DatabaseJobInputter.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
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/// @file   protocols/features/DatabaseJobInputter.hh
/// @brief  header file for DatabaseJobInputter class
/// @author Matthew O'Meara (mattjomeara@gmail.com)


#ifndef INCLUDED_protocols_features_DatabaseJobInputter_hh
#define INCLUDED_protocols_features_DatabaseJobInputter_hh

// Unit Headers
#include <protocols/jd2/JobInputter.hh>
#include <protocols/features/DatabaseJobInputter.fwd.hh>
#include <protocols/jd2/Job.fwd.hh>
// AUTO-REMOVED #include <protocols/features/ProteinSilentReport.hh>

// Project Headers
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <protocols/features/ProteinSilentReport.fwd.hh>

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

//C++ Headers
#include <string>
#include <map>
#include <set>

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

namespace protocols {
namespace features {

///@details This is the simplest implementation of JobInputter, which
///reads from -s/-l and Database files.
class DatabaseJobInputter : public protocols::jd2::JobInputter
{
public:

  DatabaseJobInputter();

  virtual ~DatabaseJobInputter();

  static void register_options();

  /// @brief load options from option sytem
  void
  load_options_from_option_system();

  /// @brief Set database name
  void
  set_database_name(std::string const & database_name);

  /// @brief Get database name
  std::string
  get_database_name() const;

  /// @brief Set database postreSQL schema
  void
  set_database_pq_schema(std::string const & database_pq_schema);

  /// @brief Get database postreSQL schema
  std::string
  get_database_pq_schema() const;

  /// @brief Get score function
  core::scoring::ScoreFunctionOP
  get_scorefunction();

  /// @brief Set score function
  void
  set_scorefunction(core::scoring::ScoreFunctionOP scorefunction );

  /// @brief set struct_ids from a list of strings of hex-uuid representations
  void
  set_struct_ids_from_strings(
  utility::vector1<std::string> const & struct_id_strings);

  /// @brief set input tags using a database SELECT command
  void
  set_struct_ids_from_sql(utility::vector1<std::string> const & sql);

//  /// @brief Get input tags
//  void
//  get_tags(utility::vector1< std::string > & tags);

  /// @brief this function is responsible for filling the pose reference with
  /// the pose indicated by the job.  The Job object (within its InnerJob)
  /// contains a PoseCOP.  This function needs to either fill the pose
  /// reference from the InnerJob or, on first demand of a pose from that
  /// InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill
  /// the reference.  This implementation uses pose_from_pdb
  virtual void pose_from_job( core::pose::Pose & pose, protocols::jd2::JobOP job );

  /// @brief this function determines what jobs exist from -in::file::silent and
  /// -in::file::tags.
  virtual void fill_jobs( protocols::jd2::Jobs & jobs );

  /// @brief Return the type of input source that the DatabaseJobInputter is currently
  ///  using.
  /// @return Always <em>DATABASE</em>.
  virtual protocols::jd2::JobInputterInputSource::Enum input_source() const;

private:
  core::scoring::ScoreFunctionOP scfxn_;
  protocols::features::ProteinSilentReportOP protein_silent_report_;
  std::string database_name_;
  std::string database_pq_schema_;
  core::Size input_protocol_id_;
  std::map< std::string, boost::uuids::uuid > tag_structures_;
  std::map< std::string, std::set< core::Size > > tag_residues_;
}; // DatabaseJobInputter

} // namespace features
} // namespace protocols

#endif //INCLUDED_protocols_features_DatabaseJobInputter_hh