openbabel-3.1.1/src/typer.cpp

/**********************************************************************
typer.cpp - Open Babel atom typer.

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

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 <openbabel/babelconfig.h>

#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/ring.h>
#include <openbabel/obiter.h>
#include <openbabel/oberror.h>
#include <openbabel/typer.h>
#include <openbabel/elements.h>

// private data headers with default parameters
#include "atomtyp.h"

#ifdef WIN32
#pragma warning (disable : 4786)
#endif

using namespace std;

namespace OpenBabel
{
  // Initialize globals declared in typer.h
  THREAD_LOCAL OBAromaticTyper  aromtyper;
  THREAD_LOCAL OBAtomTyper      atomtyper;

  /*! \class OBAtomTyper typer.h <openbabel/typer.h>
    \brief Assigns atom types, hybridization, and formal charges

    The OBAtomTyper class is designed to read in a list of atom typing
    rules and apply them to molecules. The code that performs atom
    typing is not usually used directly as atom typing, hybridization
    assignment, and charge are all done
    automatically when their corresponding values are requested of
    atoms:
    \code
    atom->GetType();
    atom->GetFormalCharge();
    atom->GetHyb();
    \endcode
  */
  OBAtomTyper::OBAtomTyper()
  {
    _init = false;
    _dir = BABEL_DATADIR;
    _envvar = "BABEL_DATADIR";
    _filename = "atomtyp.txt";
    _subdir = "data";
    _dataptr = AtomTypeData;
  }

  void OBAtomTyper::ParseLine(const char *buffer)
  {
    vector<string> vs;
    OBSmartsPattern *sp;

    if (EQn(buffer,"INTHYB",6))
      {
        tokenize(vs,buffer);
        if (vs.size() < 3)
          {
            obErrorLog.ThrowError(__FUNCTION__, " Could not parse INTHYB line in atom type table from atomtyp.txt", obInfo);
            return;
          }

        sp = new OBSmartsPattern;
        if (sp->Init(vs[1]))
          _vinthyb.push_back(pair<OBSmartsPattern*,int> (sp,atoi((char*)vs[2].c_str())));
        else
          {
            delete sp;
            sp = nullptr;
            obErrorLog.ThrowError(__FUNCTION__, " Could not parse INTHYB line in atom type table from atomtyp.txt", obInfo);
            return;
          }
      }
    else if (EQn(buffer,"EXTTYP",6))
      {
        tokenize(vs,buffer);
        if (vs.size() < 3)
          {
            obErrorLog.ThrowError(__FUNCTION__, " Could not parse EXTTYP line in atom type table from atomtyp.txt", obInfo);
            return;
          }
        sp = new OBSmartsPattern;
        if (sp->Init(vs[1]))
          _vexttyp.push_back(pair<OBSmartsPattern*,string> (sp,vs[2]));
        else
          {
            delete sp;
            sp = nullptr;
            obErrorLog.ThrowError(__FUNCTION__, " Could not parse EXTTYP line in atom type table from atomtyp.txt", obInfo);
            return;
          }
      }
  }

  OBAtomTyper::~OBAtomTyper()
  {
    vector<pair<OBSmartsPattern*,int> >::iterator i;
    for (i = _vinthyb.begin();i != _vinthyb.end();++i)
      {
        delete i->first;
        i->first = nullptr;
      }

    vector<pair<OBSmartsPattern*,string> >::iterator j;
    for (j = _vexttyp.begin();j != _vexttyp.end();++j)
      {
        delete j->first;
        j->first = nullptr;
      }

  }

  void OBAtomTyper::AssignTypes(OBMol &mol)
  {
    if (!_init)
      Init();

    obErrorLog.ThrowError(__FUNCTION__,
                          "Ran OpenBabel::AssignTypes", obAuditMsg);

    mol.SetAtomTypesPerceived();

    vector<vector<int> >::iterator j;
    vector<pair<OBSmartsPattern*,string> >::iterator i;

    for (i = _vexttyp.begin(); i != _vexttyp.end(); ++i) {
      std::vector<std::vector<int> > mlist;
      if (i->first->Match(mol, mlist))
      {
        for (j = mlist.begin(); j != mlist.end(); ++j)
          mol.GetAtom((*j)[0])->SetType(i->second);
      }
    }

