BuildAlaPose.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/protein_interface_design/movers/BuildAlaPose.cc
/// @brief
/// @author Sarel Fleishman (sarelf@u.washington.edu), Jacob Corn (jecorn@u.washington.edu)

// Unit headers
#include <protocols/protein_interface_design/movers/BuildAlaPose.hh>
#include <protocols/protein_interface_design/movers/BuildAlaPoseCreator.hh>

// Package headers
#include <protocols/rosetta_scripts/util.hh>

// AUTO-REMOVED #include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <basic/Tracer.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
// AUTO-REMOVED #include <core/pack/task/operation/TaskOperations.hh>
#include <utility/tag/Tag.hh>

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

//Auto Headers
#include <core/conformation/Residue.hh>
#include <core/id/types.hh>
#include <core/kinematics/Jump.hh>
#include <protocols/simple_moves/DesignRepackMover.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.BuildAlaPose" );

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

protocols::moves::MoverOP
BuildAlaPoseCreator::create_mover() const {
  return new BuildAlaPose;
}

std::string
BuildAlaPoseCreator::mover_name()
{
  return "build_Ala_pose";
}

BuildAlaPose::BuildAlaPose() : simple_moves::DesignRepackMover( BuildAlaPoseCreator::mover_name() ) {}
BuildAlaPose::BuildAlaPose(
  bool const partner1,
  bool const partner2,
  core::Real interface_distance_cutoff
) :
  simple_moves::DesignRepackMover( BuildAlaPoseCreator::mover_name() )
{
  repack_partner1_=design_partner1_=partner1;
  repack_partner2_=design_partner2_=partner2;
  interface_distance_cutoff_ = interface_distance_cutoff;
  runtime_assert( interface_distance_cutoff_ >= 0 );
}

BuildAlaPose::~BuildAlaPose() {}

void
BuildAlaPose::apply( pose::Pose & pose )
{
  using namespace core::scoring;
  using namespace core::pack::task::operation;

  allowed_aas_.assign( core::chemical::num_canonical_aas, false );
  allowed_aas_[ core::chemical::aa_ala ] = true;
/*  if( repack_partner1_ ^ repack_partner2_ ){
    bool const prevent_chain1( !repack_partner1_ );
    bool const prevent_chain2( !repack_partner2_ );
    core::Size const prevent_chain_begin( pose.conformation().chain_begin( prevent_chain1 ? 1 : 2 ) );
    core::Size const prevent_chain_end( pose.conformation().chain_end( prevent_chain2 ? 2 : 1 ) );
    for( core::Size res=prevent_chain_begin; res<=prevent_chain_end; ++res )
      prevent_repacking_.push_back( res );
  } */
  setup_packer_and_movemap( pose );

  using namespace core::scoring;
  core::scoring::ScoreFunctionOP scorefxn( ScoreFunctionFactory::create_score_function( STANDARD_WTS, SCORE12_PATCH ) );
  pack::pack_rotamers( pose, *scorefxn, task_ );
  (*scorefxn)( pose );
  /// Now handled automatically.  scorefxn->accumulate_residue_total_energies( pose );
}

std::string
BuildAlaPose::get_name() const {
  return BuildAlaPoseCreator::mover_name();
}

void
BuildAlaPose::parse_my_tag( TagPtr const tag, DataMap &data, protocols::filters::Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  design_partner1_ = tag->getOption<bool>( "partner1", 0 );
  design_partner2_ = tag->getOption<bool>( "partner2", 1 );
  repack_partner1_ = design_partner1_;
  repack_partner2_ = design_partner2_;
  interface_distance_cutoff_ = tag->getOption<core::Real>( "interface_cutoff_distance", 8.0 );

  task_factory( protocols::rosetta_scripts::parse_task_operations( tag, data ) );
  TR<<"defined BuildAlaPose mover "<<" for partners "<<( repack_partner1_ ? "1" : "" )<<( repack_partner2_ ? "2": "" )<<" with distance cutoff "<<
    interface_distance_cutoff_<<std::endl;
}

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

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