RotamerBoltzmannWeight.hh

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// vi: set ts=2 sw=2 noet:
//
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// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file protocols/simple_filters/RotamerBoltzmannWeight.hh
/// @brief Reports to Tracer which residues are designable in a taskfactory
/// @author Sarel Fleishman (sarelf@uw.edu)

#ifndef INCLUDED_protocols_simple_filters_RotamerBoltzmannWeight_hh
#define INCLUDED_protocols_simple_filters_RotamerBoltzmannWeight_hh


// Project Headers
#include <protocols/filters/Filter.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/simple_filters/RotamerBoltzmannWeight.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/chemical/AA.hh>

#include <utility/vector1.hh>

//Auto Headers
// Unit headers

namespace protocols {
namespace simple_filters {

class RotamerBoltzmannWeight : public protocols::filters::Filter
{
private:
  typedef protocols::filters::Filter parent;
public:
  /// @brief default ctor
  RotamerBoltzmannWeight();
  ///@brief Constructor with a single target residue
  virtual bool apply( core::pose::Pose const & pose ) const;
  virtual void report( std::ostream & out, core::pose::Pose const & pose ) const;
  virtual core::Real report_sm( core::pose::Pose const & pose ) const;
  virtual protocols::filters::FilterOP clone() const;
  virtual protocols::filters::FilterOP fresh_instance() const;
  core::Real compute( core::pose::Pose const & pose ) const;
  virtual ~RotamerBoltzmannWeight();
  core::pack::task::TaskFactoryOP task_factory() const;
  void task_factory( core::pack::task::TaskFactoryOP task_factory );
  void parse_my_tag( utility::tag::TagPtr const tag,
    protocols::moves::DataMap &,
    protocols::filters::Filters_map const &,
    protocols::moves::Movers_map const &,
    core::pose::Pose const & );
  void parse_def( utility::lua::LuaObject const & def,
          utility::lua::LuaObject const & score_fxns,
          utility::lua::LuaObject const & tasks );

  utility::vector1< core::Size > first_pass_ala_scan( core::pose::Pose const & pose ) const; // return a list of residues that pass the ddG threshold
  core::Real compute_Boltzmann_weight( core::pose::Pose const & pose, core::Size const resi ) const;
  void rb_jump( core::Size const jump );
  core::Size rb_jump() const;
  void sym_dof_names( std::string const dof_names );
  std::string sym_dof_names() const;
  void repacking_radius( core::Real const rad );
  core::Real repacking_radius() const;
  core::Real ddG_threshold() const;
  void ddG_threshold( core::Real const ddG );
  void scorefxn( core::scoring::ScoreFunctionOP scorefxn );
  core::scoring::ScoreFunctionOP scorefxn() const;
  core::Real temperature() const;
  void temperature( core::Real const temp );
  bool unbound() const;
  void unbound( bool const u );
  void threshold_probability( core::chemical::AA const aa_type, core::Real const probability );
  core::Real threshold_probability( core::chemical::AA const aa_type ) const;
  void energy_reduction_factor( core::Real const factor );
  core::Real energy_reduction_factor() const;
  core::Real interface_interaction_energy( core::pose::Pose const & pose, core::Size const res ) const;
  bool compute_entropy_reduction() const;
  void compute_entropy_reduction( bool const cer );
  void repack( bool const repack );
  bool repack() const;
  bool skip_ala_scan() const;
  void skip_ala_scan( bool const s );
  std::string type() const;
  void type( std::string const & s );
  bool write2pdb() const;
  void write2pdb( bool const write );
  core::Real compute_modified_ddG( core::pose::Pose const & pose, std::ostream & out ) const;
  void write_to_pdb( core::Size const residue, std::string const residue_name, core::Real const boltzmann_weight ) const;
private:
  core::pack::task::TaskFactoryOP task_factory_;
  core::Size rb_jump_; // dflt 1.
  std::string sym_dof_names_; // dflt "".
  bool unbound_; // dflt true. what is the reference state for computing the boltz weight
  core::scoring::ScoreFunctionOP scorefxn_;
  core::Real temperature_; //dflt 0.8 ; this is actually kT rather than just T
  core::Real ddG_threshold_; //dflt 1.5 a preliminary alanine scan will identify all allowed positions that also have at least ddG_threshold_ effect on binding for further analysis.
  core::Real repacking_radius_; // dflt 6.0. how much to repack with each rotamer
  utility::vector1< core::Real > threshold_probabilities_per_residue_; // dflt 0.1; the rotamer probability below which the energy_reduction_factor kicks in
  core::Real energy_reduction_factor_;//dflt 0.5; by how much to decrease the binding energy

  bool compute_entropy_reduction_; //dflt false; compute the difference between the bound and unbound states
  bool repack_; //dflt true; carry out ddG (true) or dG (false) calculations
/// the following are mutable b/c they only sum up data in the filter. They do not affect
/// how the filter is run (so the filter will remain logically constant, despite these variables)
/// Mutability here allows the variables to be changed even in const methods.
  mutable std::map< core::Size, core::Real > ddGs_;//save the ddG values for a final report
  mutable std::map< core::Size, core::Real > rotamer_probabilities_;//ditto for the probabilities
  std::string type_;
  bool skip_ala_scan_;//dflt false; if true, only considers the task_factory
  bool fast_calc_; //default false for now
  bool no_modified_ddG_;
  std::string target_residues_;
  bool write2pdb_;
};

} // simple_filters
} // protocols

#endif //INCLUDED_protocols_simple_filters_RotamerBoltzmannWeightFilter_HH_