MOL2File.h

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

#ifndef BALL_FORMAT_MOL2FILE_H
#define BALL_FORMAT_MOL2FILE_H

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

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

#ifndef BALL_KERNEL_ATOMCONTAINER_H
# include <BALL/KERNEL/atomContainer.h>
#endif

namespace BALL
{
  class Atom;
  class System;

  class BALL_EXPORT MOL2File
    : public GenericMolFile
  {
    public:

    struct BALL_EXPORT SetStruct
    {
      String      name;
      bool        is_static;
      String      obj_type;
      String      sub_type;
      String      status;
      String      comment;
      Size        number_of_members;

      vector<Index>  static_members;
      String         dynamic_rule;
    };


    static const String TRIPOS;


    MOL2File();

    MOL2File(const String& filename, File::OpenMode open_mode = std::ios::in);

    virtual ~MOL2File();



    virtual bool write(const System& system);

    virtual bool read(System& system);

    virtual Molecule* read();

    virtual bool write(const Molecule& molecule);

    const MOL2File& operator = (const MOL2File& file);

    Size getNumberOfSets() const { return sets_.size(); }

    SetStruct& getSet(Position i) { return sets_[i]; }

    const SetStruct& getSet(Position i) const { return sets_[i]; }


    protected:

    void readAtomSection_();

    void readBondSection_();

    void  readMoleculeSection_();

    void readSetSection_();

    void readSubstructureSection_();

    void readCommentSection_();

    String getSybylType_(const Atom& atom) const;

    bool nextLine_();

    void clear_();

    bool buildAll_(Molecule& molecule);

    bool containsAtomChilds_(AtomContainerConstIterator& frag_it);

    struct BALL_EXPORT AtomStruct
    {
      String    name;
      Vector3   position;
      String    type;
      Position  substructure;
      String    substructure_name;
      float     charge;
    };

    struct BALL_EXPORT BondStruct
    {
      Position  atom1;
      Position  atom2;
      String    type;
    };

    struct BALL_EXPORT MoleculeStruct
    {
      String      name;
      Size        number_of_atoms;
      Size        number_of_bonds;
      Size        number_of_substructures;
      Size        number_of_features;
      Size        number_of_sets;
      String      type;
      String      charge_type;
      String      comment;
    };

    struct BALL_EXPORT SubstructureStruct
    {
      String      name;
      Size        root_atom;
      String      substructure_type;
      Size        dictionary_type;
      String      chain;
      String      sub_type;
      Size        inter_bonds;
      String      comment;
    };

    struct BALL_EXPORT CommentStruct
    {
      String name;
      String value;
    };


    vector<AtomStruct>          atoms_;
    vector<BondStruct>          bonds_;
    vector<SetStruct>           sets_;
    vector<SubstructureStruct>  substructures_;
    vector<CommentStruct> comments_;
    MoleculeStruct              molecule_;

    Size  number_of_lines_;
    static const Size MAX_LENGTH_;
    char buffer_[4096];
    String line_;
    bool found_next_header_;
  };
} // namespace BALL

#endif // BALL_FORMAT_MOL2FILE_H