DnaInterfaceMultiStateDesign.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file DnaInterfaceMultiStateDesign.hh
/// @brief
/// @author ashworth

#ifndef INCLUDED_protocols_dna_DnaInterfaceMultiStateDesign_hh
#define INCLUDED_protocols_dna_DnaInterfaceMultiStateDesign_hh

#include <protocols/dna/DnaInterfaceMultiStateDesign.fwd.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>

#include <protocols/dna/DnaChains.fwd.hh>
#include <protocols/dna/DnaDesignDef.fwd.hh>

#include <protocols/multistate_design/MultiStatePacker.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
// AUTO-REMOVED #include <protocols/genetic_algorithm/GeneticAlgorithm.hh>

#include <core/pose/Pose.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <utility/tag/Tag.fwd.hh>

#include <protocols/genetic_algorithm/GeneticAlgorithm.fwd.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace dna {

///@brief wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework
// could also derive from DnaInterfacePacker(?)
class DnaInterfaceMultiStateDesign : public protocols::simple_moves::PackRotamersMover {
public:
  typedef multistate_design::PosType PosType;
  typedef core::pack::task::PackerTaskCOP PackerTaskCOP;
  typedef genetic_algorithm::GeneticAlgorithmOP GeneticAlgorithmOP;

public:
  DnaInterfaceMultiStateDesign();
  virtual ~DnaInterfaceMultiStateDesign();
  virtual void apply( Pose & );
  virtual std::string get_name() const;
  void copy_dna_chains( DnaChainsOP );
  void copy_targeted_dna( DnaDesignDefOPs const & );
  void output_results( Pose & );

  ///@brief parse XML (specifically in the context of the parser/scripting scheme)
  virtual void parse_my_tag(
    TagPtr const,
    moves::DataMap &,
    protocols::filters::Filters_map const &,
    moves::Movers_map const &,
    Pose const & );
  ///@brief required in the context of the parser/scripting scheme
  virtual moves::MoverOP fresh_instance() const;
  ///@brief required in the context of the parser/scripting scheme
  virtual moves::MoverOP clone() const;

private:
  void initialize( Pose & );

  using protocols::simple_moves::PackRotamersMover::run;

  void run();
  void add_dna_states( Pose const & , PackerTaskCOP );

private:
  GeneticAlgorithmOP gen_alg_;
  // direct use of MultiStatePacker is only for outputting results
  // (GeneticAlgorithm also holds pointer to it and uses it heavily)
  multistate_design::MultiStatePackerOP multistate_packer_;
  DnaChainsOP dna_chains_;
  DnaDesignDefOPs targeted_dna_;
  // option flags/parameters: constructor defaults to command line options
  // parse_my_tag method may change them
  core::Size generations_, pop_size_, num_packs_, pop_from_ss_, numresults_;
  core::Real fraction_by_recombination_, mutate_rate_, boltz_temp_, anchor_offset_;
  // checkpointing options
  std::string checkpoint_prefix_;
  core::Size checkpoint_interval_;
  bool checkpoint_gz_, checkpoint_rename_;

};

} // namespace dna
} // namespace protocols

#endif