Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | List of all members
protocols::features::OrbitalsFeatures Class Reference

#include <OrbitalsFeatures.hh>

Public Member Functions

 OrbitalsFeatures ()
 
 OrbitalsFeatures (OrbitalsFeatures const &src)
 
virtual ~OrbitalsFeatures ()
 
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...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
 collect all the feature data for the pose More...
 
void report_hpol_orbital_interactions (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID const struct_id, utility::sql_database::sessionOP db_session)
 get statistics based upon polar hydrogen to orbital distance/angle More...
 
void report_haro_orbital_interactions (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID const struct_id, utility::sql_database::sessionOP db_session)
 get statistics based upon aromatic hydrogen to orbital distance/angle More...
 
void set_OrbH_features_data (core::conformation::Residue &res1, core::conformation::Residue &res2, core::Size const Aindex, core::Size const Hindex, core::Size const Orbindex, numeric::xyzVector< core::Real > const Orbxyz, core::Size &resNum2, std::string &orbName1, std::string &htype2, std::string &res2name, core::Size &orbNum1, core::Size &hpolNum2, core::Real &cosAOH, core::Real &cosDHO, core::Real &chiBDHO, core::Real &chiBAOH, core::Real &AOH_angle, core::Real &DHO_angle, core::Real &chiBAHD, core::Real &cosAHD, core::Real &OrbHdist)
 
void set_OrbOrb_features_data (core::conformation::Residue &res1, core::conformation::Residue &res2, core::Size Aindex, core::Size Dindex, core::Size Orbindex1, core::Size Orbindex2, numeric::xyzVector< core::Real > const &Orbxyz1, numeric::xyzVector< core::Real > const &Orbxyz2, core::Size &resNum2, std::string &orbName1, std::string &res2name, std::string &OrbName2, core::Size &orbNum1, core::Size &OrbNum2, core::Real &cosAOO, core::Real &cosDOO, core::Real &chiBAOO, core::Real &chiBDOO, core::Real &AOO_angle, core::Real &DOO_angle, core::Real &OrbHdist, core::Real &cosAOD, core::Real &AOD_angle, core::Real &chiBAHD, core::Real &cosAHD)
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 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 &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Private Member Functions

void write_HPOL_orbital_table_schema (utility::sql_database::sessionOP db_session) const
 generate the HPOL_orbital table schema More...
 
void write_HARO_orbital_table_schema (utility::sql_database::sessionOP db_session) const
 generate the HARO_orbital table schema More...
 
void write_orbital_orbital_table_schema (utility::sql_database::sessionOP db_session) const
 generate the HPOL_orbital table schema More...
 

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, StructureID 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...
 
- Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T relevant_residues_mode_
 

Constructor & Destructor Documentation

protocols::features::OrbitalsFeatures::OrbitalsFeatures ( )

References basic::options::OptionKeys::in::add_orbitals, basic::options::option, and utility_exit_with_message.

protocols::features::OrbitalsFeatures::OrbitalsFeatures ( OrbitalsFeatures const &  src)

References basic::options::OptionKeys::in::add_orbitals, basic::options::option, and utility_exit_with_message.

protocols::features::OrbitalsFeatures::~OrbitalsFeatures ( )
virtual

Member Function Documentation

utility::vector1< std::string > protocols::features::OrbitalsFeatures::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.

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

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References report_hpol_orbital_interactions().

void protocols::features::OrbitalsFeatures::report_haro_orbital_interactions ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID const  struct_id,
utility::sql_database::sessionOP  db_session 
)

get statistics based upon aromatic hydrogen to orbital distance/angle

void protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID const  struct_id,
utility::sql_database::sessionOP  db_session 
)

get statistics based upon polar hydrogen to orbital distance/angle

References core::conformation::Residue::atom(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atoms_with_orb_index(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::bonded_orbitals(), core::conformation::Residue::Haro_index(), core::conformation::Residue::Hpol_index(), core::pose::Pose::n_residue(), core::conformation::Residue::name3(), core::conformation::Residue::orbital_xyz(), core::pose::Pose::residue(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), set_OrbH_features_data(), set_OrbOrb_features_data(), and core::conformation::Atom::xyz().

