geometry.h

/* Copyright 2004
Stanford University

This file is part of the DSR PDB Library.

The DSR PDB Library is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation; either version 2.1 of the License, or (at your
option) any later version.

The DSR PDB Library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details.

You should have received a copy of the GNU Lesser General Public License
along with the DSR PDB Library; see the file COPYING.LIB.  If not, write to
the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
MA 02111-1307, USA. */

#ifndef DSR_PDB_GEOMETRY_H
#define DSR_PDB_GEOMETRY_H

#include <dsrpdb/Protein.h>
#include <dsrpdb/iterator.h>
#include <vector>
#include <cassert>
#include <dsrpdb/geometry_internal.h>

namespace dsrpdb {

  template <class Ait, class Voit>
  inline void coordinates(Ait ab, Ait ae, Voit out){
    internal::filtered_coordinates(ab, ae, Yes(), out);
  }
  

  template <class Ait, class Voit>
  inline void backbone_coordinates(Ait ab, Ait ae, Voit out){
    internal::filtered_coordinates(ab, ae, Is_backbone(), out);
  }
  

  template <class Ait, class Voit>
  inline void ca_coordinates(Ait ab, Ait ae, Voit out){
    internal::filtered_coordinates(ab, ae, Is_CA(), out);
  }
  
  



  template <class Voit, class Boit>
  inline void coordinates_and_bonds(const Protein &p, Voit out, Boit bout){
    internal::filtered_coordinates_and_bonds(p, Yes(), out, bout);
  }


  template <class Voit, class Boit>
  inline void backbone_coordinates_and_bonds(const Protein &p, Voit out, Boit bout){
    internal::filtered_coordinates_and_bonds(p, Is_backbone(), out, bout);
  }



  template <class Voit, class Boit>
  inline void ca_coordinates_and_bonds(const Protein &p,Voit out, Boit bout){
    internal::filtered_coordinates_and_bonds(p, Is_CA(), out, bout);
  }



  template <class Voit, class Boit>
  inline int simplified_coordinates_and_bonds(const Protein &p,Voit out, Boit bout){
    int index=-1;
    std::vector<int> ca_indices;
    //const Residue::Atom_label als[]={ Residue::AL_CA};
    for (Protein::Const_residues_iterator rit= p.residues_begin(); 
         rit != p.residues_end(); ++rit){
      //for (unsigned int i=0; i< 3; ++i){
      if (rit->has_atom(Residue::AL_N)){
        *out= rit->atom(Residue::AL_N).cartesian_coords();
        ++out;
        ++index;
        if (index != 0) {
          *bout = std::pair<int,int>(index-1, index);
          ++bout;
        }
      }
      if (rit->has_atom(Residue::AL_CA)){
        *out= rit->atom(Residue::AL_CA).cartesian_coords();
        ++out;
        
        ++index;
        if (index != 0) {
          *bout = std::pair<int,int>(index-1, index);
          ++bout;
        }
        ca_indices.push_back(index);
      }
      if (rit->has_atom(Residue::AL_C)){
        *out= rit->atom(Residue::AL_C).cartesian_coords();
        ++out;
        ++index;
        if (index != 0) {
          *bout = std::pair<int,int>(index-1, index);
          ++bout;
        }
      }
    }
    int nbackbone=index+1;
    int rindex=0;
    for (Protein::Const_residues_iterator rit= p.residues_begin(); 
         rit != p.residues_end(); ++rit){
      //for (unsigned int i=0; i< 3; ++i){
      if (rit->has_atom(Residue::AL_CA)){
        
        *out = rit->sidechain_point();
        ++out;
        
        ++index;

        *bout = std::pair<int,int>(ca_indices[rindex], index);
        ++bout;
        
        ++rindex;
      }
    }
    return nbackbone;
  }
}

#endif