coord_util.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file src/protocols/comparative_modeling/coord_util.cc
/// @author James Thompson

// AUTO-REMOVED #include <core/io/silent/SilentStruct.hh>
#include <core/pose/Pose.hh>

#include <core/id/SequenceMapping.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/conformation/Residue.hh>

#include <ObjexxFCL/FArray2D.hh>

#include <numeric/xyzVector.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace comparative_modeling {

void gather_coords(
  core::pose::Pose const & model,
  core::pose::Pose const & native,
  core::sequence::SequenceAlignment const & aln,
  int & natoms,
  ObjexxFCL::FArray2D< core::Real > & p1a,
  ObjexxFCL::FArray2D< core::Real > & p2a,
  std::string const & atom_name = "CA"
) {
  using core::Size;
  using namespace core::id;
  using namespace core::sequence;
  SequenceMapping mapping( aln.sequence_mapping(1,2) );

  natoms = 0;
  for ( Size ii = 1; ii <= model.total_residue(); ++ii ) {
    if (!model.residue(ii).is_protein()) continue;
    Size const native_ii( mapping[ii] );
    bool skip(
      native_ii == 0 ||
      native_ii > native.total_residue()
    );
    if ( !skip ) ++natoms;
  }
  p1a.dimension(3,natoms);
  p2a.dimension(3,natoms);

  Size n_gap(0);
  for ( Size ii = 1; ii <= model.total_residue(); ++ii ) {
    if (!model.residue(ii).is_protein()) continue;
    Size const native_ii(mapping[ii]);
    bool skip(
      native_ii == 0 ||
      native_ii > native.total_residue()
    );
    if ( skip ) {
      n_gap++;
    } else {
      using core::Real;
      numeric::xyzVector< Real > model_xyz ( model.residue(ii).xyz(atom_name) );
      numeric::xyzVector< Real > native_xyz( native.residue(native_ii).xyz(atom_name) );
      for ( Size jj = 1; jj <= 3; ++jj ) {
        p1a(jj,ii - n_gap) = native_xyz[jj-1];
        p2a(jj,ii - n_gap) = model_xyz [jj-1];
      }
    }
  }
} // gather_coords

}
}