    // Special cases
    vector<OBAtom*>::iterator a;
    OBAtom* atom;
    for (atom = mol.BeginAtom(a); atom; atom = mol.NextAtom(a)) {
      // guanidinium. Fixes PR#1800964
      if (strncasecmp(atom->GetType(),"C2", 2) == 0) {
        int guanidineN = 0;
        OBAtom *nbr;
        vector<OBBond*>::iterator k;
        for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k)) {
          if (strncasecmp(nbr->GetType(),"Npl", 3) == 0 ||
              strncasecmp(nbr->GetType(),"N2", 2) == 0 ||
              strncasecmp(nbr->GetType(),"Ng+", 3) == 0)
            ++guanidineN;
        }
        if (guanidineN == 3)
          atom->SetType("C+");

      } // end C2 carbon for guanidinium

    } // end special cases
  }

  void OBAtomTyper::AssignHyb(OBMol &mol)
  {
    if (!_init)
      Init();

    aromtyper.AssignAromaticFlags(mol);

    mol.SetHybridizationPerceived();
    obErrorLog.ThrowError(__FUNCTION__,
                          "Ran OpenBabel::AssignHybridization", obAuditMsg);

    OBAtom *atom;
    vector<OBAtom*>::iterator k;
    for (atom = mol.BeginAtom(k);atom;atom = mol.NextAtom(k))
      atom->SetHyb(0);

    vector<vector<int> >::iterator j;
    vector<pair<OBSmartsPattern*,int> >::iterator i;

    for (i = _vinthyb.begin(); i != _vinthyb.end(); ++i) {
      std::vector<std::vector<int> > mlist;
      if (i->first->Match(mol, mlist))
      {
        for (j = mlist.begin(); j != mlist.end(); ++j)
          mol.GetAtom((*j)[0])->SetHyb(i->second);
      }
    }

    // check all atoms to make sure *some* hybridization is assigned
    for (atom = mol.BeginAtom(k);atom;atom = mol.NextAtom(k))
      if (atom->GetHyb() == 0) {
        switch (atom->GetExplicitDegree()) {
          case 0:
          case 1:
          case 2:
            atom->SetHyb(1);
            break;
          case 3:
            atom->SetHyb(2);
            break;
          case 4:
            atom->SetHyb(3);
            break;
          default:
            atom->SetHyb(atom->GetExplicitDegree());
        }
      }
  }

  /*! \class OBRingTyper typer.h <openbabel/typer.h>
    \brief Assigns ring types

    The OBRingTyper class is designed to read in a list of ring typing
    rules and apply them to molecules. The code that performs ring
    typing is not usually used directly as ring typing is done
    automatically when the ring type is requested of rings:
    \code
    vector<OBRing*>::iterator i;
    vector<OBRing*> rlist = mol.GetSSSR();

    for (i = rlist.begin();i != rlist.end();++i)
    cout << "ring type = " << (*i)->GetType() << endl;
    \endcode
  */
  OBRingTyper::OBRingTyper()
  {
    _init = false;
    _dir = BABEL_DATADIR;
    _envvar = "BABEL_DATADIR";
    _filename = "ringtyp.txt";
    _subdir = "data";
    //_dataptr = RingTypeData;
  }

  void OBRingTyper::ParseLine(const char *buffer)
  {
    vector<string> vs;
    OBSmartsPattern *sp;

    if (EQn(buffer,"RINGTYP",7)) {
      tokenize(vs,buffer);
      if (vs.size() < 3) {
        obErrorLog.ThrowError(__FUNCTION__, " Could not parse RING line in ring type table from ringtyp.txt", obInfo);
        return;
      }
      sp = new OBSmartsPattern;
      if (sp->Init(vs[2]))
        _ringtyp.push_back(pair<OBSmartsPattern*,string> (sp,vs[1]));
      else {
        delete sp;
        sp = nullptr;
        obErrorLog.ThrowError(__FUNCTION__, " Could not parse RING line in ring type table from ringtyp.txt", obInfo);
        return;
      }
    }
  }

