MMFF94Processors.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: MMFF94Processors.h,v 1.1.8.1 2007/03/25 21:25:18 oliver Exp $ 
//

#ifndef BALL_MOLMEC_MMFF94_PROCESSORS_H
#define BALL_MOLMEC_MMFF94_PROCESSORS_H

#ifndef BALL_MOLMEC_MMFF94_MMFF94PARAMETERS_H
# include <BALL/MOLMEC/MMFF94/MMFF94Parameters.h>
#endif

#ifndef BALL_DATATYPE_HASHSET_H
# include <BALL/DATATYPE/hashSet.h>
#endif

#ifndef BALL_DATATYPE_STRINGHASHMAP_H
# include <BALL/DATATYPE/stringHashMap.h>
#endif

#ifndef BALL_KERNEL_BOND_H
# include <BALL/KERNEL/bond.h>
#endif

#ifndef BALL_STRUCTURE_ATOMTYPER_H
# include <BALL/STRUCTURE/atomTyper.h>
#endif

#include <vector>

namespace BALL 
{
  using std::vector;

  class MMFF94ESParameters;
  class Molecule;
  class System;

  class BALL_EXPORT MMFF94AtomTyper
    : public AtomTyper
  {
    public:

    struct AromaticType
    {
      String new_type;
      Position atomic_number;
      bool     cation;
      bool     anion;
    };

    BALL_CREATE(MMFF94AtomTyper)

    
    MMFF94AtomTyper();

    MMFF94AtomTyper(const MMFF94AtomTyper& t);

    virtual ~MMFF94AtomTyper() {};

    virtual void assignTo(System& s);

    virtual bool setupHydrogenTypes(Parameters& p, const String& section);

    virtual bool setupSymbolsToTypes(Parameters& p, const String& section);

    virtual bool setupAromaticTypes(Parameters& p, const String& section);

    void collectHeteroAtomTypes(const MMFF94AtomTypes& atom_types);

    protected:

    bool assignAromaticType_5_(Atom& atom, Position L5, bool anion, bool cation);

    StringHashMap<String> partner_type_to_htype_;
    StringHashMap<Position> id_to_type_;
    HashMap<String, AromaticType> aromatic_types_5_map_;
    HashSet<String> cation_atoms_;
    MMFF94AtomTypes* atom_types_;
    HashSet<Position> hetero_atom_types_;
  };


  class BALL_EXPORT MMFF94ChargeProcessor
    : public UnaryProcessor<Atom>
  {
    public:

    BALL_CREATE(MMFF94ChargeProcessor)

    
    MMFF94ChargeProcessor();

    MMFF94ChargeProcessor(const MMFF94ChargeProcessor& cp);
 
    virtual ~MMFF94ChargeProcessor() {};

    const MMFF94ChargeProcessor& operator = (const MMFF94ChargeProcessor& cp)
      ;

    virtual void clear()
      ;
    
    virtual bool start();

    virtual bool finish();

    virtual Processor::Result operator () (Atom& atom);

    void assignFormalCharge(Atom& atom);
    
    const HashSet<Atom*>& getUnassignedAtoms() { return unassigned_atoms_;}

    void setESParameters(const MMFF94ESParameters& es) { es_parameters_ = &es; }

    void setup(const String& filename);

    void setAromaticRings(const vector<HashSet<Atom*> >& rings) { aromatic_rings_ = rings;}

    protected:

    void assignPartialCharges_();

    vector<Atom*>               atoms_;
    HashSet<Atom*>              unassigned_atoms_;
    const MMFF94ESParameters*   es_parameters_;
    HashMap<String, float>      types_to_charges_;
    HashSet<String>             rule_types_;
    vector<HashSet<Atom*> >     aromatic_rings_;
  };
  
} // namespace BALL

#endif // BALL_MOLMEC_MMFF94_PROCESSORS_H