HBondFeatures.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/HBondFeatures.hh
/// @brief  report HBond geometry and scores to features Statistics Scientific Benchmark
/// @author Matthew O'Meara (mattjomeara@gmail.com)

#ifndef INCLUDED_protocols_features_HBondFeatures_hh
#define INCLUDED_protocols_features_HBondFeatures_hh

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

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

// Project Headers
#include <core/types.hh>
#include <core/id/AtomID_Map.fwd.hh>
#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 <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/hbonds/HBondSet.fwd.hh>
#include <core/scoring/hbonds/HBondOptions.fwd.hh>

// Utility Headers
#include <utility/vector1.hh>
#include <utility/tag/Tag.fwd.hh>

// C++ Headers
#include <string>

namespace protocols{
namespace features{

/// @brief How a hydrogen bond should be defined See note for
/// definition_type_ below.
enum HBDefType {
  hbdef_NONE = 1,
  hbdef_ENERGY, // define what constitutes a hydrogen bond by its energy
  hbdef_AHDIST, // define what constitutes a hydrogen bond by the A-H distance
  hbdef_MAX = hbdef_AHDIST
};



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

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

  HBondFeatures( HBondFeatures const & src );

  virtual ~HBondFeatures();

  ///@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;

private:
  void
  write_hbond_chem_types_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_sites_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_sites_pdb_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_site_environment_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_site_atoms_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbonds_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_lennard_jones_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_geom_coords_table_schema(
    utility::sql_database::sessionOP db_session) const;

  void
  write_hbond_dehydrons_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 get what criteria should be used to define what
  ///constitutes a hydrogen bond
  // Undefined, commenting out to fix PyRosetta build  HBDefType definition_type() const;

  ///@brief set what criteria should be used to define what
  ///constitutes a hydrogen bond
  // Undefined, commenting out to fix PyRosetta build  void definition_type( HBDefType definition_type );


  ///@brief get the definition threshold that should be
  ///used to define what constitutes a hydrogen bond
  // Undefined, commenting out to fix PyRosetta build  core::Real definition_threshold() const;

  ///@brief set the definition threshold that should be
  ///used to define what constitutes a hydrogen bond
  // Undefined, commenting out to fix PyRosetta build  void definition_threshold( core::Real definition_threshold );

  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 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
  insert_site_row(
    core::pose::Pose const & pose,
    boost::uuids::uuid struct_id,
    core::Size site_id,
    core::Size resNum,
    core::Size atmNum,
    bool is_donor,
    utility::sql_database::sessionOP db_session);

  void
  insert_site_pdb_row(
    core::pose::Pose const & pose,
    core::Size resNum,
    core::Size atmNum,
    core::Size heavy_atmNum,
    boost::uuids::uuid struct_id,
    core::Size site_id,
    utility::sql_database::sessionOP db_session);

  void
  insert_site_environment_row(
    core::pose::Pose const & pose,
    core::Size resNum,
    core::Size atmNum,
    boost::uuids::uuid struct_id,
    core::Size site_id,
    core::id::AtomID_Map< core::Real > const & atom_sasa_s,
    core::id::AtomID_Map< core::Real > const & atom_sasa_m,
    core::id::AtomID_Map< core::Real > const & atom_sasa_l,
    core::id::AtomID_Map< utility::vector1< core::scoring::hbonds::HBondCOP > > const & site_partners,
    core::id::AtomID_Map< core::Real > const & site_hbond_energies,
    utility::sql_database::sessionOP db_session);

  void
  insert_site_atoms_row(
    core::pose::Pose const & pose,
    core::Size resNum,
    core::Size atmNum,
    boost::uuids::uuid struct_id,
    core::Size site_id,
    utility::sql_database::sessionOP db_session);

  void
  insert_hbond_row(
    core::scoring::hbonds::HBond const & hbond,
    boost::uuids::uuid struct_id,
    core::Size hbond_id,
    core::id::AtomID_Map< core::Size > const & site_ids,
    core::id::AtomID_Map< utility::vector1< core::scoring::hbonds::HBondCOP > > const & site_partners,
    utility::sql_database::sessionOP db_session);

  void
  insert_hbond_geom_coords(
    core::pose::Pose const & pose,
    core::scoring::hbonds::HBondOptions const & hbond_options,
    core::scoring::hbonds::HBond const & hbond,
    boost::uuids::uuid struct_id,
    core::Size hbond_id,
    utility::sql_database::sessionOP db_session);

  void
  insert_hbond_lennard_jones_row(
    core::pose::Pose const & pose,
    core::scoring::hbonds::HBond const & hbond,
    boost::uuids::uuid struct_id,
    core::Size hbond_id,
    utility::sql_database::sessionOP db_session);

  void
  insert_hbond_dehydron_row(
    core::pose::Pose const & pose,
    core::scoring::hbonds::HBond const & hbond,
    boost::uuids::uuid struct_id,
    core::Size hbond_id,
    utility::sql_database::sessionOP db_session);


private:

  core::scoring::ScoreFunctionOP scfxn_;

  // The standard Rosetta definition of a hydrogen bond is when the
  // hbond energy < 0.  However, to detect the distribution around
  // this threhsold it can be useful to define hydrogen bonds
  // differently, either by a higher energy thershold or using some
  // other threshold, like the distance between the acceptor and the
  // hydrogen.
  HBDefType definition_type_;
  core::Real definition_threshold_;
};

} // namespace
} // namespace

#endif // include guard