  OBRingTyper::~OBRingTyper()
  {
    vector<pair<OBSmartsPattern*,string> >::iterator i;
    for (i = _ringtyp.begin();i != _ringtyp.end();++i) {
      delete i->first;
      i->first = nullptr;
    }
  }

  void OBRingTyper::AssignTypes(OBMol &mol)
  {
    if (!_init)
      Init();

    obErrorLog.ThrowError(__FUNCTION__,
                          "Ran OBRing::AssignTypes", obAuditMsg);

    mol.SetRingTypesPerceived();

    vector<vector<int> >::iterator j2;
    vector<pair<OBSmartsPattern*,string> >::iterator i2;

    vector<OBRing*>::iterator i;
    vector<int>::iterator j;
    vector<OBRing*> rlist = mol.GetSSSR();

    unsigned int member_count;
    for (i2 = _ringtyp.begin();i2 != _ringtyp.end();++i2) { // for each ring type
      std::vector<std::vector<int> > mlist;
      if (i2->first->Match(mol, mlist)) {
        for (j2 = mlist.begin();j2 != mlist.end();++j2) { // for each found match

          for (i = rlist.begin();i != rlist.end();++i) { // for each ring
            member_count = 0;

            for(j = j2->begin(); j != j2->end(); ++j) { // for each atom in the match
              if ((*i)->IsMember(mol.GetAtom(*j)))
                member_count++;
            }

            if ((*i)->Size() == member_count)
              (*i)->SetType(i2->second);
          }
        }
      }
    }
  }

  // Start of helper functions for AssignOBAromaticityModel
  enum ExocyclicAtom { NO_EXOCYCLIC_ATOM, EXO_OXYGEN, EXO_NONOXYGEN };

  static ExocyclicAtom FindExocyclicAtom(OBAtom *atm)
  {
    FOR_BONDS_OF_ATOM(bond, atm) {
      if (bond->GetBondOrder() == 2 && !bond->IsInRing()) {
        unsigned int atomicnum = bond->GetNbrAtom(atm)->GetAtomicNum();
        switch (atomicnum) {
        case OBElements::Oxygen:
          return EXO_OXYGEN;
        default:
          return EXO_NONOXYGEN;
        }
      }
    }
    return NO_EXOCYCLIC_ATOM;
  }

  static bool HasExocyclicBondToOxygenMinus(OBAtom *atm)
  {
    FOR_BONDS_OF_ATOM(bond, atm) {
      if (bond->GetBondOrder() == 1 && !bond->IsInRing()) {
        OBAtom* nbr = bond->GetNbrAtom(atm);
        if (nbr->GetAtomicNum() == OBElements::Oxygen && nbr->GetFormalCharge() == -1)
          return true;
      }
    }
    return false;
  }

  static bool HasExocyclicDblBondToOxygen(OBAtom *atm)
  {
    FOR_BONDS_OF_ATOM(bond, atm) {
      if (bond->GetBondOrder() == 2 && !bond->IsInRing() &&
          bond->GetNbrAtom(atm)->GetAtomicNum() == OBElements::Oxygen)
        return true;
    }
    return false;
  }

  static bool HasExocyclicDblBondToHet(OBAtom *atm)
  {
    FOR_BONDS_OF_ATOM(bond, atm) {
      if (bond->GetBondOrder() == 2 && !bond->IsInRing()) {
        unsigned int atomicnum = bond->GetNbrAtom(atm)->GetAtomicNum();
        switch (atomicnum) {
        case OBElements::Carbon:
        case OBElements::Hydrogen:
          break;
        default:
          return true;
        }
      }
    }
    return false;
  }
  // End of predicates for AssignOBAromaticityModel

  static bool AssignOBAromaticityModel(OBAtom *atm, int &min, int &max)
  {
    // The Open Babel aromaticity model
    //
    // Return minimum and maximum pi-electrons contributed to an aromatic system
    // The return value indicates a potentially aromatic atom (i.e. any patterns matched)
    //
    // The original code used SMARTS patterns organised in increasing order of
    // prioirity (i.e. later matches overrode earlier ones). These SMARTS patterns
    // are now implemented in the code below, but are included in the comments
    // for reference (Case 1->22).

