StrandBundleFeatures.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:
// :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
// (c) addressed to university of washington uw techtransfer, email: license@u.washington.edu.

/// @file strandBundleFeatures.hh
/// @brief
/// @author Doo Nam Kim (started with Tim Jacobs' code)

#ifndef INCLUDED_protocols_features_strand_assembly_StrandBundleFeatures_hh
#define INCLUDED_protocols_features_strand_assembly_StrandBundleFeatures_hh

//Unit
#include <protocols/features/strand_assembly/StrandBundleFeatures.fwd.hh>

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

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

//Devel
#include <protocols/features/strand_assembly/StrandFragment.hh>

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

// for string return
#include <string>

namespace protocols {
namespace features {
namespace strand_assembly {

class StrandBundleFeatures : public protocols::features::FeaturesReporter {

public:

  StrandBundleFeatures();

  void init_from_options();

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

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

  ///@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;

  ///@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<StrandFragment> get_full_strands(boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session);
  utility::vector1<StrandFragment> get_i_strand_from_full_strand_pairs(boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session);
  utility::vector1<StrandFragment> get_j_strand_from_full_strand_pairs(boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session);
  
  bool find_antiparallel                   (core::pose::Pose const & pose, StrandFragment strand_i, StrandFragment strand_j);
  bool find_parallel                       (core::pose::Pose const & pose, StrandFragment strand_i, StrandFragment strand_j);

  core::Real check_sheet_dis_antiparallel        (core::pose::Pose const & pose, StrandFragment strand_i, StrandFragment strand_j);
  core::Real check_sheet_dis_parallel            (core::pose::Pose const & pose, StrandFragment strand_i, StrandFragment strand_j);

  core::Real sheet_torsion                 (core::pose::Pose const & pose, StrandFragment strand_i, StrandFragment strand_j); 
  core::Real shortest_dis_sidechain (core::pose::Pose const & pose, StrandFragment strand_i, StrandFragment strand_j);  
  core::Real shortest_dis_sidechain (core::Real val_shortest_dis_sidechain_1,
                     core::Real val_shortest_dis_sidechain_2,
                     core::Real val_shortest_dis_sidechain_3,
                     core::Real val_shortest_dis_sidechain_4);  

  core::Real shortest_dis_pairs (core::Real return_of_check_sheet_dis_antiparallel_1,
                   core::Real return_of_check_sheet_dis_antiparallel_2,
                   core::Real return_of_check_sheet_dis_antiparallel_3,
                   core::Real return_of_check_sheet_dis_antiparallel_4);  
private:

  core::Size min_strand_size_;
  core::Size max_strand_size_;
  core::Real min_O_N_dis_;
  core::Real max_O_N_dis_;
  core::Real min_sheet_dis_;
  core::Real max_sheet_dis_;
  core::Real min_sheet_torsion_;
  core::Real max_sheet_torsion_;  
};

} //namespace strand_assembly
} //namespace features
} //namespace protocols

#endif