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core::chemical::ResidueDatabaseIO Class Reference

#include <ResidueDatabaseIO.hh>

Inheritance diagram for core::chemical::ResidueDatabaseIO:
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Collaboration diagram for core::chemical::ResidueDatabaseIO:
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Public Member Functions

 ResidueDatabaseIO ()
 
virtual ~ResidueDatabaseIO ()
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const
 generate the table schemas and write them to the database More...
 
void initialize (utility::sql_database::sessionOP db_session)
 write the schema More...
 
core::Real get_version ()
 
void write_residuetype_to_database (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
core::chemical::ResidueTypeOP read_residuetype_from_database (chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types, std::string const &residue_type_set_name, std::string const &residue_type_name, utility::sql_database::sessionOP db_session)
 
utility::vector1< std::string > get_all_residues_in_database (utility::sql_database::sessionOP db_session)
 

Private Member Functions

void write_residue_type_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type table schema More...
 
void write_residue_type_atom_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_atom table schema More...
 
void write_residue_type_bond_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_bond table schema More...
 
void write_residue_type_cut_bond_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_cut_bond table schema More...
 
void write_residue_type_chi_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_chi table schema More...
 
void write_residue_type_chi_rotamer_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_chi_rotamer table schema More...
 
void write_residue_type_proton_chi_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_proton_chi table schema More...
 
void write_residue_type_property_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_property table schema More...
 
void write_residue_type_variant_type_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_variant_type table schema More...
 
void write_residue_type_icoor_table_schema (utility::sql_database::sessionOP db_session) const
 generate the residue_type_icoor table schema More...
 
std::string get_atom_name_from_database_atom_index (std::string residue_name, core::Size atom_index, utility::sql_database::sessionOP db_session)
 
void report_residue_type (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 this needs to get called after read_residue_type_atom More...
 
void report_residue_type_atom (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_atom (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_bond (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_bond (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_cut_bond (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_cut_bond (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_chi (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_chi (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_chi_rotamer (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_chi_rotamer (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_proton_chi (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_proton_chi (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_properties (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_properties (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_variant (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_variant (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 
void report_residue_type_icoor (std::string const &residue_type_set_name, core::chemical::ResidueType const &res_type, utility::sql_database::sessionOP db_session)
 
void read_residue_type_icoor (std::string const &residue_type_set_name, std::string const &residue_type_name, core::chemical::ResidueType &res_type, utility::sql_database::sessionOP db_session)
 

Private Attributes

core::Real version_
 
std::map< std::pair
< std::string, core::Size >
, std::string > 		atom_name_id_cache_
 

Detailed Description

Definition at line 33 of file ResidueDatabaseIO.hh.

Constructor & Destructor Documentation

core::chemical::ResidueDatabaseIO::ResidueDatabaseIO ( )

Definition at line 50 of file ResidueDatabaseIO.cc.

core::chemical::ResidueDatabaseIO::~ResidueDatabaseIO ( )
virtual

Definition at line 55 of file ResidueDatabaseIO.cc.

Member Function Documentation

utility::vector1< std::string > core::chemical::ResidueDatabaseIO::get_all_residues_in_database ( utility::sql_database::sessionOP  db_session)

Definition at line 663 of file ResidueDatabaseIO.cc.

Referenced by core::chemical::ChemicalManager::residue_type_set().

std::string core::chemical::ResidueDatabaseIO::get_atom_name_from_database_atom_index ( std::string  residue_name,
core::Size  atom_index,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 513 of file ResidueDatabaseIO.cc.

References atom_name_id_cache_.

Referenced by read_residue_type(), read_residue_type_bond(), read_residue_type_chi(), and read_residue_type_cut_bond().

core::Real core::chemical::ResidueDatabaseIO::get_version ( )

Definition at line 454 of file ResidueDatabaseIO.cc.

References version_.

Referenced by protocols::features::ResidueTypesFeatures::ResidueTypesFeatures().

void core::chemical::ResidueDatabaseIO::initialize ( utility::sql_database::sessionOP  db_session)

write the schema

Definition at line 449 of file ResidueDatabaseIO.cc.

References write_schema_to_db().

void core::chemical::ResidueDatabaseIO::read_residue_type ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

this needs to get called after read_residue_type_atom

Definition at line 585 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::aa(), get_atom_name_from_database_atom_index(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::name3(), core::chemical::name_from_aa(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueType::set_lower_connect_atom(), core::chemical::ResidueType::set_RotamerLibraryName(), core::chemical::ResidueType::set_upper_connect_atom(), and version_.

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_atom ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 709 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_atom().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_bond ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 768 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_bond(), and get_atom_name_from_database_atom_index().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_chi ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 878 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_chi(), and get_atom_name_from_database_atom_index().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_chi_rotamer ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 936 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_chi_rotamer().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_cut_bond ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 823 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_cut_bond(), and get_atom_name_from_database_atom_index().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_icoor ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1216 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::atom_name(), core::kinematics::distance(), core::chemical::ResidueType::natoms(), protocols::swa::phi(), core::chemical::ResidueType::set_atom_base(), core::chemical::ResidueType::set_icoor(), core::chemical::ResidueType::set_ideal_xyz(), and core::kinematics::Stub::spherical().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_properties ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1078 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_property().