    if (!atm->IsInRing()) {
      min = 0; max = 0; return false;
    }

    unsigned int elem = atm->GetAtomicNum();
    int chg = atm->GetFormalCharge();
    unsigned int deg = atm->GetExplicitDegree() + atm->GetImplicitHCount();
    unsigned int val = atm->GetExplicitValence() + atm->GetImplicitHCount();

    switch (elem) {
    case OBElements::Carbon:
      switch (chg) {
      case 0:
        if (val == 4 && deg == 3) {
          if (HasExocyclicDblBondToHet(atm)) {
            min = 0; max = 0; return true;
          }
          else {
            min = 1; max = 1; return true;
          }
        }
        break;
      case 1:
        if (val == 3) {
          switch (deg) {
          case 3:
            min = 0; max = 0; return true;
          case 2:
            min = 1; max = 1; return true;
          }
        }
        break;
      case -1:
        if (val == 3) {
          switch (deg) {
          case 3:
            min = 2; max = 2; return true;
          case 2:
            min = 1; max = 1; return true;
          }
        }
        break;
      }
      break;

    case OBElements::Nitrogen: // nitrogen
    case OBElements::Phosphorus: // phosphorus
      switch (chg) {
      case 0:
        switch (val) {
        case 3:
          switch (deg) {
          case 3:
            min = 2; max = 2; return true;
          case 2:
            min = 1; max = 1; return true;
          }
          break;
        case 5:
          if (deg == 3) {
            ExocyclicAtom exoatom = FindExocyclicAtom(atm);
            switch (exoatom) {
            case EXO_OXYGEN:
              min = 1; max = 1; return true;
            case EXO_NONOXYGEN:
              min = 2; max = 2; return true;
            default:
              ;
            }
          }
        }
        break;
      case 1:
        if (val == 4 && deg == 3) {
          min = 1; max = 1; return true;
        }
        break;
      case -1:
        if (val == 2 && deg == 2) {
          min = 2; max = 2; return true;
        }
      }
      break;

    case OBElements::Oxygen:
    case OBElements::Selenium:
      switch (chg) {
      case 0:
        if (val == 2 && deg == 2) {
          min = 2; max = 2; return true;
        }
      case 1:
        if (val == 3 && deg == 2) {
          min = 1; max = 1; return true;
        }
      }
      break;

    case OBElements::Sulfur:
      switch (chg) {
      case 0:
        switch (val) {
        case 2:
          if (deg == 2) {
            min = 2; max = 2; return true;
          }
          break;
        case 4:
          if (deg == 3 && HasExocyclicDblBondToOxygen(atm)) {
            min = 2; max = 2; return true;
          }
        }
        break;
      case 1:
        if (val == 3) {
          switch (deg) {
          case 2:
            min = 1; max = 1; return true;
          case 3:
            if (HasExocyclicBondToOxygenMinus(atm)) {
              min = 2; max = 2; return true;
            }
          }
        }
      }
      break;

    case OBElements::Boron:
      if (chg == 0 && val == 3) {
        switch (deg) {
        case 2:
          min = 1; max = 1; return true;
        case 3:
          min = 0; max = 0; return true;
        }
      }
      break;

    case OBElements::Arsenic:
      switch (chg) {
      case 0:
        if (val == 3) {
          switch (deg) {
          case 2:
            min = 1; max = 1; return true;
          case 3:
            min = 2; max = 2; return true;
          }
        }
        break;
      case 1:
        if (val == 4 && deg == 3) {
          min = 1; max = 1; return true;
        }
      }
      break;


    case 0: // Asterisk
      if (chg == 0) {
        switch (val) {
        case 2:
          switch (deg) {
          case 2:
          case 3:
            min = 0; max = 2; return true;
          }
          break;
        case 3:
          switch (deg) {
          case 2:
          case 3:
            min = 0; max = 1; return true;
          }
          break;
        }
      }
      break;
    }

    min = 0; max = 0; // nothing matched
    return false;
  }

  class OBAromaticTyperMolState
  {
  public:
    OBAromaticTyperMolState(OBMol &mol) : mol(mol)
    {
      _vpa.resize(mol.NumAtoms() + 1);
      _velec.resize(mol.NumAtoms() + 1);
      _root.resize(mol.NumAtoms() + 1);
      _visit.resize(mol.NumAtoms() + 1);
    }
    void AssignAromaticFlags();
  private:
    OBMol &mol;
    std::vector<bool>             _vpa;   //!< potentially aromatic atoms
    std::vector<bool>             _visit;
    std::vector<bool>             _root;
    std::vector<std::pair<int, int> >   _velec;   //!< # electrons an atom contributes

