MissingDensityToJumpMover.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.
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// (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/simple_moves/MissingDensityToJumpMover.cc
/// @brief  Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density.
/// @author TJ Brunette (tjbrunette@gmail.com), May 2011

// Unit Headers
#include <protocols/simple_moves/MissingDensityToJumpMover.hh>

// P
// tracer
#include <basic/Tracer.hh>

#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/types.hh>

#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
// AUTO-REMOVED #include <core/chemical/ChemicalManager.hh>
// AUTO-REMOVED #include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
// AUTO-REMOVED #include <core/chemical/AtomType.hh>

#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/conformation/ResidueFactory.hh>

#include <core/kinematics/FoldTree.hh>

#include <utility/vector1.hh>

using basic::T;
using basic::Error;
using basic::Warning;

// C++ Headers

// ObjexxFCL Headers

namespace protocols {
namespace simple_moves {
static basic::Tracer TR("protocols.mover.MissingDensityToJumpMover");
/// MissingDensityToJumpMover

  MissingDensityToJumpMover::MissingDensityToJumpMover(): protocols::moves::Mover( MissingDensityToJumpMover::get_name() ){}


MissingDensityToJumpMover::~MissingDensityToJumpMover() {}

void
MissingDensityToJumpMover::apply( core::pose::Pose & pose ) {
  using namespace core;
  using namespace core::conformation;
  using namespace core::chemical;
  Size const nres( pose.total_residue() );  
 for ( Size i=1; i< nres; ++i ) {//don't have to go to last residue thus < rather than <=
    if ( pose.residue_type(i).is_polymer() && !pose.residue_type(i).is_lower_terminus() && !pose.fold_tree().is_cutpoint(i) ) {
      Residue const &current_rsd(pose.residue(i));
      Residue const &next_rsd(pose.residue(i+1));
      core::Real bondlength = ( current_rsd.atom( current_rsd.upper_connect_atom() ).xyz() - next_rsd.atom( next_rsd.lower_connect_atom() ).xyz() ).length();
      if( bondlength > 2.5 ){
        TR << "[ WARNING ] missing density found at residue " << i << std::endl;
        core::kinematics::FoldTree update_tree(pose.fold_tree());
        update_tree.new_jump(i,i+1,i);
        pose.fold_tree(update_tree);
        core::pose::add_variant_type_to_pose_residue( pose, chemical::UPPER_TERMINUS, i);
        core::pose::add_variant_type_to_pose_residue( pose, chemical::LOWER_TERMINUS, i+1 );
      }
    }
  }
}
  
std::string MissingDensityToJumpMover::get_name() const {
  return "MissingDensityToJumpMover";
}
  
} // moves
} // protocols