InterfaceRecapitulationMover.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/DesignRepackMover.cc
/// @brief
/// @author Sarel Fleishman (sarelf@u.washington.edu), Jacob Corn (jecorn@u.washington.edu)

// Unit headers
#include <protocols/protein_interface_design/movers/InterfaceRecapitulationMover.hh>
#include <protocols/protein_interface_design/movers/InterfaceRecapitulationMoverCreator.hh>

// Package headers
#include <protocols/protein_interface_design/ReportPSSMDifference.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>

// Project Headers
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <protocols/protein_interface_design/design_utils.hh>

#include <core/pack/task/PackerTask.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <utility/tag/Tag.hh>

#include <basic/Tracer.hh>

// Utility Headers

// Unit Headers

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

#include <protocols/jd2/Job.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

//Auto Headers
#include <utility/excn/Exceptions.hh>
#include <protocols/simple_moves/DesignRepackMover.hh>



using namespace core;

// option key includes

using namespace core::scoring;

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


namespace protocols {
namespace protein_interface_design {
namespace movers {

using namespace protocols::moves;

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

protocols::moves::MoverOP
InterfaceRecapitulationMoverCreator::create_mover() const {
  return new InterfaceRecapitulationMover;
}

std::string
InterfaceRecapitulationMoverCreator::mover_name()
{
  return "InterfaceRecapitulation";
}

InterfaceRecapitulationMover::InterfaceRecapitulationMover() :
  Mover( InterfaceRecapitulationMoverCreator::mover_name() ),
  saved_pose_( NULL ),
  design_mover_( NULL ),
  design_mover2_( NULL ),
  pssm_( false )
  {}

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

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

core::pose::PoseCOP
InterfaceRecapitulationMover::get_reference_pose() const
{
  return saved_pose_;
}

void
InterfaceRecapitulationMover::set_reference_pose( core::pose::PoseOP pose )
{
  saved_pose_ = pose;
}

InterfaceRecapitulationMover::~InterfaceRecapitulationMover() {}

void
InterfaceRecapitulationMover::apply( core::pose::Pose & pose ){
  runtime_assert( saved_pose_ );
  runtime_assert( design_mover_ || design_mover2_ );
  core::pack::task::PackerTaskCOP task;
  if( design_mover_ ){
    design_mover_->apply( pose );
    task = design_mover_->task();
  }
  else{
    design_mover2_->apply( pose );
    task = design_mover2_->task();
  }
  core::Size designable_positions( 0 );
  for( Size i( 1 ); i<= pose.total_residue(); ++i )
    if( task->being_designed( i ) ) ++designable_positions;

  protocols::jd2::JobDistributor* jd = protocols::jd2::JobDistributor::get_instance();
  ReportPSSMDifferences rsd;
  if ( pssm_ && !rsd.load_pssm_data( jd->current_job()->input_tag() ) ){
    pssm_ = false;
  }

  if (!pssm_){
    ReportSequenceDifferences rsd( core::scoring::ScoreFunctionFactory::create_score_function( STANDARD_WTS, SCORE12_PATCH ) );
    rsd.calculate( *get_reference_pose(), pose );
    std::map< core::Size, std::string > const res_names1( rsd.res_name1() );
    core::Size const mutated( res_names1.size() );
    core::Real const rate( (core::Real) mutated / designable_positions );
    TR<<"Your design mover mutated "<<mutated<<" positions out of "<<designable_positions<<" designable positions. Sequence recovery is: "<<1-rate<<std::endl;
  }
  else{
    core::Real pssm = rsd.calculate( *get_reference_pose(), pose, task );
    TR << "PSSM-Score: " << pssm << " at " << designable_positions << " designable positions. Mean score is " << pssm / (core::Real)designable_positions << std::endl;
  }

}

std::string
InterfaceRecapitulationMover::get_name() const {
  return InterfaceRecapitulationMoverCreator::mover_name();
}

void
InterfaceRecapitulationMover::parse_my_tag( utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const & movers, core::pose::Pose const & pose ){
  set_reference_pose( new core::pose::Pose( pose ) );
  std::string const mover_name( tag->getOption<std::string>( "mover_name" ) );
  std::map< std::string const, MoverOP >::const_iterator find_mover( movers.find( mover_name ));
  bool const mover_found( find_mover != movers.end() );
  if( mover_found ){
    design_mover_ = dynamic_cast< simple_moves::DesignRepackMover * >( find_mover->second() );
    if( !design_mover_ ){
      design_mover2_ = dynamic_cast< protocols::simple_moves::PackRotamersMover * >( find_mover->second() );
      if( !design_mover2_ )
        throw utility::excn::EXCN_RosettaScriptsOption( "dynamic cast failed in tag in RecapitulateMover. Make sure that the mover is either PackRotamers or DesignRepackMover derived" );
    }
    pssm_ = tag->getOption<bool>( "pssm", false );
  }
}

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