Referenced by report_features().

void protocols::features::OrbitalsFeatures::set_OrbH_features_data ( core::conformation::Residue &  res1,
core::conformation::Residue &  res2,
core::Size const  Aindex,
core::Size const  Hindex,
core::Size const  Orbindex,
numeric::xyzVector< core::Real > const  Orbxyz,
core::Size &  resNum2,
std::string &  orbName1,
std::string &  htype2,
std::string &  res2name,
core::Size &  orbNum1,
core::Size &  hpolNum2,
core::Real &  cosAOH,
core::Real &  cosDHO,
core::Real &  chiBDHO,
core::Real &  chiBAOH,
core::Real &  AOH_angle,
core::Real &  DHO_angle,
core::Real &  chiBAHD,
core::Real &  cosAHD,
core::Real &  OrbHdist 
)

References core::conformation::Residue::actcoord(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_type(), core::conformation::Residue::bonded_neighbor(), cos_of(), numeric::dihedral_radians(), numeric::xyzVector< class >::distance(), dot(), core::chemical::orbitals::OrbitalType::name(), core::chemical::AtomType::name(), core::conformation::Residue::name3(), numeric::xyzVector< class >::normalize(), core::conformation::Residue::orbital_type(), core::conformation::Residue::seqpos(), core::conformation::Residue::update_actcoord(), core::conformation::Residue::xyz(), core::conformation::Atom::xyz(), and protocols::kinmatch::xyz().

Referenced by report_hpol_orbital_interactions().

void protocols::features::OrbitalsFeatures::set_OrbOrb_features_data ( core::conformation::Residue &  res1,
core::conformation::Residue &  res2,
core::Size  Aindex,
core::Size  Dindex,
core::Size  Orbindex1,
core::Size  Orbindex2,
numeric::xyzVector< core::Real > const &  Orbxyz1,
numeric::xyzVector< core::Real > const &  Orbxyz2,
core::Size &  resNum2,
std::string &  orbName1,
std::string &  res2name,
std::string &  OrbName2,
core::Size &  orbNum1,
core::Size &  OrbNum2,
core::Real &  cosAOO,
core::Real &  cosDOO,
core::Real &  chiBAOO,
core::Real &  chiBDOO,
core::Real &  AOO_angle,
core::Real &  DOO_angle,
core::Real &  OrbHdist,
core::Real &  cosAOD,
core::Real &  AOD_angle,
core::Real &  chiBAHD,
core::Real &  cosAHD 
)

References core::conformation::Residue::actcoord(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), cos_of(), numeric::dihedral_radians(), numeric::xyzVector< class >::distance(), dot(), core::chemical::orbitals::OrbitalType::name(), core::conformation::Residue::name3(), numeric::xyzVector< class >::normalize(), core::conformation::Residue::orbital_type(), core::conformation::Residue::seqpos(), core::conformation::Residue::update_actcoord(), core::conformation::Atom::xyz(), core::conformation::Residue::xyz(), and protocols::kinmatch::xyz().

Referenced by report_hpol_orbital_interactions().

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

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::OrbitalsFeatures::write_HARO_orbital_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the HARO_orbital table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

void protocols::features::OrbitalsFeatures::write_HPOL_orbital_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the HPOL_orbital table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

void protocols::features::OrbitalsFeatures::write_orbital_orbital_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the HPOL_orbital table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by write_schema_to_db().

void protocols::features::OrbitalsFeatures::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_HARO_orbital_table_schema(), write_HPOL_orbital_table_schema(), and write_orbital_orbital_table_schema().

The documentation for this class was generated from the following files:
Generated on Wed Sep 10 2014 11:44:38 for Rosetta Protocols by   doxygen 1.8.7