DomainAssembly.hh

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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.

/// @brief

#ifndef INCLUDED_protocols_hybridization_DomainAssembly_hh
#define INCLUDED_protocols_hybridization_DomainAssembly_hh

// libRosetta headers
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/loops/loops_main.hh>
#include <core/pose/Pose.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>

#include <protocols/relax/FastRelax.hh>
#include <protocols/viewer/viewers.hh>

#include <protocols/moves/Mover.hh>
#include <protocols/moves/CompositionMover.hh>

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

// AUTO-REMOVED #include <basic/Tracer.hh>
#include <core/types.hh>
#include <utility/vector1.hh>

// option key includes
#include <basic/options/option.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>

#include <core/kinematics/Jump.hh>
#include <numeric/random/random.hh>
#include <core/scoring/ScoreFunction.hh>

namespace protocols {
//namespace comparative_modeling {
namespace hybridization {

class DomainAssembly : public protocols::moves::Mover {

public:
DomainAssembly(
         utility::vector1 < core::pose::PoseOP > & poses,
         utility::vector1 < core::Real > & domain_assembly_weights
         );

void run();

DomainAssembly(core::pose::PoseOP pose1,
  core::pose::PoseOP pose2,
  core::scoring::ScoreFunctionOP scorefxn)
{
  pose1_ = pose1;
  pose2_ = pose2;
  scorefxn_ = scorefxn;
}
  
void apply(
       core::pose::Pose & pose
       );
  
std::string
get_name() const {
  return "DomainAssembly";
}

private:
  utility::vector1 < core::pose::PoseOP > poses_;

  core::pose::PoseOP pose1_;
    core::pose::PoseOP pose2_;
    core::scoring::ScoreFunctionOP scorefxn_;
}; // class DomainAssembly

}  //  namespace hybridization
//}  //  //namespace comparative_modeling
}  //  namespace protocols

#endif  // PROTOCOLS_COMPARATIVE_MODELING_HYBRIDIZE_HYBRIDIZEFOLDTREEDYNAMIC_HH_