query.h

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/**********************************************************************
  query.h - OBQuery, OBQueryAtom & OBQueryBond classes.

  Copyright (C) 2010 by Tim Vandermeersch

  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; either version 2 of the License, or
  (at your option) any later version.

  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.

  You should have received a copy of the GNU General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
  02110-1301, USA.
 **********************************************************************/
#ifndef OB_QUERY_H
#define OB_QUERY_H

#include <openbabel/bond.h> // TODO: Move OBBond code out of this header
#include <openbabel/bitvec.h>
#include <openbabel/tokenst.h>

namespace OpenBabel {

  class OBQueryBond;
  class OBMol;


  class OBAPI OBQueryAtom
  {
    public:
      friend class OBQuery;
      friend class OBQueryBond;
      OBQueryAtom(int atomicNum = 6, bool isInRing = false, bool isAromatic = false) :
        m_atomicNum(atomicNum), m_isInRing(isInRing), m_isAromatic(isAromatic) {}

      virtual ~OBQueryAtom() {}

      unsigned int GetIndex() const
      {
        return m_index;
      }
      const std::vector<OBQueryBond*>& GetBonds() const
      {
        return m_bonds;
      }
      const std::vector<OBQueryAtom*>& GetNbrs() const
      {
        return m_nbrs;
      }
      virtual bool Matches(const OBAtom *atom) const
      {
        if (atom->GetAtomicNum() != m_atomicNum)
          return false;
        if (atom->IsAromatic() != m_isAromatic)
          return false;
        if (m_isInRing)
          if (!atom->IsInRing())
            return false;
        return true;
      }
    protected:
      unsigned int m_index;
      unsigned int m_atomicNum;
      bool m_isInRing, m_isAromatic;
      std::vector<OBQueryBond*> m_bonds;
      std::vector<OBQueryAtom*> m_nbrs;
  };

  class OBAPI OBQueryBond
  {
    public:
      friend class OBQuery;
      OBQueryBond(OBQueryAtom *begin, OBQueryAtom *end, int order = 1, bool aromatic = false) :
          m_begin(begin), m_end(end), m_order(order), m_aromatic(aromatic)
      {
        m_begin->m_bonds.push_back(this);
        m_end->m_bonds.push_back(this);
        m_begin->m_nbrs.push_back(m_end);
        m_end->m_nbrs.push_back(m_begin);
      }

      virtual ~OBQueryBond() {}

      unsigned int GetIndex() const
      {
        return m_index;
      }
      OBQueryAtom* GetBeginAtom() const { return m_begin; }
      OBQueryAtom* GetEndAtom() const { return m_end; }
      virtual bool Matches(const OBBond *bond) const
      {
        if (m_aromatic)
          return bond->IsAromatic();
        return bond->GetBondOrder() == m_order;
      }
    protected:
      unsigned int m_index;
      OBQueryAtom *m_begin, *m_end;
      unsigned int m_order;
      bool m_aromatic;
  };

  class OBAPI OBQuery
  {
    public:
      ~OBQuery();
      unsigned int NumAtoms() const
      {
        return m_atoms.size();
      }
      unsigned int NumBonds() const
      {
        return m_bonds.size();
      }
      const std::vector<OBQueryAtom*>& GetAtoms() const
      {
        return m_atoms;
      }
      const std::vector<OBQueryBond*>& GetBonds() const
      {
        return m_bonds;
      }
      OBQueryBond* GetBond(OBQueryAtom *begin, OBQueryAtom *end) const
      {
        for (unsigned int i = 0; i < begin->GetBonds().size(); ++i)
          if (begin->GetNbrs()[i] == end)
            return begin->GetBonds()[i];
        return 0;
      }
      void AddAtom(OBQueryAtom *atom)
      {
        atom->m_index = m_atoms.size();
        m_atoms.push_back(atom);
      }
      void AddBond(OBQueryBond *bond)
      {
        bond->m_index = m_bonds.size();
        m_bonds.push_back(bond);
      }
    protected:
      std::vector<OBQueryAtom*> m_atoms;
      std::vector<OBQueryBond*> m_bonds;
  };

  OBAPI OBQuery* CompileMoleculeQuery(OBMol *mol, const OBBitVec &mask = OBBitVec());

  OBAPI OBQuery* CompileSmilesQuery(const std::string &smiles, const OBBitVec &mask = OBBitVec());

}

#endif