
327			}
328			for(i=0;i <NumBonds(); i++) {
329			bcurrentState[i]=binitState[i];
330			}
331			}
332			}
333			if (!expand_successful)
334			{
335			#ifdef HAVE_SSTREAM
336			stringstream errorMsg;
337			#else
338			strstream errorMsg;
339			#endif
340			errorMsg << "Kekulize Error for molecule " << GetTitle() << endl;
341	tim	819	obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo);
342	tim	741	}
343
344			// Set the double bonds
345			// std::cout << "Set double bonds\n";
346			for(i=0;i <NumBonds(); i++) {
347			bond = GetBond(i);
348			// std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " ";
349			if (bond->GetBO()==5 && bcurrentState[i] == DOUBLE) {
350			bond->SetKDouble();
351			bond->SetBO(2);
352			//std::cout << "double\n";
353			}
354			//else
355			//std::cout << "single\n";
356			//else if (bond->IsAromatic() && bond->GetBO() != 2)
357			// bond->SetBO(1);
358			}
359
360			return;
361			}
362
363
364			/////////////////////////////////////////////////////////////////////////////////////////
365			//! \brief recursively assign single and double bonds according to the electronical state
366			//! of the atoms of the current bond
367			int OBMol::expand_kekulize(OBAtom atom1, OBAtom atom2, std::vector<int> &currentState, std::vector<int> &initState, std::vector<int> &bcurrentState, std::vector<int> &binitState, std::vector<bool> &mark)
368			{
369			int done;
370			int Idx1=atom1->GetIdx(), Idx2=atom2->GetIdx();
371			OBBond *bond;
372			std::vector<OBEdgeBase*>::iterator i;
373			OBAtom *nbr;
374			int natom;
375
376			mark[Idx1]= true;
377			bond = atom1->GetBond(atom2);
378			int bIdx = bond->GetIdx();
379
380			//cout << "assign bond state for atoms " << Idx1 << " and " << Idx2 << endl;
381			if (currentState[Idx1] == 1 && currentState[Idx2] == 1) {
382			currentState[Idx1]=0;
383			currentState[Idx2]=0;
384			// set bond to double
385			//std::cout << "bond " << Idx1 << " " << Idx2 << " double\n";
386			bcurrentState[bIdx]=DOUBLE;
387			}
388			else if (currentState[Idx1] == 0 && currentState[Idx2] == 1 \|\|
389			currentState[Idx1] == 2 && currentState[Idx2] == 1 \|\|
390			currentState[Idx1] == 2 && currentState[Idx2] == 2) {
391			//std::cout << "bond " << Idx1 << " " << Idx2 << " single\n";
392			// leave bond to single
393			}
394			else if (currentState[Idx1] == 1 && currentState[Idx2] == 0 \|\|
395			currentState[Idx1] == 1 && currentState[Idx2] == 2) {
396			mark[Idx1]=false;
397			//std::cout << "bond " << Idx1 << " " << Idx2 << " error\n";
398			return (0); // error
399			}
400			else if (currentState[Idx1] == 0 && currentState[Idx2] == 0
401			\|\| currentState[Idx1] == 2 && currentState[Idx2] == 0) {
402			//std::cout << "bond " << Idx1 << " " << Idx2 << " done\n";
403			mark[Idx2]=true;
404			return (1); //done
405			}
406			else if (currentState[Idx1] == 0 && currentState[Idx2] == 2) {
407			currentState[Idx2]=0;
408			//std::cout << "bond " << Idx1 << " " << Idx2 << " leave single\n";
409			// leave bond to single
410			}
411			else {
412
413			#ifdef HAVE_SSTREAM
414			stringstream errorMsg;
415			#else
416			strstream errorMsg;
417			#endif
418
419			errorMsg << "unexpected state:" << "atom " << Idx1 << " " << currentState[Idx1]
420			<< " atom " << Idx2 << " " << currentState[Idx2] << endl;
421	tim	819	obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug);
422	tim	741	return(false);
423			}
424
425			//int c;
426			//for(c=1; c < currentState.size(); c++) {
427			//cout << c << "\t";
428			//}
429			//cout << endl;
430			//for(c=1; c < currentState.size(); c++) {
431			//cout << currentState[c] << "\t";
432			//}
433			//cout << endl;
434
435			vector<int> previousState = currentState; // Backup the atom
436			vector<int> bpreviousState = bcurrentState; // and the bond states before expanding again
437
438			bool return_false=false;
439			// for each neighbor of atom 2 not already kekulized
440			for (nbr = atom2->BeginNbrAtom(i);nbr;nbr = atom2->NextNbrAtom(i))
441			{
442			natom = nbr->GetIdx();
443			if(initState[natom] == -1) //neighbor atom not in the cycle, try next one
444			continue;
445			if ( !mark[natom] ) {
446			done = expand_kekulize(atom2, nbr, currentState, initState, bcurrentState, binitState, mark);
447			if ( !done ) // kekulize failed
448			return_false =true;
449			else
450			return_false =false;
451			}
452
