CartesianHybridize.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.

/// @file
/// @brief
/// @author Yifan Song
/// @author Frank DiMaio


#ifndef INCLUDED_protocols_hybridization_CartesianHybridize_hh
#define INCLUDED_protocols_hybridization_CartesianHybridize_hh

#include <protocols/hybridization/InsertChunkMover.hh>
#include <protocols/hybridization/CartesianHybridize.fwd.hh>

#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/util/kinematics_util.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/FragSet.hh>

#include <core/scoring/ScoreFunction.hh>

#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>

#include <protocols/moves/Mover.hh>

#include <ObjexxFCL/format.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/model_quality/maxsub.hh>

#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>

#include <boost/unordered/unordered_map.hpp>

namespace protocols {
//namespace comparative_modeling {
namespace hybridization {

using namespace core;
using namespace protocols::moves;
using namespace protocols::loops;
  
class CartesianHybridize: public protocols::moves::Mover {
public:
  CartesianHybridize();

  CartesianHybridize(
    utility::vector1 < core::pose::PoseOP > const & templates_in,
    utility::vector1 < core::Real > const & template_wts_in,
    utility::vector1 < protocols::loops::Loops > const & template_chunks_in, 
    utility::vector1 < protocols::loops::Loops > const & template_contigs_in,
    core::fragment::FragSetOP fragments9_in );

  // initialize options to defaults
  void init();

  // run the protocol
  void apply(core::pose::Pose & pose);

  // set the centroid scorefunction
  void set_scorefunction(core::scoring::ScoreFunctionOP scorefxn_in);

  // set options
  void set_increase_cycles(core::Real increase_cycles_in) { increase_cycles_=increase_cycles_in; }
  void set_no_global_frame(bool no_global_frame_in) { no_global_frame_=no_global_frame_in; }
  void set_linmin_only(bool linmin_only_in) { linmin_only_=linmin_only_in; }
  void set_cartfrag_overlap(core::Size cartfrag_overlap_in) { cartfrag_overlap_=cartfrag_overlap_in; }

  //
  std::string get_name() const { return "CartesianHybridize"; }

protected:
  // apply a homologue fragment
  void apply_frag( core::pose::Pose &pose, core::pose::Pose &templ, protocols::loops::Loop &frag, bool superpose=true);

  // apply a sequence fragment
  void apply_frame( core::pose::Pose & pose, core::fragment::Frame &frame );

private:
  // parameters
  core::Real increase_cycles_;
  core::Size ncycles_, cartfrag_overlap_;
  bool no_global_frame_, linmin_only_;

  // fragments
  utility::vector1 < core::pose::PoseOP > templates_;
  utility::vector1 < core::Real > template_wts_;
  utility::vector1 < protocols::loops::Loops > template_contigs_;
  core::fragment::FragSetOP fragments9_;
  boost::unordered_map<core::Size, core::fragment::Frame> library_;

  // scorefunctions
  core::scoring::ScoreFunctionOP lowres_scorefxn_, min_scorefxn_, bonds_scorefxn_, nocst_scorefxn_;
}; //class CartesianHybridize
  
} // hybridize 
//} // comparative_modeling 
} // protocols

#endif