kekulizer.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_KEKULIZER_H
#define BALL_STRUCTURE_KEKULIZER_H

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

#ifndef BALL_DATATYPE_HASHMAP_H
# include <BALL/DATATYPE/hashMap.h>
#endif 

#include <set>

namespace BALL
{
  class Atom;
  class Molecule;
  class Bond;

  class BALL_EXPORT Kekuliser
  {
    struct BALL_EXPORT AtomInfo
    {
      // needed for sorting:
      bool operator < (const AtomInfo& info) const;
      AtomInfo& operator = (const AtomInfo& ai) ;

      // THE atom 
      Atom* atom;

      // bond to be set to a double bond
      Bond* double_bond;

      // aromatic bonds
      std::vector<Bond*> abonds;

      // position of the partner atoms in the vector of AtomInfos
      std::vector<Position> partner_id;

      // current number of double bonds for this atom
      Index curr_double;

      // minumum possible number of double bonds for this atom
      Index min_double;
      
      // maximum possible number of double bonds for this atom
      Index max_double;
      
      // number of double bonds for this atom to be uncharged
      Index uncharged_double;
    };

    public:

    BALL_CREATE(Kekuliser)

    
    Kekuliser();

    virtual ~Kekuliser() {}

    bool setup(Molecule& ac);

    void setAromaticRings(const std::vector<std::set<Atom*> >& rings) { aromatic_rings_ = rings;}
    
    void setRings(const std::vector<std::set<Atom*> >& rings) { rings_ = rings;}
    
    const std::vector<Bond*>& getUnassignedBonds() const { return unassigned_bonds_; }

    void clear();

    void dump();

    void setUseFormalCharges(bool state) { use_formal_charges_ = state;}

    bool useFormalCharges() const { return use_formal_charges_;}

    protected:

    bool fixAromaticRings_();
    void fixAromaticSystem_(Position it);
    virtual Size getPenalty_(Atom& atom, Index charge);

    void getMaximumValence_();

    // merge aromatic rings:
    void calculateAromaticSystems_();
    void collectSystems_(Atom& atom);
    void collectAromaticAtoms_();
    bool hasAromaticBonds_(Atom& atom);
    void applySolution_(Position pos);
    Position calculateDistanceScores_();

    bool use_formal_charges_;

    std::vector<std::set<Atom*> > aromatic_systems_;
    std::vector<std::set<Atom*> > aromatic_rings_;
    std::vector<std::set<Atom*> > rings_;
    std::vector<Bond*>          unassigned_bonds_;

    // atoms that take part in an aromatic bond:
    std::set<const Atom*>     aromatic_atoms_;
    std::set<const Atom*>     all_aromatic_atoms_;
    HashMap<Atom*, Index>   max_valence_;

    std::set<Atom*>           current_aromatic_system_;

    // current aromatic system:
    std::vector<AtomInfo>         atom_infos_;
    Molecule*               molecule_;
    Size                    lowest_penalty_;
    Size                    current_penalty_;

    std::vector<std::vector<AtomInfo> > solutions_;
  };

} // namespace BALL

#endif // BALL_STRUCTURE_KEKULIZER_H

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