DnaInterfacePacker.hh

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// vi: set ts=2 noet:
//
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/// @file DnaInterfacePacker.hh
/// @author ashworth
/// @brief Intended to perform anything one would want to do in a DNA interface that uses a single incarnation of the RotamerSets/InteractionGraph combo.
/// @details For basic packing/designing, the more basic PackRotamersMover can be used instead, provided it receives the appropriate TaskFactory/TaskOperations. This derived class, however, takes advantage of the reusability of packer data to accomplish some higher-level functions, such as rapid estimations of multi-state specificity, reversions, and mutational scanning.

#ifndef INCLUDED_protocols_dna_DnaInterfacePacker_hh
#define INCLUDED_protocols_dna_DnaInterfacePacker_hh

#include <protocols/dna/DnaInterfacePacker.fwd.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <protocols/filters/Filter.fwd.hh>

#include <protocols/dna/typedefs.hh>
// AUTO-REMOVED #include <protocols/dna/DnaDesignDef.hh>
#include <protocols/dna/DnaChains.fwd.hh>
#include <protocols/dna/PDBOutput.fwd.hh>

#include <core/types.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/optimization/MinimizerOptions.fwd.hh>
#include <core/pack/interaction_graph/InteractionGraphBase.fwd.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/tag/Tag.fwd.hh>

#include <map>
#include <string>

#include <protocols/dna/DnaDesignDef.fwd.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace dna {

class ResTypeSequence_lt;

typedef std::map< ResTypeSequence, core::Real, ResTypeSequence_lt > SequenceScores;

class ResTypeSequence_lt {
public:
  bool operator() ( ResTypeSequence const & a, ResTypeSequence const & b ) const;
};

class DnaInterfacePacker : public protocols::simple_moves::PackRotamersMover {

public:
  typedef utility::tag::TagPtr TagPtr;
  typedef core::scoring::ScoreFunctionOP ScoreFunctionOP;

public:
  DnaInterfacePacker();

  DnaInterfacePacker(
    ScoreFunctionOP,
    bool minimize = false,
    std::string filename_root = "dnapacker"
  );

  virtual ~DnaInterfacePacker(); // important for properly "releasing" owning pointer data

  virtual moves::MoverOP fresh_instance() const;
  virtual moves::MoverOP clone() const;
  virtual std::string get_name() const;

  virtual void apply( Pose & );

  bool initialized() const;

  ///@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 & );

  core::Real unbound_score( Pose const &, bool output_pdb = false, std::string pdbname = "" );

  std::pair< core::Real, core::Real > measure_specificity( Pose & );
  std::pair< SequenceScores, SequenceScores > measure_bp_specificities( Pose & );
  std::pair< SequenceScores, SequenceScores >
    measure_specificities( Pose &, ResTypeSequences const & );

  void reversion_scan(
    Pose &,
    core::Real bound_score = 0.,
    core::Real binding_score = 0.,
    std::pair< core::Real, core::Real > specificities = std::make_pair(0.,0.) );

  // setters, getters, and book-keeping methods
  void reference_pose( Pose const & );
  PoseCOP reference_pose() const;
  void targeted_dna( DnaDesignDefOPs const & );
  DnaDesignDefOPs const & targeted_dna() const;
  void pdboutput( PDBOutputOP );
  void set_filename_root( std::string const & name ) { filename_root_ = name; }
  std::string dna_seq_tag( Pose const &, ResTypeSequence const & ) const;
  ResTypeSequence get_targeted_sequence( Pose const & ) const;
  ResTypeSequence current_working_sequence( Pose const & ) const;
  std::string current_dna_design_string( Pose const & ) const;
  std::string allowed_types() const;
  void clear_initialization();
  std::string pdbname() { return pdbname_; }

private: // methods
  void standard_packing( Pose & );
  void post_packing( Pose &, ResTypeSequence const &, Size );
  void protein_scan( Pose & );
  void init_standard( Pose & );
  void make_dna_sequence_combinations();
  void add_complementary_sequence( ResTypeSequence & );
  core::Real calculate_specificity( Pose const &, ResTypeSequence const &, SequenceScores const & );

private: // data
  PoseCOP reference_pose_;
  DnaDesignDefOPs targeted_dna_;
  DnaChainsOP dna_chains_;
  ResTypeSequences dna_sequences_;
  bool minimize_;
  std::string filename_root_;
  bool binding_E_;
  bool probe_specificity_;
  bool reversion_scan_;
  bool protein_scan_;
  std::string allowed_types_;
  bool base_only_;
  bool include_dna_potentials_in_specificity_calculations_;
  core::Size num_repacks_;
  core::Size specificity_repacks_;
  core::optimization::MinimizerOptionsOP minimize_options_;
  core::kinematics::MoveMapOP min_movemap_;
  PDBOutputOP pdboutput_;
  utility::vector1< core::chemical::ResidueTypeCOP > reference_residue_types_;
  bool initialization_state_;
  std::string pdbname_;
};

} // namespace dna
} // namespace protocols

#endif