RotamerFeatures.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:
//
// (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   protocols/features/RotamerFeatures.hh
/// @brief  report idealized torsional DOFs Statistics Scientific Benchmark
/// @author Matthew O'Meara

#ifndef INCLUDED_protocols_features_RotamerFeatures_hh
#define INCLUDED_protocols_features_RotamerFeatures_hh

// Unit Headers
#include <protocols/features/FeaturesReporter.hh>
#include <protocols/features/RotamerFeatures.fwd.hh>
#include <basic/database/schema_generator/Schema.hh>


#include <protocols/features/RotamerFeatures.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.hh>
#include <core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>


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

// Project Headers
#include <core/types.hh>
#include <utility/vector1.fwd.hh>

// C++ Headers
#include <string>

#include <utility/vector1.hh>


namespace protocols{
namespace features{

//@brief Extract from the dunbrack Energy term the model for the
// rotamer conformation.
template < core::Size T >
class RotamerInitializer {

public:
  static
  bool
  initialize_rotamer(
    core::conformation::Residue const & residue,
    core::pack::dunbrack::RotamerLibraryScratchSpace & scratch,
    core::Size & rotamer_bin
  ) {
    using namespace core::pack::dunbrack;

    SingleResidueRotamerLibraryCAP generic_rotlib =
      RotamerLibrary::get_instance().get_rsd_library( residue.type() );

    if(!generic_rotlib){
      return false;
    }

    RotamericSingleResidueDunbrackLibrary< T > const & rotlib(
      dynamic_cast< RotamericSingleResidueDunbrackLibrary< T > const & >(
        * generic_rotlib));

    RotVector rotamer_vector;
    Size4 rotamer_fixed_vector;
    core::Size packed_rotno;

    // can't use get_rotamer_from_chi_static because it's private. Perhaps it should be made public?
    rotlib.get_rotamer_from_chi(residue.chi(), rotamer_vector);

    if(rotamer_vector.size() > 4){
      //eg LYS_p:dimethylated, perhaps there is a more direct way to
      //detect cases like this?
      return false;
    }

    copy(rotamer_vector.begin(), rotamer_vector.end(), rotamer_fixed_vector.begin());

    packed_rotno = rotlib.rotwell_2_packed_rotno(rotamer_vector);
    if(packed_rotno == 0){
      packed_rotno = rotlib.find_another_representative_for_unlikely_rotamer(
        residue, rotamer_fixed_vector);
      rotlib.packed_rotno_2_rotwell(packed_rotno, rotamer_vector);
    }
    rotamer_bin = rotlib.rotwell_2_rotno(rotamer_vector);

    PackedDunbrackRotamer< T, core::Real > interpolated_rotamer;
    rotlib.interpolate_rotamers(
      residue, scratch, packed_rotno, interpolated_rotamer);

    return true;

  }

};


class RotamerFeatures : public protocols::features::FeaturesReporter {
public:
  RotamerFeatures(){}

  RotamerFeatures(
    RotamerFeatures const & ) :
    FeaturesReporter()
  {}

  virtual ~RotamerFeatures(){}

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

private:
  ///@brief generate the residue_rotamers table schema
  void
  write_residue_rotamers_table_schema(
    utility::sql_database::sessionOP db_session) const;

public:
  ///@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 return string with class name
  std::string
  type_name() const;

  ///@brief collect all the feature data for the pose
  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);

  void
  delete_record(
    boost::uuids::uuid struct_id,
    utility::sql_database::sessionOP db_session);
};

} // namespace
} // namespace

#endif // include guard