minimol.h

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//C Copyright (C) 2000-2006 Kevin Cowtan and University of York
//L
//L  This library is free software and is distributed under the terms
//L  and conditions of version 2.1 of the GNU Lesser General Public
//L  Licence (LGPL) with the following additional clause:
//L
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//L     not covered by this licence.)'
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//L  Note that this clause grants an additional right and does not impose
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//L  You can redistribute it and/or modify the library under the terms of
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//L  later version.
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//L  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
//L  Lesser General Public License for more details.
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#ifndef CLIPPER_MINIMOL
#define CLIPPER_MINIMOL


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


namespace clipper {

  namespace MM {
    enum MODE { UNIQUE, ANY };
    enum COPY { COPY_NONE, COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, MEMBERS=COPY_M, PROPERTIES=COPY_P, CHILDREN=COPY_C };
  }



  class MAtom : public Atom, public PropertyManager
  {
  public:
    MAtom() {}  
    MAtom( const clipper::Atom& atom );  

    const String& id() const { return id_; }
    void set_id( const String& s );      

    String name() const { return id_.substr(0,4); }
    void set_name( const String s, const String altconf="" );  

    //-- const String& element() const;  //!< get element e.g. H, C, Zn2+
    //-- const Coord_orth& coord_orth() const;      //!< get orth coordinate
    //-- const ftype& occupancy() const;            //!< get occupancy
    //-- const ftype& u_iso() const;                //!< get isotropic U
    //-- const U_aniso_orth& u_aniso_orth() const;  //!< get anisotropic U
    //-- void set_element( const String& s );             //!< set element
    //-- void set_coord_orth( const Coord_orth& s );      //!< set coord_orth
    //-- void set_occupancy( const ftype& s );            //!< set occupancy
    //-- void set_u_iso( const ftype& s );                //!< set u_iso
    //-- void set_u_aniso_orth( const U_aniso_orth& s );  //!< set u_aniso
    //-- void transform( const RTop_orth rt );  //!< apply transform to object
    const Atom& atom() const { return *this; }  
    Atom& atom() { return *this; }              

    MAtom& copy( const MAtom& other, const MM::COPY& mode );

    static String id_tidy( const String& id );  
    static bool id_match( const String& id1, const String& id2, const MM::MODE& mode );  
  private:
    String id_;
  };


  class MMonomer : public PropertyManager
  {
  public:
    const String& id() const { return id_; }  
    void set_id( const String& s );           

    const String& type() const { return type_; }   
    void set_type( const String& s );  

    int seqnum() const { return id_.i(); }  
    void set_seqnum( const int s, const String inscode="" ); 

    // the following methods are similar for all levels of the hierarchy
    Atom_list atom_list() const;           
    void transform( const RTop_orth rt );  

    int size() const { return children.size(); }
    const MAtom& operator[] ( const int& i ) const { return children[i]; }
    MAtom& operator[] ( const int& i ) { return children[i]; }
    const MAtom& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const;
    MAtom& find( const String& n, const MM::MODE mode=MM::UNIQUE );
    MMonomer select( const String& sel, const MM::MODE mode=MM::UNIQUE ) const;
    int lookup( const String& str, const MM::MODE& mode ) const;
    void insert( const MAtom& add, int pos=-1 );  

    friend MMonomer operator& ( const MMonomer& m1, const MMonomer& m2 );
    friend MMonomer operator| ( const MMonomer& m1, const MMonomer& m2 );

