AtomGraph.cc

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   src/core/conformation/AtomGraph.cc
/// @author Sam DeLuca

///@detail right now there isnt a canonical mapping from nodes back to atom objects.

#include <core/conformation/AtomGraph.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Conformation.hh>

#include <core/conformation/AtomGraphData.hh>
#include <core/graph/UpperEdgeGraph.hh>

#include <utility/vector1.hh>


namespace core {
namespace conformation {

void
atom_graph_from_conformation(
  Conformation const & conformation,
  AtomGraphOP atom_graph
)
{
  //TODO: doing this because I don't want to pull in an entire pose :( gotta be a better way
  platform::Size num_atoms = 0;
  for (platform::Size resid = 1; resid <= conformation.size(); ++resid)
  {
    num_atoms += conformation.residue_type(resid).natoms();
  }
  num_atoms++;
  atom_graph->set_num_vertices(num_atoms);
  platform::Size index_id = 1;

  for ( platform::Size resid=1 ;resid <= conformation.size(); ++resid ) {
    core::conformation::Residue current_res(conformation.residue(resid));
    for(platform::Size atomno=1; atomno <= current_res.natoms(); ++atomno )
    {
      AtomGraphVertexData current_vertex = atom_graph->get_vertex(index_id).data();
      current_vertex.xyz() = current_res.xyz(atomno);
      current_vertex.atom_name() = current_res.atom_name(atomno);
      core::Real lj_radius = current_res.atom_type(atomno).lj_radius();
      current_vertex.atom_radius_squared() = lj_radius*lj_radius;


      num_atoms++;
    }
  }

}


platform::Size
annotated_atom_graph_from_conformation(
    Conformation const & conformation,
    AtomGraphOP atom_graph,
    PointPosition const & additional_point

)
{
  //TODO: doing this because I don't want to pull in an entire pose :( gotta be a better way
  platform::Size num_atoms = 0;
  for (platform::Size resid = 1; resid <= conformation.size(); ++resid)
  {
    num_atoms += conformation.residue_type(resid).natoms();
  }
  num_atoms++;
  atom_graph->set_num_vertices(num_atoms);
  platform::Size index_id = 1;
  for ( platform::Size resid=1 ;resid <= conformation.size(); ++resid ) {
    core::conformation::Residue current_res(conformation.residue(resid));
    for(platform::Size atomno=1; atomno <= current_res.natoms(); ++atomno )
    {
      AtomGraphVertexData current_vertex = atom_graph->get_vertex(index_id).data();
      current_vertex.xyz() = current_res.xyz(atomno);
      current_vertex.atom_name() = current_res.atom_name(atomno);
      current_vertex.residue_id() = resid;
      //num_atoms++;
    }
  }
  //add the additional point
  atom_graph->get_vertex(num_atoms).data().xyz() = additional_point;

  return num_atoms; //this is the ID of the additional point
}


}
}