SwitchChainOrderMover.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 SwitchChainOrderMover.cc
/// @brief

// Unit headers
#include <protocols/simple_moves/SwitchChainOrderMover.hh>
#include <protocols/simple_moves/SwitchChainOrderMoverCreator.hh>
#include <protocols/moves/DataMapObj.hh>
#include <protocols/moves/DataMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <basic/Tracer.hh>
#include <core/pose/util.hh>
using basic::T;
using basic::Error;
using basic::Warning;
static basic::Tracer TR("protocols.simple_moves.SwitchChainOrderMover");
#include <utility/tag/Tag.hh>

// AUTO-REMOVED #include <core/chemical/AtomType.hh>
#include <utility/vector1.hh>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH
#include <core/pose/Pose.hh>
#include <core/conformation/Conformation.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>

namespace protocols {
namespace simple_moves {

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

protocols::moves::MoverOP
SwitchChainOrderMoverCreator::create_mover() const {
  return new SwitchChainOrderMover;
}

std::string
SwitchChainOrderMoverCreator::mover_name()
{
  return "SwitchChainOrder";
}

SwitchChainOrderMover::SwitchChainOrderMover()
  : moves::Mover("SwitchChainOrder"),
  residue_numbers_( NULL )
{
}

void
SwitchChainOrderMover::apply( Pose & pose )
{
  core::pose::Pose new_pose(pose);
  core::kinematics::FoldTree new_ft;
  new_ft.clear();
  core::conformation::Conformation const conf( pose.conformation() );
  core::Size chain_count( 1 );
  utility::vector1< core::Size > new_residue_numbers;
  new_residue_numbers.clear();
  utility::vector1< core::Size > positions_in_new_pose;
  positions_in_new_pose.clear();
  foreach( char const chaini, chain_order() ){
    core::Size const chain( chaini - '0' );
    runtime_assert( chain > 0 && chain <= conf.num_chains() );
    core::Size const chain_begin( conf.chain_begin( chain ) );
    core::Size const chain_end(   conf.chain_end(   chain ) );

    core::Size const new_chain_begin( positions_in_new_pose.size() + 1 );
    for( core::Size i = chain_begin; i<=chain_end; ++i )
      positions_in_new_pose.push_back( i );
    core::Size const new_chain_end( positions_in_new_pose.size() );
    if( residue_numbers_() != NULL ){
      foreach( core::Size const residue_number, residue_numbers_->obj ){
        if( residue_number >= chain_begin && residue_number <= chain_end )
          new_residue_numbers.push_back( residue_number - ( chain_begin - new_chain_begin ) );
      }
    }
    new_ft.add_edge( new_chain_begin, new_chain_end, -1 );
    if( chain_count > 1 )
      new_ft.add_edge( 1, new_chain_begin, chain_count - 1 );
    chain_count++;
  }
  new_ft.reorder( 1 );
  core::pose::create_subpose( pose, positions_in_new_pose, new_ft, new_pose );
  new_pose.update_residue_neighbors();
  new_pose.pdb_info( new core::pose::PDBInfo( new_pose, true ) ); //reinitialize the PDBInfo
  pose.clear();
  pose = new_pose;
  pose.conformation().detect_disulfides();
  ( *scorefxn() ) ( pose );
  pose.update_residue_neighbors();
  TR<<"New pose's foldtree "<<pose.fold_tree()<<std::endl;
  if( residue_numbers_() != NULL ){
    residue_numbers_->obj = new_residue_numbers;
    TR<<"new residue numbers: ";
    foreach( core::Size const res, residue_numbers_->obj )
      TR<<res<<", ";
    TR<<std::endl;
  }
}

std::string
SwitchChainOrderMover::get_name() const {
  return SwitchChainOrderMoverCreator::mover_name();
}

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

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

void
SwitchChainOrderMover::parse_my_tag(
  utility::tag::TagPtr const tag,
  protocols::moves::DataMap & data,
  protocols::filters::Filters_map const &,
  protocols::moves::Movers_map const &,
  core::pose::Pose const & )
{
  chain_order( tag->getOption< std::string >( "chain_order" ) );
  std::string const residue_numbers_setter( tag->getOption< std::string >( "residue_numbers_setter", "" ) );
  scorefxn( protocols::rosetta_scripts::parse_score_function( tag, data, "score12" ) );
  if( residue_numbers_setter != "" )
    residue_numbers_ = protocols::moves::get_set_from_datamap< protocols::moves::DataMapObj< utility::vector1< core::Size > > >( "residue_numbers", residue_numbers_setter, data );

}

void
SwitchChainOrderMover::chain_order( std::string const co ){
  chain_order_ = co;
}

std::string
SwitchChainOrderMover::chain_order() const
{
  return chain_order_;
}

void
SwitchChainOrderMover::scorefxn( core::scoring::ScoreFunctionOP s ) { scorefxn_ = s; }

core::scoring::ScoreFunctionOP
SwitchChainOrderMover::scorefxn() const { return scorefxn_; }

} // simple_moves
} // protocols