clipper_mmdb.h

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//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
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#ifndef CLIPPER_MMDB
#define CLIPPER_MMDB


#include "../core/coords.h"

#include <mmdb/mmdb_manager.h>


namespace clipper {

  namespace mmdb {
    typedef ::CAtom CAtom;
    typedef ::CResidue CResidue;
    typedef ::CChain CChain;
    typedef ::CModel CModel;
    typedef ::CMMDBManager CMMDBManager;

    typedef ::PCAtom PCAtom;
    typedef ::PCResidue PCResidue;
    typedef ::PCChain PCChain;
    typedef ::PCModel PCModel;
    typedef ::PCMMDBManager PCMMDBManager;

    typedef ::PPCAtom PPCAtom;
    typedef ::PPCResidue PPCResidue;
    typedef ::PPCChain PPCChain;
    typedef ::PPCModel PPCModel;
    typedef ::PPCMMDBManager PPCMMDBManager;
  }

  // PDB 'sigma' classes (should be depracated)


  class Sig_Coord_orth : public Vec3<>
  {
  public:
    Sig_Coord_orth() {}    
    explicit Sig_Coord_orth( const Vec3<>& v ) :
      Vec3<>( v ) {}  
    Sig_Coord_orth( const ftype& sigx, const ftype& sigy, const ftype& sigz ) :
      Vec3<>( sigx, sigy, sigz ) {}    
    const ftype& sigx() const { return (*this)[0]; }  
    const ftype& sigy() const { return (*this)[1]; }  
    const ftype& sigz() const { return (*this)[2]; }  
  };


  class Sig_U_aniso_orth : public Mat33sym<>
  {
  public:
    Sig_U_aniso_orth() {};
    explicit Sig_U_aniso_orth( const Mat33sym<>& m ) : Mat33sym<>(m) {}
    Sig_U_aniso_orth( const ftype& su11, const ftype& su22, const ftype& su33,
                 const ftype& su12, const ftype& su13, const ftype& su23 ) :
      Mat33sym<>( su11, su22, su33, su12, su13, su23 ) {}
  };



  class MMDBAtom : public mmdb::CAtom
  {
  public:
    MMDBAtom() {}
    MMDBAtom( const mmdb::CAtom& a ) : mmdb::CAtom(a) {}

    // standard atom properties
    String id() const;              
    String element() const;         
    Coord_orth coord_orth() const;  
    ftype occupancy() const;        
    ftype u_iso() const;            
    U_aniso_orth u_aniso_orth() const;  
    void set_id( const String& n );                  
    void set_element( const String& n );             
    void set_coord_orth( const Coord_orth& v );      
    void set_occupancy( const ftype& v );            
    void set_u_iso( const ftype& v );                
    void set_u_aniso_orth( const U_aniso_orth& v );  
    Sig_Coord_orth sig_coord_orth() const;  // stupid sigmas
    ftype sig_occupancy() const;
    ftype sig_u_iso() const;
    Sig_U_aniso_orth sig_u_aniso_orth() const;
    void set_sig_coord_orth( const Sig_Coord_orth& s );
    void set_sig_occupancy( const ftype& s );
    void set_sig_u_iso( const ftype& s );
    void set_sig_u_aniso_orth( const Sig_U_aniso_orth& s );
    // other atom properties
    String altconf() const;         
    int serial_num() const;         
    String charge() const;          
  };


  class MMDBResidue : public mmdb::CResidue
  {
  public:
    MMDBResidue() {}
    MMDBResidue( const mmdb::CResidue& a ) : mmdb::CResidue(a) {}
 
    // standard residue properties
    String type() const;
    int seqnum() const;
    String inscode() const;
    void set_type( const String& n );
    void set_seqnum( const int& n );
    void set_inscode( const String& n );
  };


  class MMDBChain : public mmdb::CChain
  {
  public:
    MMDBChain() {}
    MMDBChain( const mmdb::CChain& a ) : mmdb::CChain(a) {}

    // chain properties
    String id() const;
    void set_id( const String& n );
  };


  class MMDBModel : public mmdb::CModel
  {
  public:
    MMDBModel()  {}
    MMDBModel( const mmdb::CModel& a ) : mmdb::CModel(a) {}

    // model properties
    String id() const;
    void set_id( const String& n );
  };


  class MMDBManager : public mmdb::CMMDBManager
  {
  public:
    enum TYPE { Default=-1, PDB, CIF, Binary };
    MMDBManager();   
    ~MMDBManager();  
    Spacegroup spacegroup() const;                        
    Cell cell() const;                                    
    void set_spacegroup( const Spacegroup& spacegroup );  
    void set_cell( const Cell& cell );                    
    //-- int ReadCoorFile( char* name );                       //!< For file i/o see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_rdwr.html
    //-- void select( int hnd, int typ, char* str, int key );  //!< For selection functions see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_selfnc.html
    //-- PCModel GetModel ( int  modelNo );                    //!< For accessor functions see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_surf.html
    //-- int AddModel ( PCModel  model );                      //!< For editing functions see http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_edit.html
  };


  class MMDBAtom_list : public Atom_list
  {
  public:
    MMDBAtom_list( const mmdb::PPCAtom ppcatom, const int natom );
  };


} // namespace clipper

#endif

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