RNA_IdealCoord.cc

Go to the documentation of this file.

// -*- 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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
/// @file   protocols/rna/RNA_IdealCoord.cc
/// @brief  Apply ideal RNA geometry to a residue or a pose
/// @author  Fang-Chieh Chou

// Unit headers
#include <protocols/rna/RNA_IdealCoord.hh>
#include <utility/vector1.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/TorsionID.hh>
#include <core/id/AtomID.hh>
#include <core/scoring/rna/RNA_FittedTorsionInfo.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/database/open.hh>

// Numeric headers
#include <numeric/conversions.hh>
#include <numeric/constants.hh>

//// C++ headers
#include <string>
#include <cmath>

using namespace core;
using namespace core::pose;
using namespace core::scoring::rna;

namespace protocols {
namespace rna {

//////////////////////////////////////////////////////
RNA_IdealCoord::RNA_IdealCoord():
  path_( basic::database::full_name("chemical/rna/ideal_geometry/") )
{
  init();
}

RNA_IdealCoord::~RNA_IdealCoord() {}

/////////////////////////////////////////////////////
bool RNA_IdealCoord::is_torsion_exists(Pose const & pose, id::TorsionID const & torsion_id) const {
  using namespace core::id;
  Size res_index = torsion_id.rsd();
  if ( res_index < 1 || res_index > pose.total_residue() ) return false;

  AtomID id1,id2,id3,id4;
  bool fail = pose.conformation().get_torsion_angle_atom_ids( torsion_id, id1, id2, id3, id4 );
  return (! fail);
}
/////////////////////////////////////////////////////
void RNA_IdealCoord::init() {
  //Names of the pdb files
  utility::vector1 < std::string > pdb_file_list;
  pdb_file_list.push_back( path_ + "/A_n_std.pdb" );
  pdb_file_list.push_back( path_ + "/A_s_std.pdb" );
  pdb_file_list.push_back( path_ + "/G_n_std.pdb" );
  pdb_file_list.push_back( path_ + "/G_s_std.pdb" );
  pdb_file_list.push_back( path_ + "/C_n_std.pdb" );
  pdb_file_list.push_back( path_ + "/C_s_std.pdb" );
  pdb_file_list.push_back( path_ + "/U_n_std.pdb" );
  pdb_file_list.push_back( path_ + "/U_s_std.pdb" );

  //Initialize the reference poses
  chemical::ResidueTypeSetCAP rsd_set = chemical::ChemicalManager::get_instance()->residue_type_set ( "rna" );
  Pose ref_pose;
  for (Size i = 1; i <= pdb_file_list.size(); ++i) {
    import_pose::pose_from_pdb ( ref_pose, *rsd_set, pdb_file_list[i] );
    ref_pose_list_.push_back(ref_pose);
  }
}

/////////////////////////////////////////////////////
void RNA_IdealCoord::apply( Pose & pose, Size const seqpos, bool const is_north, bool const keep_backbone_torsion ) const {

  using namespace core::id;
  using namespace core::chemical;
  using namespace core::conformation;

  Residue const & res = pose.residue( seqpos );
  if ( !res.is_RNA() ) return;

  //Figure out the residue_type.
  Size res_class = 0;
  if ( res.aa() == na_rad ) {
    res_class = 1;
  } else if ( res.aa() == na_rgu ) {
    res_class = 3;
  } else if ( res.aa() == na_rcy ) {
    res_class = 5;
  } else if ( res.aa() == na_ura ) {
    res_class = 7;
  }
  if (! is_north) ++res_class;

  //Record the torsions in starting pose
  utility::vector1 < TorsionID > saved_torsion_id;
  utility::vector1 < Real > saved_torsions;
  if (keep_backbone_torsion) {
    saved_torsion_id.push_back( TorsionID( seqpos,   id::BB,  ALPHA   ) );
    saved_torsion_id.push_back( TorsionID( seqpos,   id::BB,  BETA    ) );
    saved_torsion_id.push_back( TorsionID( seqpos,   id::BB,  GAMMA   ) );
    saved_torsion_id.push_back( TorsionID( seqpos,   id::BB,  EPSILON ) );
    saved_torsion_id.push_back( TorsionID( seqpos,   id::BB,  ZETA    ) );
    saved_torsion_id.push_back( TorsionID( seqpos,   id::CHI, 1       ) );
    saved_torsion_id.push_back( TorsionID( seqpos,   id::CHI, 4       ) );
    saved_torsion_id.push_back( TorsionID( seqpos-1, id::BB,  ZETA    ) );
    saved_torsion_id.push_back( TorsionID( seqpos+1, id::BB,  ALPHA   ) );
    for (Size i = 1; i <= saved_torsion_id.size(); ++i) {
      bool const is_exists = is_torsion_exists( pose, saved_torsion_id[i] );
      if (is_exists) {
        saved_torsions.push_back( pose.torsion( saved_torsion_id[i] ) );
      } else {
        saved_torsions.push_back( -9999 );
      }
    }
  }

  //Apply ideal dofs
  std::map <Size, Size> res_map;
  res_map.insert( std::pair <Size, Size> (seqpos, 2) ); //Only the center res (#2) matters in ref_pose
  Pose const & ref_pose = ref_pose_list_[res_class];
  copy_dofs_match_atom_names(pose, ref_pose, res_map);

  //Copy back the original torsions
  if (keep_backbone_torsion) {
    for (Size i = 1; i <= saved_torsion_id.size(); ++i) {
      if (saved_torsions[i] > -1000) {
        pose.set_torsion( saved_torsion_id[i], saved_torsions[i] );
      }
    }
  }
}
/////////////////////////////////////////////////////
//Apply ideal coords to whole pose.
//pucker_conformations: 0 for skipping, 1 for North, 2 for South
void RNA_IdealCoord::apply( Pose & pose, utility::vector1 < Size > const & pucker_conformations, bool const keep_backbone_torsion ) const {
  if ( pose.total_residue() != pucker_conformations.size() ) {
    utility_exit_with_message("RNA_IdealCoord::apply--pose.total_resdiue() != pucker_conformations.size() !!!!");
  }
  for (Size i = 1; i <= pose.total_residue(); ++i) {
    switch ( pucker_conformations[i] ) {
      case 0: //Skip
        break;
      case 1: //North
        apply(pose, i, true, keep_backbone_torsion);
        break;
      case 2: //South
        apply(pose, i, false, keep_backbone_torsion);
        break;
      default :
        utility_exit_with_message("RNA_IdealCoord::apply--Invalid value for pucker_conformations!!!!");
    }
  }
}
/////////////////////////////////////////////////

}
}