MOLFile.h

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

#ifndef BALL_FORMAT_MOLFILE_H
#define BALL_FORMAT_MOLFILE_H

#ifndef BALL_FORMAT_GENERICMOLFILE_H
# include <BALL/FORMAT/genericMolFile.h>
#endif

#ifndef BALL_MATHS_VECTOR3_H
# include <BALL/MATHS/vector3.h>
#endif

namespace BALL 
{
  class System;
  class Atom;
  class Molecule;

  class BALL_EXPORT MOLFile
    : public GenericMolFile
  {
    public:


    BALL_EXPORT struct Property
    {
      static const String ATOM_MASS_DIFFERENCE;
      static const String ATOM_HYDROGEN_COUNT;
      static const String ATOM_STEREO_CARE_BOX;
      static const String ATOM_VALENCE;
      static const String ATOM_H0_DESIGNATOR;
      static const String ATOM_REACTION_COMPONENT_TYPE;
      static const String ATOM_REACTION_COMPONENT_NUMBER;
      static const String ATOM_INVERSION_RETENTION;
      static const String ATOM_EXACT_CHANGE;

      static const String BOND_STEREO;
      static const String BOND_TOPOLOGY;
      static const String BOND_REACTING_CENTER_STATUS;
    };

    class BALL_EXPORT CountsStruct
    {
      public:
      Size    number_of_atoms;
      Size    number_of_bonds;
      Size    number_of_atom_lists;
      bool    chiral;
      Size    number_of_stext_entries;
      Size    number_of_reaction_components;
      Size    number_of_reactants;
      Size    number_of_products;
      Size    number_of_intermediates;
      String  version;
    };

    class BALL_EXPORT AtomStruct
    {
      public:
      Vector3   position;
      String    symbol;
      Index     mass_difference;
      Index     charge;
      Index     parity;
      Size      hydrogen_count;
      bool      stereo_care_box;
      Size      valence;
      bool      H0_designator;
      Position  reaction_component_type;
      Position  reaction_component_number;
      Position  number;
      Position  inversion_retention;
      bool      exact_change;
    };

    class BALL_EXPORT BondStruct
    {
      public:
      Position  first_atom;
      Position  second_atom;
      Position  type;
      Position  stereo;
      Position  topology;
      Position  reacting_center_status;
    };


    MOLFile();

    MOLFile(const String& filename, File::OpenMode open_mode = std::ios::in);

    virtual ~MOLFile();
    

    
    virtual bool write(const Molecule& molecule);

    virtual bool write(const System& system);
    
    virtual bool read(System& system);

    virtual Molecule* read();
      
    const MOLFile& operator = (const MOLFile& file);


    protected:

    static const String counts_format_;

    static const String atom_format_;

    static const String bond_format_;

    Molecule* readCTAB_(std::vector<Atom*>& atom_map);

    bool readCountsLine_(CountsStruct& counts);

    bool readAtomLine_(AtomStruct& atom);

    bool readBondLine_(BondStruct& bond);

    void writeCountsLine_(const CountsStruct& counts);

    void writeAtomLine_(const AtomStruct& atom);

    void writeBondLine_(const BondStruct& bond);
  };
} // namespace BALL

#endif // BALL_FORMAT_MOLFILE_H