AddChainBreak.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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file protocols/protein_interface_design/movers/AddChainBreak.cc
/// @brief
/// @author Sarel Fleishman (sarelf@u.washington.edu)

// Unit headers
#include <protocols/protein_interface_design/movers/AddChainBreak.hh>
#include <protocols/protein_interface_design/movers/AddChainBreakCreator.hh>
#include <core/pose/util.hh>
// Package headers
#include <core/chemical/VariantType.hh>
// Project headers
#include <utility/tag/Tag.hh>
#include <basic/Tracer.hh>
#include <core/pose/Pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH

//Auto Headers
#include <utility/vector0.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace protein_interface_design {
namespace movers {

using namespace core;
using namespace std;
using namespace core::scoring;
using namespace protocols::moves;

static basic::Tracer TR( "protocols.protein_interface_design.movers.AddChainBreak" );

std::string
AddChainBreakCreator::keyname() const
{
  return AddChainBreakCreator::mover_name();
}

protocols::moves::MoverOP
AddChainBreakCreator::create_mover() const {
  return new AddChainBreak;
}

std::string
AddChainBreakCreator::mover_name()
{
  return "AddChainBreak";
}

AddChainBreak::AddChainBreak() :
  protocols::moves::Mover( AddChainBreakCreator::mover_name() ),
  resnum_( "" ),
  change_foldtree_( true ),
  find_automatically_( false ),
  automatic_distance_cutoff_( 2.5 )
{}

AddChainBreak::~AddChainBreak() {}

protocols::moves::MoverOP
AddChainBreak::clone() const {
  return (protocols::moves::MoverOP( new AddChainBreak( *this ) ) );
}

void
AddChainBreak::parse_my_tag( TagPtr const tag, DataMap &, protocols::filters::Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  /// resnum & pdb_num are now equivalent
  if( tag->hasOption( "resnum" ) )
    resnum_ = tag->getOption< std::string > ("resnum" );
  else if( tag->hasOption( "pdb_num" ) ){
    resnum_ = tag->getOption< std::string > ("pdb_num" );
  }
  if( tag->hasOption( "find_automatically" ) ){
    find_automatically( tag->getOption< bool >( "find_automatically" ) );
    automatic_distance_cutoff( tag->getOption< core::Real >( "distance_cutoff", 2.5 ));
  }
  change_foldtree( tag->getOption< bool >( "change_foldtree", true ) );
  TR<<"resnum: "<<resnum_<<" change foldtree "<<change_foldtree()<<" find cutpoints automatically "<<find_automatically()<<std::endl;
}//end parse my tag

void
AddChainBreak::apply( core::pose::Pose & pose )
{
  using namespace core::chemical;
  using namespace pose;
  core::kinematics::FoldTree f( pose.fold_tree() );

  if( resnum() != "" ){
    core::Size const resn( core::pose::parse_resnum( resnum(), pose ) );

    if( change_foldtree() ){
      f.new_jump( resn, resn+1, resn );
    }
    if(pose.residue(resn  ).is_upper_terminus()) core::pose::remove_upper_terminus_type_from_pose_residue(pose,resn);
    if(pose.residue(resn+1).is_lower_terminus()) core::pose::remove_lower_terminus_type_from_pose_residue(pose,resn+1);
    add_variant_type_to_pose_residue( pose, CUTPOINT_LOWER, resn );
    add_variant_type_to_pose_residue( pose, CUTPOINT_UPPER, resn +1);
  }
  utility::vector1< core::Size > cuts;
  cuts.clear();
  if( find_automatically() ){
    for( core::Size i = 1; i < pose.total_residue(); ++i ){
      core::Real const distance( pose.residue( i ).xyz( "C" ).distance( pose.residue( i + 1 ).xyz( "N" ) ) );
      if( distance >= automatic_distance_cutoff() ){
        cuts.push_back( i );
        TR<<"Detecting cut at "<<i<<" with distance "<<distance<<std::endl;
      }
    }
  }
  foreach( core::Size const res, cuts ){
    add_variant_type_to_pose_residue( pose, CUTPOINT_LOWER, res );
    add_variant_type_to_pose_residue( pose, CUTPOINT_UPPER, res +1);
    if( change_foldtree() ){
      f.new_jump( res, res+1, res );
    }
  }
  if( change_foldtree() ){
    pose.fold_tree( f );
    TR<<"New fold tree: "<<pose.fold_tree()<<std::endl;
  }
}

std::string
AddChainBreak::get_name() const {
  return AddChainBreakCreator::mover_name();
}

} //movers
} //protein_interface_design
} //protocols