CartesianSampler.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_CartesianSampler_hh
#define INCLUDED_protocols_hybridization_CartesianSampler_hh

#include <protocols/hybridization/InsertChunkMover.hh>
#include <protocols/hybridization/CartesianSampler.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 <numeric/random/WeightedSampler.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 CartesianSampler: public protocols::moves::Mover {
public:
  CartesianSampler();
  CartesianSampler( utility::vector1<core::fragment::FragSetOP> fragments_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) { scorefxn_=scorefxn_in; }

  // set options
  void set_ncycles(core::Size ncycles_in) { ncycles_=ncycles_in; }
  void set_overlap(core::Size overlap_in) { overlap_=overlap_in; }

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

  void parse_my_tag(
    utility::tag::TagPtr const tag, 
    moves::DataMap & data,
    filters::Filters_map const & ,
    moves::Movers_map const & ,
    core::pose::Pose const & pose );

  virtual protocols::moves::MoverOP clone() const;
  virtual protocols::moves::MoverOP fresh_instance() const;

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

  // 
  void compute_fragment_bias( core::pose::Pose & pose );

  void update_fragment_library_pointers( );

private:
  // parameters
  core::Size ncycles_, overlap_;

  // fragments
  utility::vector1<core::fragment::FragSetOP> fragments_;
  utility::vector1<boost::unordered_map<core::Size, core::fragment::Frame> > library_;

  // fragment bias
  std::string fragment_bias_strategy_;
  utility::vector1<numeric::random::WeightedSampler> frag_bias_;
  std::set<core::Size> user_pos_;

  // scorefunctions
  core::scoring::ScoreFunctionOP scorefxn_;
}; //class CartesianSampler
  
} // hybridize 
//} // comparative_modeling 
} // protocols

#endif