    //! "Anti-alias" potentially aromatic flags around a molecule
    //! (aromatic atoms need to have >= 2 neighboring ring atoms)
    void PropagatePotentialAromatic(OBAtom*);
    // Documentation in typer.cpp
    void SelectRootAtoms(bool avoidInnerRingAtoms = true);
    //! Remove 3-member rings from consideration
    void ExcludeSmallRing();
    //! Check aromaticity starting from the root atom, up to a specified depth
    void CheckAromaticity(OBAtom *root, int searchDepth);
    // Documentation in typer.cpp
    bool TraverseCycle(OBAtom *root, OBAtom *atom, OBBond *prev,
      std::pair<int, int> &er, int depth);
  };

  void OBAromaticTyperMolState::AssignAromaticFlags()
  {
    OBBond *bond;
    OBAtom *atom;
    vector<OBAtom*>::iterator i;
    vector<OBBond*>::iterator j;

    //unset all aromatic flags
    for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
      atom->SetAromatic(false);
    for (bond = mol.BeginBond(j); bond; bond = mol.NextBond(j))
      bond->SetAromatic(false);

    // New code using lookups instead of SMARTS patterns
    FOR_ATOMS_OF_MOL(atom, mol) {
      unsigned int idx = atom->GetIdx();
      _vpa[idx] = AssignOBAromaticityModel(&(*atom), _velec[idx].first, _velec[idx].second);
    }

    //propagate potentially aromatic atoms
    for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
      if (_vpa[atom->GetIdx()])
        PropagatePotentialAromatic(atom);

    //select root atoms
    SelectRootAtoms();

    ExcludeSmallRing(); //remove 3 membered rings from consideration

    //loop over root atoms and look for aromatic rings

    for (atom = mol.BeginAtom(i); atom; atom = mol.NextAtom(i))
      if (_root[atom->GetIdx()])
        CheckAromaticity(atom, 14);

    //for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
    //	  if (atom->IsAromatic())
    //		  cerr << "aro = " <<atom->GetIdx()  << endl;

    //for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
    //if (bond->IsAromatic())
    //cerr << bond->GetIdx() << ' ' << bond->IsAromatic() << endl;
  }

  /*! \class OBAromaticTyper typer.h <openbabel/typer.h>
    \brief Assigns aromatic typing to atoms and bonds

    The OBAromaticTyper class applies a set of
    aromatic perception rules to molecules. The code
    that performs typing is not usually used directly -- it is usually
    done automatically when their corresponding values are requested of atoms
    or bonds.
    \code
    atom->IsAromatic();
    bond->IsAromatic();
    \endcode
  */

  void OBAromaticTyper::AssignAromaticFlags(OBMol &mol)
  {
    if (mol.HasAromaticPerceived())
      return;
    mol.SetAromaticPerceived();
    obErrorLog.ThrowError(__FUNCTION__,
                          "Ran OpenBabel::AssignAromaticFlags", obAuditMsg);

    OBAromaticTyperMolState molstate(mol);
    molstate.AssignAromaticFlags();
  }

  /** \brief Traverse a potentially aromatic cycle starting at @p root.
      \return  True if the cycle is likely aromatic
      \param root  The initial, "root" atom in traversing this ring
      \param atom  The current atom to visit and check
      \param prev  The bond traversed in moving to this @p atom
      \param er    The min and max number of pi electrons for this ring
      \param depth The maximum number of atoms to visit in a ring (e.g., 6)

      This method traverses a potentially aromatic ring, adding up the possible
      pi electrons for each atom. At the end (e.g., when @p atom == @p root)
      the Huekel 4n+2 rule is checked to see if there is a possible electronic
      configuration which corresponds to aromaticity.
  **/
  bool OBAromaticTyperMolState::TraverseCycle(OBAtom *root, OBAtom *atom, OBBond *prev,
                                      std::pair<int,int> &er,int depth)
  {
    if (atom == root)
      {
        int i;
        for (i = er.first;i <= er.second;++i)
          if (i%4 == 2 && i > 2)
            return(true);

        return(false);
      }

    if (!depth || !_vpa[atom->GetIdx()] || _visit[atom->GetIdx()])
      return(false);

    bool result = false;

    depth--;
    er.first  += _velec[atom->GetIdx()].first;
    er.second += _velec[atom->GetIdx()].second;

    _visit[atom->GetIdx()] = true;
    OBAtom *nbr;
    vector<OBBond*>::iterator i;
    for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
      if (*i != prev && (*i)->IsInRing() && _vpa[nbr->GetIdx()])
        {
          if (TraverseCycle(root,nbr,(OBBond*)(*i),er,depth))
            {
              result = true;
              ((OBBond*) *i)->SetAromatic();
            }
        }

