HelixBundleFeatures.hh

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// vi: set ts=2 noet:
// :notabs=false:tabSize=4:indentsize=4:
//
// (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
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/// @file HelixBundleFeatures.hh
/// @brief
/// @author Tim Jacobs

#ifndef INCLUDED_protocols_features_helixAssembly_HelixBundleFeatures_hh
#define INCLUDED_protocols_features_helixAssembly_HelixBundleFeatures_hh

//Unit
#include <protocols/features/helixAssembly/HelixBundleFeatures.fwd.hh>

//External
#include <boost/uuid/uuid.hpp>

//Protocols
#include <protocols/features/FeaturesReporter.hh>
#include <protocols/simple_filters/InterfaceSasaFilter.hh>

//Devel
#include <protocols/features/helixAssembly/HelicalFragment.hh>

//Utility
#include <utility/vector1.hh>

namespace protocols {
namespace features {
namespace helixAssembly {

struct FragmentPair
{
  FragmentPair(HelicalFragmentOP frag1, HelicalFragmentOP frag2):
  fragment_1(frag1),
  fragment_2(frag2)
  {}

  HelicalFragmentOP fragment_1;
  HelicalFragmentOP fragment_2;
  
  core::Real end_1_distance;
  core::Real end_2_distance;
  core::Real fa_attr;
  core::Real fa_fraction;
  core::Real crossing_angle;
};
  
class HelixBundleFeatures : public protocols::features::FeaturesReporter
{

public:

  HelixBundleFeatures();

  virtual
  std::string
  type_name() const  {
    return "HelixBundleFeatures";
  };

  ///@brief generate the table schemas and write them to the database
  virtual
  void
  write_schema_to_db(
    utility::sql_database::sessionOP db_session
  ) const;

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

  ///@brief return the set of features reporters that are required to
  ///also already be extracted by the time this one is used.
  utility::vector1<std::string>
  features_reporter_dependencies() const;
  
  bool
  valid_frag_set(
    std::set<HelicalFragmentOP> const & frag_set
  );

  bool
  check_cap_distances(
    core::pose::Pose const & pose,
    utility::vector1<HelicalFragmentOP> const & frag_set
  );

  ///@brief collect all the feature data for the pose
  virtual
  core::Size
  report_features(
    core::pose::Pose const & pose,
    utility::vector1<bool> const & relevant_residues,
    boost::uuids::uuid struct_id,
    utility::sql_database::sessionOP db_session
  );

  utility::vector1<HelicalFragmentOP>
  get_helix_fragments(
    boost::uuids::uuid struct_id,
    utility::sql_database::sessionOP db_session
  );
  
  void
  calc_pc_and_com(
    core::pose::Pose const & pose,
    HelicalFragmentOP fragment
  );
  
  ///@brief create a bundle-pose from the combination of fragments
  /// and record the "interface" SASA for each helix against the
  /// rest of the bundle
  void
  record_helix_sasas(
    core::pose::Pose const & pose,
    std::set<HelicalFragmentOP> const & frag_set
  );
  
  utility::vector1<FragmentPair>
  get_helix_pairs(
    core::pose::Pose const & pose,
    utility::vector1<HelicalFragmentOP> helix_fragments
  );
  
  ///@brief calculate the shared fa_attr for each pair of helices
  /// in the bundle
  void
  calc_fa_energy(
    core::pose::Pose const & pose,
    FragmentPair & fragment_pair
  );
  
  ///@brief calculate the crossing angles of the helix fragment in the bundle set
  void
  calc_crossing_angles(
    core::pose::Pose const & pose,
    FragmentPair & fragment_pair
  );
  
private:

  //Maximum allowable distance, in angstroms, between any two helix ends
  core::Real helix_cap_dist_cutoff_;
  
  //number of helices in the bundle
  core::Size bundle_size_;
  
  //number of residues in each helix
  core::Size helix_size_;
  
  //minimum residue_normalized fa_attr between two helix fragments in order to be considered
  //interacting
  core::Real min_per_residue_fa_attr_;
  
  //minimum fraction of
  core::Real min_interacting_set_fraction_;
  
  //maximum degrees off parallel for crossing angle
  core::Real max_degrees_off_parallel_;
  
  protocols::simple_filters::InterfaceSasaFilter sasa_filter_;
  
  core::scoring::ScoreFunctionOP scorefxn_;
};

} //namespace helixAssembly
} //namespace features
} //namespace protocols

#endif