SmotifFeatures.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 SmotifFeatures.hh
///
/// @brief
/// @author Tim Jacobs

#ifndef INCLUDED_protocols_features_SmotifFeature_hh
#define INCLUDED_protocols_features_SmotifFeature_hh

// Unit Headers
#include <protocols/features/FeaturesReporter.hh>
#include <protocols/features/SmotifFeatures.fwd.hh>

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

// Project Headers
#include <core/pose/Pose.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <utility/vector1.fwd.hh>

#include <numeric/xyzVector.fwd.hh>

// C++ Headers
#include <string>

#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>


namespace protocols{
namespace features{

struct SecondaryStructureSegment{
  core::Size segment_id;
  core::Size residue_begin;
  core::Size residue_end;
  std::string dssp;
};

class SmotifFeatures : public protocols::features::FeaturesReporter {
public:
  SmotifFeatures();

  SmotifFeatures(
    core::scoring::ScoreFunctionOP scfxn);

  SmotifFeatures( SmotifFeatures const & src );

  virtual ~SmotifFeatures();

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

  ///@brief generate the table schemas and write them to the database
  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;

  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*/);

  utility::vector1<SecondaryStructureSegment>
  get_ss_segments(
    boost::uuids::uuid struct_id,
    utility::sql_database::sessionOP db_session);

  /* Undefined, commenting out to fix PyRosetta build  numeric::xyzVector<core::Real>
  pca(utility::vector1< numeric::xyzVector< core::Real > > coords); */

  ///@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
    );
};

} // namespace
} // namespace

#endif // include guard