453			}
454			if (return_false) { // no good solution found
455			//cout << "return_false:no good solution\n" << endl;
456			//cout << "reset state of " << Idx1 << " and " << Idx2 << " from " << currentState[Idx1]
457			//<< " " << currentState[Idx2] << " to ";
458
459			// retrieve the states that might have been changed during kekulize expansion
460			currentState = previousState;
461
462
463			bcurrentState = bpreviousState;
464
465
466			// reset the bond and the atom states
467			if (bcurrentState[bIdx] == DOUBLE)
468			currentState[Idx1]=initState[Idx1];
469
470			currentState[Idx2]=initState[Idx2];
471			bcurrentState[bIdx]=binitState[bIdx]; // should be always single
472			mark[Idx2]=false;
473
474			//cout << currentState[Idx1] << " " << currentState[Idx2] << endl;
475			return (false);
476			}
477			// atom 2 cannot make any bond, should not have 1 electron
478			if (currentState[Idx2] == 1) {
479			// currentState[Idx1]=initState[Idx1];
480			//cout << "return true but " << Idx2 << " state = 1\n";
481			mark[Idx1]=false;
482			return (false);
483			}
484			else {
485			// if we found a good solution, then the state of Idx2 may have shifted from 1 to 0 during the kekulization
486			// If it is the case, we should check if there is a remaining unmarked neighbor because it is possible
487			// that kekulizing from this neigbor failed just because Idx2 was equal to 1
488
489			if(previousState[Idx2] == 1) {
490			// Since now Idx2 is equal to 0 because it kekulized well the kekulizing of the failed neigbor could be successfull
491			// If there is still an unmarked neigbor try to kekulize it again
492			//mark[Idx2]=true;
493			return_false=false;
494			//cout << "retry kekulizing from " << Idx2 << endl;
495
496			for (nbr = atom2->BeginNbrAtom(i);nbr;nbr = atom2->NextNbrAtom(i))
497			{
498			natom = nbr->GetIdx();
499			if(initState[natom] == -1) //neighbor atom not in the cycle, try next one
500			continue;
501			if ( !mark[natom] ) {
502			//cout << "atom " << natom << " not marked, expand again" << endl;
503			done = expand_kekulize(atom2, nbr, currentState, initState, bcurrentState, binitState, mark);
504			if ( !done ) // kekulize failed
505			return_false =true;
506			else
507			return_false =false;
508			}
509
510			}
511
512			// if we cannot kekulize the remaining neigbor again then we have to return false
513			// we do not have to reset the states because the kekulize will fail anyway
514			if(return_false) {
515			//cout << "rekekulize failed" << endl;
516			return(false);
517			}
518			else {
519			//cout << "rekekulized successfull" << endl;
520			return (true);
521			}
522
523			}
524
525
526			//cout << "return_true: good solution" << endl;
527			return (true);
528			}
529			}
530
531			//! Give the priority to give two electrons instead of 1
532			int OBMol::getorden( OBAtom *atom)
533			{
534			if ( atom->IsSulfur() ) return 1;
535			if ( atom->IsOxygen() ) return 2;
536			if ( atom->GetAtomicNum() == 34 ) return 3;
537			if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->GetValence() == 3) return 5;
538			if ( atom->IsAmideNitrogen() ) return 4;
539			if ( atom->IsNitrogen() && atom->GetFormalCharge() == -1) return 6;
540			if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->IsInRingSize(5) ) return 7;
541			if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 ) return 8;
542			if ( atom->IsCarbon() && atom->GetFormalCharge() == -1) return 9;
543			//if ( atom->IsCarbon() ) return 9;
544
545			return (100); //no atom found
546			}
547
548			//! Recursively find the aromatic atoms with an aromatic bond to the current atom
549			void OBMol::expandcycle (OBAtom *atom, OBBitVec &avisit)
550			{
551			OBAtom *nbr;
552			// OBBond *bond;
553			std::vector<OBEdgeBase*>::iterator i;
554			int natom;
555			//for each neighbour atom test if it is in the aromatic ring
556			for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
557			{
558			natom = nbr->GetIdx();
559			// if (!avisit[natom] && nbr->IsAromatic() && ((OBBond) i)->IsAromatic()) {
560			if (!avisit[natom] && ((OBBond) i)->GetBO()==5) {
561			avisit.SetBitOn(natom);
562			expandcycle(nbr, avisit);
563			}
564			}
565			}
566
567			} // end namespace OpenBabel
568
569			//! \file kekulize.cpp
570			//! \brief Alternate algorithm to kekulize a molecule (OBMol::NewPerceiveKekuleBonds()).