    _visit[atom->GetIdx()] = false;
    if (result)
      atom->SetAromatic();

    er.first  -= _velec[atom->GetIdx()].first;
    er.second -= _velec[atom->GetIdx()].second;

    return(result);
  }

  void OBAromaticTyperMolState::CheckAromaticity(OBAtom *atom,int depth)
  {
    OBAtom *nbr;
    vector<OBBond*>::iterator i;

    pair<int,int> erange;
    for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
      if ((*i)->IsInRing()) // check all rings, regardless of assumed aromaticity
        {
          erange = _velec[atom->GetIdx()];

          if (TraverseCycle(atom,nbr,(OBBond *)*i,erange,depth-1))
            {
              atom->SetAromatic();
              ((OBBond*) *i)->SetAromatic();
            }
        }
  }

  void OBAromaticTyperMolState::PropagatePotentialAromatic(OBAtom *atom)
  {
    int count = 0;
    OBAtom *nbr;
    vector<OBBond*>::iterator i;

    for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
      if ((*i)->IsInRing() && _vpa[nbr->GetIdx()])
        count++;

    if (count < 2)
      {
        _vpa[atom->GetIdx()] = false;
        if (count == 1)
          for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
            if ((*i)->IsInRing() && _vpa[nbr->GetIdx()])
              PropagatePotentialAromatic(nbr);
      }
  }

  /**
   * \brief Select the root atoms for traversing atoms in rings.
   *
   * Picking only the begin atom of a closure bond can cause
   * difficulties when the selected atom is an inner atom
   * with three neighbour ring atoms. Why ? Because this atom
   * can get trapped by the other atoms when determining aromaticity,
   * because a simple visited flag is used in the
   * OBAromaticTyper::TraverseCycle() method.
   *
   * Ported from JOELib, copyright Joerg Wegner, 2003 under the GPL version 2
   * Improved by Fabian (fab5) in 2009 -- PR#2889708
   *
   * @param mol the molecule
   * @param avoidInnerRingAtoms inner closure ring atoms with more than 2 neighbours will be avoided
   *
   */
  void OBAromaticTyperMolState::SelectRootAtoms(bool avoidInnerRingAtoms)
  {
    OBBond *bond;
    OBAtom *atom, *nbr, *nbr2;
    OBRing *ring;
    //    vector<OBAtom*>::iterator i;
    vector<OBBond*>::iterator j, l, nbr2Iter;
    vector<OBRing*> sssRings = mol.GetSSSR();
    vector<OBRing*>::iterator k;

    int rootAtom;
    int ringNbrs;
    int heavyNbrs;
    int newRoot = -1;
    vector<int> tmpRootAtoms;
    vector<int> tmp;

    vector<OBBond*> cbonds;
    vector< vector<OBRing*> > ringAtoms; // store ring pointers on an atom basis

    //generate list of closure bonds
    for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j))
      {
        if( bond->IsClosure() )
          {
            cbonds.push_back(bond);
            if(avoidInnerRingAtoms)
              {
                tmpRootAtoms.push_back(bond->GetBeginAtomIdx());
              }
          }
      }

    if(avoidInnerRingAtoms)
      {
        //for every atom fill vector with ring pointer it's associated with
        ringAtoms.resize(mol.NumAtoms()+1);
        for (k = sssRings.begin();k != sssRings.end();++k)
          {
            tmp = (*k)->_path;
            for (unsigned int j (0),j_end(tmp.size()); j < j_end; ++j)
              {
                ringAtoms[tmp[j]].push_back(*k);
              }
          }
      }


    //loop over closure bonds
    for(OBBondIterator bd(cbonds.begin()),bd_end(cbonds.end());bd!=bd_end;++bd)
      {
        bond = *bd;

        // BASIC APPROACH
        // pick beginning atom at closure bond
        // this is really ready, isn't it ! ;-)
        rootAtom = bond->GetBeginAtomIdx();
        _root[rootAtom] = true;

