KinematicControl.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 KinematicControl.cc
/// @brief
/// @detailed
/// @author Oliver Lange
///


// Unit Headers
#include <protocols/abinitio/KinematicControl.hh>

// Package Headers
// AUTO-REMOVED #include <protocols/jumping/JumpSetup.hh>

// Project Headers
#include <core/chemical/VariantType.hh>
#include <core/pose/Pose.hh>

// AUTO-REMOVED #include <core/fragment/OrderedFragSet.hh>
// AUTO-REMOVED #include <core/fragment/FragSetCollection.hh>

#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/ShortestPathInFoldTree.hh>



#include <core/scoring/ScoreFunction.hh>

#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/jumping/util.hh>
// AUTO-REMOVED #include <protocols/jumping/PairingLibrary.hh>


// ObjexxFCL Headers
// AUTO-REMOVED #include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>

// Utility headers
// AUTO-REMOVED #include <numeric/random/random.hh>
// AUTO-REMOVED #include <utility/io/izstream.hh>
// AUTO-REMOVED #include <utility/io/ozstream.hh>

#include <basic/Tracer.hh>
// AUTO-REMOVED #include <basic/options/option.hh>
// AUTO-REMOVED #include <basic/options/keys/OptionKeys.hh>


//// C++ headers
// AUTO-REMOVED #include <fstream>

//Auto Headers
#include <core/chemical/AtomType.hh>
#include <core/pose/util.hh>
#include <utility/vector1.hh>


static basic::Tracer tr("protocols.abinitio",basic::t_info);

namespace protocols {
namespace abinitio {

using namespace core;

bool KinematicControl::prepare_pose_for_sampling( pose::Pose& pose ) const {
  pose.fold_tree( sampling_fold_tree() );
  if ( jump_mover() ) jump_mover()->apply_at_all_positions( pose ); //make sure each jump is initialized
  jumping::safe_secstruct( pose ); //make sure that secstruct is valid (in the sense of FragmentMover::valid_ss)
  return true;
}

//@brief find all cutpoints that are only present in the "sampling" fold-tree.
void
find_sampling_cuts(
  kinematics::FoldTree const& sampling,
  kinematics::FoldTree const& final,
  utility::vector1< Size >& sample_cuts )
{
  sample_cuts.clear();
  for ( Size i = 1; i <= (Size) sampling.num_cutpoint(); i++ ) {
    if ( !final.is_cutpoint( sampling.cutpoint( i ) ) ) sample_cuts.push_back( sampling.cutpoint( i ));
  }
}

void
KinematicControl::add_chainbreak_variants( pose::Pose &pose ) const {
  utility::vector1< Size > sample_cuts;
  find_sampling_cuts( pose.fold_tree(), final_fold_tree(), sample_cuts );
  for ( utility::vector1< Size >::const_iterator it = sample_cuts.begin(), eit = sample_cuts.end();
  it != eit; ++ it ) {
    core::pose::add_variant_type_to_pose_residue( pose, chemical::CUTPOINT_LOWER, *it );
    core::pose::add_variant_type_to_pose_residue( pose, chemical::CUTPOINT_UPPER, *it+1 );
  }
}

void
KinematicControl::add_chainbreak_variants( pose::Pose &pose, Size max_dist, core::kinematics::ShortestPathInFoldTree const& sp) const {
  //remove_chainbreaks( pose ); not necessary if max_dist is monotonoically increaseing
  utility::vector1< Size > sample_cuts;
  find_sampling_cuts( pose.fold_tree(), final_fold_tree(), sample_cuts );
  for ( utility::vector1< Size >::const_iterator it = sample_cuts.begin(), eit = sample_cuts.end();
  it != eit; ++ it ) {
    if ( sp.dist( *it, *it+1 ) <= max_dist ) {
      tr.Debug << "add chainbreak variant to residues " << *it << " and " << *it+1 << std::endl;
      core::pose::add_variant_type_to_pose_residue( pose, chemical::CUTPOINT_LOWER, *it );
      core::pose::add_variant_type_to_pose_residue( pose, chemical::CUTPOINT_UPPER, *it+1 );
    }
  }
}

KinematicControl::KinematicControl() {}
KinematicControl::~KinematicControl() {}

void KinematicControl::set_movemap( core::kinematics::MoveMapCOP mm ) {
 movemap_ = mm;
  if ( jump_mover_ ) jump_mover_->set_movemap( movemap_ptr() );
}

void KinematicControl::set_strict_movemap( core::kinematics::MoveMapCOP mm ) {
 strict_movemap_ = mm;
}

core::kinematics::MoveMapCOP
KinematicControl::movemap_ptr() const {
 return movemap_;
}

core::kinematics::MoveMap const &
KinematicControl::movemap() const {
 return *movemap_;
}

//return a jump-Mover for jumps that you want to be sampled
simple_moves::FragmentMoverOP
KinematicControl::jump_mover() const {
 return jump_mover_;
}

//return a jump-Mover for jumps that you want to be sampled
void
KinematicControl::set_jump_mover( simple_moves::FragmentMoverOP jm ) {
 jump_mover_ = jm;
  if ( jump_mover_ && movemap_ ) jump_mover_->set_movemap( movemap_ );
}


void CoordinateConstraintKC::add_score_weights( scoring::ScoreFunction& scorefxn, Real progress ) const {
  scorefxn.set_weight( scoring::coordinate_constraint, ramp_ ? progress*final_weight_ : final_weight_ );
}

}
}