Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::features::HBondFeatures Class Reference

#include <HBondFeatures.hh>

Inheritance diagram for protocols::features::HBondFeatures:
Inheritance graph
[legend]
Collaboration diagram for protocols::features::HBondFeatures:
Collaboration graph
[legend]

Public Member Functions

 HBondFeatures ()
 
 HBondFeatures (core::scoring::ScoreFunctionOP scfxn)
 
 HBondFeatures (HBondFeatures const &src)
 
virtual ~HBondFeatures ()
 
std::string type_name () const
 return string with class name More...
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const
 generate the table schemas and write them to the database More...
 
utility::vector1< std::string > features_reporter_dependencies () const
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 get what criteria should be used to define what constitutes a hydrogen bond More...
 
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)
 collect all the feature data for the pose More...
 
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)
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
virtual ~FeaturesReporter ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
virtual std::string schema () const
 return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
 
core::Size report_features (core::pose::Pose const &, boost::uuids::uuid, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void load_into_pose (utility::sql_database::sessionOP, boost::uuids::uuid, core::pose::Pose &)
 
virtual void delete_record (boost::uuids::uuid, utility::sql_database::sessionOP)
 

Private Member Functions

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
 

Private Attributes

core::scoring::ScoreFunctionOP scfxn_
 
HBDefType definition_type_
 
core::Real definition_threshold_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 

Constructor & Destructor Documentation

protocols::features::HBondFeatures::HBondFeatures ( )
protocols::features::HBondFeatures::HBondFeatures ( core::scoring::ScoreFunctionOP  scfxn)
protocols::features::HBondFeatures::HBondFeatures ( HBondFeatures const &  src)
protocols::features::HBondFeatures::~HBondFeatures ( )
virtual

Member Function Documentation

utility::vector1< std::string > protocols::features::HBondFeatures::features_reporter_dependencies ( ) const
virtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::HBondFeatures::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 
)

References core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::energies(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and core::conformation::Residue::xyz().

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::conformation::Residue::abase2(), core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::eval_type(), core::scoring::hbonds::get_hbe_acc_hybrid(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), core::pose::Pose::residue(), protocols::kinmatch::xyz(), and core::conformation::Atom::xyz().

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::ScoringManager::get_instance(), core::pose::Pose::residue(), and scfxn_.

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::HBond::eval_type(), core::scoring::hbonds::hb_eval_type_weight(), scfxn_, and core::scoring::hbonds::HBond::weight().

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::pose::Pose::residue(), and protocols::kinmatch::xyz().

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::pose::Pose::is_fullatom(), and core::io::serialization::size().

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::pose::Pose::pdb_info().

Referenced by report_features().

void protocols::features::HBondFeatures::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 
)

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::pose::Pose::chain(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::chemical::AtomType::name(), core::chemical::ResidueType::name(), core::scoring::hbonds::HBondTypeManager::name_from_acc_chem_type(), core::scoring::hbonds::HBondTypeManager::name_from_don_chem_type(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Referenced by report_features().

void protocols::features::HBondFeatures::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap &  data,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual

get what criteria should be used to define what constitutes a hydrogen bond

set what criteria should be used to define what constitutes a hydrogen bond get the definition threshold that should be used to define what constitutes a hydrogen bond set the definition threshold that should be used to define what constitutes a hydrogen bond

Reimplemented from protocols::features::FeaturesReporter.

References definition_threshold_, definition_type_, protocols::moves::DataMap::get(), protocols::features::hbdef_AHDIST, protocols::features::hbdef_ENERGY, scfxn_, and type_name().

Size protocols::features::HBondFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)
virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References core::scoring::hbonds::HBond::acc_res(), core::scoring::calc_per_atom_sasa(), core::pose::Pose::conformation(), definition_threshold_, definition_type_, core::scoring::hbonds::HBond::don_res(), core::sequence::end, core::pose::Pose::energies(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), protocols::features::hbdef_AHDIST, protocols::features::hbdef_ENERGY, core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBond::hbond_energy_comparer(), core::scoring::hbonds::HBondSet::hbond_options(), core::pose::initialize_atomid_map(), insert_hbond_dehydron_row(), insert_hbond_geom_coords(), insert_hbond_lennard_jones_row(), insert_hbond_row(), insert_site_atoms_row(), insert_site_environment_row(), insert_site_pdb_row(), insert_site_row(), core::pose::Pose::is_fullatom(), core::pose::Pose::n_residue(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::conformation::Conformation::structure_moved().

string protocols::features::HBondFeatures::type_name ( ) const
virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

Referenced by parse_my_tag().

void protocols::features::HBondFeatures::write_hbond_chem_types_table_schema ( utility::sql_database::sessionOP  db_session) const
private

References core::pack::dunbrack::c, and core::scoring::hbonds::t().

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_dehydrons_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_geom_coords_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_lennard_jones_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_site_atoms_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_site_environment_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_sites_pdb_table_schema ( utility::sql_database::sessionOP  db_session) const
private

References protocols::loops::iCode.

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbond_sites_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_hbonds_table_schema ( utility::sql_database::sessionOP  db_session) const
private

Referenced by write_schema_to_db().

void protocols::features::HBondFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_hbond_chem_types_table_schema(), write_hbond_dehydrons_table_schema(), write_hbond_geom_coords_table_schema(), write_hbond_lennard_jones_table_schema(), write_hbond_site_atoms_table_schema(), write_hbond_site_environment_table_schema(), write_hbond_sites_pdb_table_schema(), write_hbond_sites_table_schema(), and write_hbonds_table_schema().

Member Data Documentation

core::Real protocols::features::HBondFeatures::definition_threshold_
private

Referenced by parse_my_tag(), and report_features().

HBDefType protocols::features::HBondFeatures::definition_type_
private

Referenced by parse_my_tag(), and report_features().

core::scoring::ScoreFunctionOP protocols::features::HBondFeatures::scfxn_
private

Referenced by insert_hbond_lennard_jones_row(), insert_hbond_row(), and parse_my_tag().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:34:58 for Rosetta 3.5 by   doxygen 1.8.4