    MMonomer& copy( const MMonomer& other, const MM::COPY& mode );

    static String id_tidy( const String& id );  
    static bool id_match( const String& id1, const String& id2, const MM::MODE& mode );  

    enum TYPE { Default, Dunbrack, Richardson };
    void protein_mainchain_build_carbonyl_oxygen( const MMonomer& next );
    int protein_sidechain_number_of_rotamers( TYPE t = default_type_ ) const;
    int protein_sidechain_number_of_rotomers() const { return protein_sidechain_number_of_rotamers(); }
    ftype protein_sidechain_build_rotamer( const int& n, TYPE t = default_type_ );
    ftype protein_sidechain_build_rotomer( const int& n ) { return protein_sidechain_build_rotamer( n ); }
    static bool protein_peptide_bond( const MMonomer& m1, const MMonomer& m2, ftype r = 1.5 );
    static double protein_ramachandran_phi( const MMonomer& m1, const MMonomer& m2 );
    static double protein_ramachandran_psi( const MMonomer& m1, const MMonomer& m2 );

    static TYPE& default_type() { return default_type_; }
  private:
    typedef MAtom CHILDTYPE;
    std::vector<CHILDTYPE> children;
    String id_, type_;
    static TYPE default_type_;
    static int rotamer_find( String res, int rota, TYPE t );
  };


  class MPolymer : public PropertyManager
  {
  public:
    const String& id() const { return id_; }  
    void set_id( const String& s );           

    // the following methods are similar for all levels of the hierarchy
    Atom_list atom_list() const;           
    void transform( const RTop_orth rt );  

    int size() const { return children.size(); }
    const MMonomer& operator[] ( const int& i ) const { return children[i]; }
    MMonomer& operator[] ( const int& i ) { return children[i]; }
    const MMonomer& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const;
    MMonomer& find( const String& n, const MM::MODE mode=MM::UNIQUE );
    MPolymer select( const String& sel, const MM::MODE mode=MM::UNIQUE ) const;
    int lookup( const String& str, const MM::MODE& mode ) const;
    void insert( const MMonomer& add, int pos=-1 );  

    friend MPolymer operator& ( const MPolymer& m1, const MPolymer& m2 );
    friend MPolymer operator| ( const MPolymer& m1, const MPolymer& m2 );

    MPolymer& copy( const MPolymer& other, const MM::COPY& mode );

    static String id_tidy( const String& id );  
    static bool id_match( const String& id1, const String& id2, const MM::MODE& mode );  
  private:
    typedef MMonomer CHILDTYPE;
    std::vector<CHILDTYPE> children;
    String id_;
  };


  class MModel : public PropertyManager
  {
  public:
    // the following methods are similar for all levels of the hierarchy
    Atom_list atom_list() const;           
    void transform( const RTop_orth rt );  

    int size() const { return children.size(); }
    const MPolymer& operator[] ( const int& i ) const { return children[i]; }
    MPolymer& operator[] ( const int& i ) { return children[i]; }
    const MPolymer& find( const String& n, const MM::MODE mode=MM::UNIQUE ) const;
    MPolymer& find( const String& n, const MM::MODE mode=MM::UNIQUE );
    MModel select( const String& sel, const MM::MODE mode=MM::UNIQUE ) const;
    int lookup( const String& str, const MM::MODE& mode ) const;
    void insert( const MPolymer& add, int pos=-1 );  

    friend MModel operator& ( const MModel& m1, const MModel& m2 );
    friend MModel operator| ( const MModel& m1, const MModel& m2 );

    MModel& copy( const MModel& other, const MM::COPY& mode );
  private:
    typedef MPolymer CHILDTYPE;
    std::vector<CHILDTYPE> children;
  };


  class MiniMol : public MModel
  {
  public:
    enum MODE { UNIQUE, ANY };  

    MiniMol();
    MiniMol( const Spacegroup& spacegroup, const Cell& cell );
    void init( const Spacegroup& spacegroup, const Cell& cell );
    const Cell& cell() const { return cell_; }
    const Spacegroup& spacegroup() const { return spacegroup_; }
    const MModel& model() const { return *this; }  
    MModel& model() { return *this; }              

    bool is_null() const;  
  private:
    Spacegroup spacegroup_;
    Cell cell_;
  };

  typedef MMonomer MResidue;

  typedef MPolymer MChain;


} // namespace clipper

#endif