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

// Unit headers
#include <protocols/protein_interface_design/movers/RepackMinimize.hh>
#include <protocols/protein_interface_design/movers/RepackMinimizeCreator.hh>

// Package headers
#include <protocols/protein_interface_design/design_utils.hh>
#include <protocols/simple_moves/symmetry/SetupForSymmetryMover.hh>

// Project headers
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>

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

//Auto Headers
#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.RepackMinimize" );

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

protocols::moves::MoverOP
RepackMinimizeCreator::create_mover() const {
  return new RepackMinimize;
}

std::string
RepackMinimizeCreator::mover_name()
{
  return "RepackMinimize";
}

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

RepackMinimize::RepackMinimize() :
  simple_moves::DesignRepackMover( RepackMinimizeCreator::mover_name() )
{
  min_rb_set_ = min_bb_set_ = min_sc_set_ = false;
  optimize_foldtree_ = true;
  automatic_repacking_definition_ = true;
}

RepackMinimize::RepackMinimize(
  ScoreFunctionCOP scorefxn_repack,
  ScoreFunctionCOP scorefxn_minimize,
  utility::vector1< core::Size > const target_residues,
  bool const repack_partner1/*=false*/,
  bool const repack_partner2/*=true*/,
  core::Real const interface_distance_cutoff/*=8.0*/,
  bool const repack_non_ala/*=true*/
) :
  simple_moves::DesignRepackMover( RepackMinimizeCreator::mover_name() )
{
  repack_partner2_ = repack_partner2;
  repack_partner1_ = repack_partner1;
  target_residues_ = target_residues;
  interface_distance_cutoff_ = interface_distance_cutoff;
  if (symmetry_ ) {
    if( scorefxn_repack ) scorefxn_repack_ = new core::scoring::symmetry::SymmetricScoreFunction( *scorefxn_repack );
    if( scorefxn_minimize ) scorefxn_minimize_ = new core::scoring::symmetry::SymmetricScoreFunction( *scorefxn_minimize );
  } else {
    if( scorefxn_repack ) scorefxn_repack_ = new core::scoring::ScoreFunction( *scorefxn_repack );
    if( scorefxn_minimize ) scorefxn_minimize_ = new ScoreFunction( *scorefxn_minimize );
  }
  repack_non_ala_ = repack_non_ala;
}

RepackMinimize::~RepackMinimize() {}

/// @details designs interface residues and minimizes the pose.
/// If minimization parameters have not been set by the user the default minimization behaviour is as follows:
/// + minimize bb/sc for all residues that are repacked.
/// + minimize bb/sc of residues that are +-1 from target residues
/// + minimize bb for all residues (minimizing over only interface residues causes large motions during minimization)
/// + minimize rb jump
/// Note that some confusion may arise from the use of repack1_ and repack2_
/// The behaviour of these variables is such that if they're false, then the
/// relevant partner is not designed but may be repacked. Turning off design_
/// precludes design across the whole system only allowing repack. At one point
/// the names should be rethought...
void
RepackMinimize::apply( pose::Pose & pose )
{
  allowed_aas_[ chemical::aa_cys ] = false;
  allowed_aas_[ chemical::aa_gly ] = false;
  allowed_aas_[ chemical::aa_pro ] = false;

if ( symmetry_ ) {
    protocols::simple_moves::symmetry::SetupForSymmetryMoverOP setup_mover = new protocols::simple_moves::symmetry::SetupForSymmetryMover;
    setup_mover->apply( pose );
  }

  setup_packer_and_movemap( pose );
  using namespace core::scoring;

  if ( symmetry_ ) {
    pack::symmetric_pack_rotamers( pose, *scorefxn_repack_, task_ );
    SymMinimizeInterface( pose, scorefxn_minimize_, curr_min_bb_, curr_min_sc_, curr_min_rb_); //, optimize_foldtree_, target_residues_ );
  } else {
    pack::pack_rotamers( pose, *scorefxn_repack_, task_ );
    MinimizeInterface( pose, scorefxn_minimize_, curr_min_bb_, curr_min_sc_, curr_min_rb_, optimize_foldtree_, target_residues_ );
  }
  pose.update_residue_neighbors();
  (*scorefxn_minimize_)( pose );
}

std::string
RepackMinimize::get_name() const {
  return RepackMinimizeCreator::mover_name();
}


void
RepackMinimize::parse_my_tag( TagPtr const tag, DataMap & data, protocols::filters::Filters_map const &filters, Movers_map const & movers, core::pose::Pose const & pose )
{
  TR<<"repack minimize mover with the following parameters:"<<std::endl;
  simple_moves::DesignRepackMover::parse_my_tag( tag, data, filters, movers, pose );
}

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