CutChainMover.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   ForceDisulfidesMover.cc
///
/// @brief
/// @author Sarel Fleishman

// unit headers
#include <protocols/simple_moves/CutChainMover.hh>
#include <protocols/simple_moves/CutChainMoverCreator.hh>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH

// type headers
#include <core/types.hh>
#include <core/id/types.hh>

// project headers
#include <protocols/moves/Mover.hh>
#include <core/pose/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/selection.hh>

// package headers
#include <core/pose/PDBInfo.hh>
#include <core/pose/carbohydrates/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/datacache/CacheableObserverType.hh>
#include <core/pose/datacache/ObserverCache.hh>

// Project headers
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>

#include <core/id/TorsionID.hh>
#include <core/id/types.hh>
#include <core/scoring/Energies.hh>

// utility header
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <utility/tag/Tag.hh>
#include <utility/string_util.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/toolbox/task_operations/DesignAroundOperation.hh>
#include <core/pack/task/PackerTask.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <core/scoring/ScoreFunction.hh>

namespace protocols {
namespace simple_moves {

static basic::Tracer TR("protocols.simple_moves.CutChainMover");

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

protocols::moves::MoverOP
CutChainMoverCreator::create_mover() const {
  return new CutChainMover;
}

std::string
CutChainMoverCreator::mover_name()
{
  return "CutChain";
}

//Default Constructor
CutChainMover::CutChainMover() :
  protocols::moves::Mover("CutChain"),
  bond_length_(4.0), //define covalent bond length cut-off
  chain_id_(1)//define default main chain
{
}


CutChainMover::~CutChainMover() {}

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

protocols::moves::MoverOP
CutChainMover::fresh_instance() const
{
  return new CutChainMover();
}

//getters
std::string
CutChainMover::get_name() const {
  return "CutChain";
}

core::Real
CutChainMover::bond_length() const {
  return bond_length_;
}

core::Size
CutChainMover::chain_id() const {
  return chain_id_;
}

//setters
void
CutChainMover::bond_length(core::Real const length){
  bond_length_ = length;
}
void
CutChainMover::chain_id(core::Size const ID){
  chain_id_ = ID;
}
void
CutChainMover::parse_my_tag( utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const & )
{
  bond_length( tag->getOption< core::Real >( "bond_length", 4.0 ) );
  chain_id( tag->getOption< core::Size >( "chain_id", 1 ) );
  TR<<" bond_length: "<<bond_length();
  TR<<"Chain id: "<<chain_id();
  TR<<std::endl;
}

void CutChainMover::apply( core::pose::Pose & pose )
{
    create_subpose(pose);
    foldTree(pose);

}

core::Size
CutChainMover::chain_cut( core::pose::Pose & pose)
{
  core::Size cut_pos = -1;
  for( core::Size resj = pose.conformation().chain_begin( chain_id_ ); resj <= pose.conformation().chain_end( chain_id_ )-1; ++resj ){
    core::Real const distance = pose.residue( resj+1 ).xyz( "N" ).distance(pose.residue( resj ).xyz( "C" ));
//      TR<<"distance is: "<<distance<<std::endl;
//      TR<<"residue name is : "<<pose.residue(resj).name1()<<std::endl;
    if( distance > bond_length()){
      cut_pos = resj;
      TR<<"Found cut at: "<<resj<<std::endl;
      break;
    }
  }
  return( cut_pos );//cut_pos is the amino acid position BEFORE the cut
}

void
CutChainMover::create_subpose(core::pose::Pose & pose)
{
  core::pose::Pose copy_pose( pose );
  pose.clear();

  //add to pose only residues from main chain
  for (core::Size resj = copy_pose.conformation().chain_begin( chain_id_); resj <= copy_pose.conformation().chain_end( chain_id_); ++resj) {
    core::conformation::Residue const & rsd( copy_pose.residue( resj) );
    pose.append_residue_by_bond( rsd );
  }

}

void
CutChainMover::foldTree (core::pose::Pose & pose){
core::Size const s1 = chain_cut(pose);
core::kinematics::FoldTree ft;
  ft.clear();
  ft.add_edge( 1, s1, -1 );
  ft.add_edge( s1, s1+1, 1 );
  ft.add_edge( s1+1, pose.conformation().chain_end( chain_id()), -1 );
TR<<"old foldtree: "<<pose.fold_tree()<<std::endl;
pose.fold_tree(ft);
TR<<"new_foldtree: "<<pose.fold_tree()<<std::endl;
pose.conformation().detect_disulfides();
}


} // simple_moves
} // protocols