        // EXTENDED APPROACH
        if (avoidInnerRingAtoms)
          {
            // count the number of neighbor ring atoms
            atom = mol.GetAtom(rootAtom);
            ringNbrs = heavyNbrs = 0;

            for (nbr = atom->BeginNbrAtom(l);nbr;nbr = atom->NextNbrAtom(l))
              {
                // we can get this from atom->GetHvyDegree()
                // but we need to find neighbors in rings too
                // so let's save some time
                if (nbr->GetAtomicNum() != OBElements::Hydrogen)
                  {
                    heavyNbrs++;
                    if (nbr->IsInRing())
                      ringNbrs++;
                  }

                // if this atom has more than 2 neighbor ring atoms
                // we could get trapped later when traversing cycles
                // which can cause aromaticity false detection
                newRoot = -1;

                if (ringNbrs > 2)
                  {
                    // try to find another root atom
                    // only loop over rings which contain rootAtom
                    for(k = ringAtoms[rootAtom].begin() ; k != ringAtoms[rootAtom].end(); ++k)
                      {
                        ring = (*k);
                        tmp = ring->_path;

                        bool checkThisRing = false;
                        int rootAtomNumber=0;
                        int idx=0;
                        // avoiding two root atoms in one ring !
                        for (unsigned int j = 0; j < tmpRootAtoms.size(); ++j)
                          {
                            idx= tmpRootAtoms[j];
                            if(ring->IsInRing(idx))
                              {
                                rootAtomNumber++;
                                if(rootAtomNumber>=2)
                                  break;
                              }
                          }
                        if(rootAtomNumber<2)
                          {
                            for (unsigned int j = 0; j < tmp.size(); ++j)
                              {
                                // find critical ring
                                if (tmp[j] == rootAtom)
                                  {
                                    checkThisRing = true;
                                  }
                                else
                                  {
                                    // second root atom in this ring ?
                                    if (_root[tmp[j]] == true)
                                      {
                                        // when there is a second root
                                        // atom this ring can not be
                                        // used for getting an other
                                        // root atom
                                        checkThisRing = false;

                                        break;
                                      }
                                  }
                              }
                          }

                        // check ring for getting another
                        // root atom to avoid aromaticity typer problems
                        if (checkThisRing)
                          {
                            // check if we can find another root atom
                            for (unsigned int m = 0; m < tmp.size(); ++m)
                              {
                                ringNbrs = heavyNbrs = 0;
                                for (nbr2 = (mol.GetAtom(tmp[m]))->BeginNbrAtom(nbr2Iter);
                                     nbr2;nbr2 = (mol.GetAtom(tmp[m]))->NextNbrAtom(nbr2Iter))
                                  {
                                    if (nbr2->GetAtomicNum() != OBElements::Hydrogen)
                                      {
                                        heavyNbrs++;

                                        if (nbr2->IsInRing())
                                          ringNbrs++;
                                      }
                                  }

                                // if the number of neighboured heavy atoms is also
                                // the number of neighboured ring atoms, the aromaticity
                                // typer could be stuck in a local traversing trap
                                if (ringNbrs <= 2 && ring->IsInRing((mol.GetAtom(tmp[m])->GetIdx())))
                                  {
                                    newRoot = tmp[m];
                                  }
                              }
                          }
                      }

                    if ((newRoot != -1) && (rootAtom != newRoot))
                      {
                        // unset root atom
                        _root[rootAtom] = false;

                        // pick new root atom
                        _root[newRoot] = true;
                      }
                  } // if (ringNbrs > 2)

              } // end for
          } // if (avoid)
      } // end for(closure bonds)
  }

  void OBAromaticTyperMolState::ExcludeSmallRing()
  {
    OBAtom *atom,*nbr1,*nbr2;
    vector<OBAtom*>::iterator i;
    vector<OBBond*>::iterator j,k;

    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
      if (_root[atom->GetIdx()])
        for (nbr1 = atom->BeginNbrAtom(j);nbr1;nbr1 = atom->NextNbrAtom(j))
          if ((*j)->IsInRing() && _vpa[nbr1->GetIdx()])
            for (nbr2 = nbr1->BeginNbrAtom(k);nbr2;nbr2 = nbr1->NextNbrAtom(k))
              if (nbr2 != atom && (*k)->IsInRing() && _vpa[nbr2->GetIdx()])
                if (atom->IsConnected(nbr2))
                  _root[atom->GetIdx()] = false;
  }

} //namespace OpenBabel;

//! \file typer.cpp
//! \brief Open Babel atom and aromaticity typer.