Referenced by read_residuetype_from_database().

void core::chemical::ResidueDatabaseIO::read_residue_type_proton_chi ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1005 of file ResidueDatabaseIO.cc.

void core::chemical::ResidueDatabaseIO::read_residue_type_variant ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::ResidueType &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1122 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::add_variant_type().

Referenced by read_residuetype_from_database().

core::chemical::ResidueTypeOP core::chemical::ResidueDatabaseIO::read_residuetype_from_database ( chemical::AtomTypeSetCAP  atom_types,
chemical::ElementSetCAP  elements,
chemical::MMAtomTypeSetCAP  mm_atom_types,
chemical::orbitals::OrbitalTypeSetCAP  orbital_atom_types,
std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
utility::sql_database::sessionOP  db_session 
)

Definition at line 485 of file ResidueDatabaseIO.cc.

References read_residue_type(), read_residue_type_atom(), read_residue_type_bond(), read_residue_type_chi(), read_residue_type_chi_rotamer(), read_residue_type_cut_bond(), read_residue_type_icoor(), read_residue_type_properties(), and read_residue_type_variant().

Referenced by core::chemical::ChemicalManager::residue_type_set().

void core::chemical::ResidueDatabaseIO::report_residue_type ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 552 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::aa(), core::chemical::ResidueType::get_RotamerLibraryName(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::ResidueType::lower_connect_atom(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueType::upper_connect_atom(), and version_.

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_atom ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 684 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::AtomType::atom_type_name(), core::chemical::Atom::charge(), core::chemical::Atom::mm_name(), core::chemical::ResidueType::name(), and core::chemical::ResidueType::natoms().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_bond ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 743 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::bonded_neighbor_types(), core::chemical::ResidueType::name(), and core::chemical::ResidueType::natoms().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_chi ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 852 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::chi_atoms(), core::chemical::ResidueType::name(), and core::chemical::ResidueType::nchi().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 913 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::chi_rotamers(), core::chemical::ResidueType::name(), and core::chemical::ResidueType::nchi().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 799 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::cut_bond_neighbor(), core::chemical::ResidueType::name(), and core::chemical::ResidueType::natoms().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_icoor ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1147 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::CONNECT, core::chemical::ResidueType::icoor(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), and core::chemical::ICoorAtomID::POLYMER_LOWER.

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_properties ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1060 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::name(), and core::chemical::ResidueType::properties().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 964 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::n_proton_chi(), core::chemical::ResidueType::name(), core::chemical::ResidueType::proton_chi_2_chi(), core::chemical::ResidueType::proton_chi_extra_samples(), and core::chemical::ResidueType::proton_chi_samples().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::report_residue_type_variant ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)
private

Definition at line 1104 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::name(), and core::chemical::ResidueType::variant_types().

Referenced by write_residuetype_to_database().

void core::chemical::ResidueDatabaseIO::write_residue_type_atom_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_atom table schema

Definition at line 114 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_bond_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_bond table schema

Definition at line 162 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_chi_rotamer_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_chi_rotamer table schema

Definition at line 273 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_chi_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_chi table schema

Definition at line 231 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_cut_bond_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_cut_bond table schema

Definition at line 198 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_icoor_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_icoor table schema

Definition at line 405 of file ResidueDatabaseIO.cc.

References core::kinematics::distance(), and protocols::swa::phi().

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_property_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_property table schema

Definition at line 343 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_proton_chi_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_proton_chi table schema

Definition at line 308 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type table schema

Definition at line 77 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residue_type_variant_type_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the residue_type_variant_type table schema

Definition at line 374 of file ResidueDatabaseIO.cc.

Referenced by write_schema_to_db().

void core::chemical::ResidueDatabaseIO::write_residuetype_to_database ( std::string const &  residue_type_set_name,
core::chemical::ResidueType const &  res_type,
utility::sql_database::sessionOP  db_session 
)

Definition at line 460 of file ResidueDatabaseIO.cc.

References core::chemical::ResidueType::name(), report_residue_type(), report_residue_type_atom(), report_residue_type_bond(), report_residue_type_chi(), report_residue_type_chi_rotamer(), report_residue_type_cut_bond(), report_residue_type_icoor(), report_residue_type_properties(), report_residue_type_proton_chi(), and report_residue_type_variant().

Referenced by protocols::features::ResidueTypesFeatures::report_features().

void core::chemical::ResidueDatabaseIO::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const

generate the table schemas and write them to the database

Definition at line 61 of file ResidueDatabaseIO.cc.

References write_residue_type_atom_table_schema(), write_residue_type_bond_table_schema(), write_residue_type_chi_rotamer_table_schema(), write_residue_type_chi_table_schema(), write_residue_type_cut_bond_table_schema(), write_residue_type_icoor_table_schema(), write_residue_type_property_table_schema(), write_residue_type_proton_chi_table_schema(), write_residue_type_table_schema(), and write_residue_type_variant_type_table_schema().

Referenced by initialize(), and protocols::features::ResidueTypesFeatures::write_schema_to_db().

Member Data Documentation

std::map<std::pair<std::string,core::Size>, std::string > core::chemical::ResidueDatabaseIO::atom_name_id_cache_
private

Definition at line 261 of file ResidueDatabaseIO.hh.

Referenced by get_atom_name_from_database_atom_index().

core::Real core::chemical::ResidueDatabaseIO::version_
private

Definition at line 259 of file ResidueDatabaseIO.hh.

Referenced by get_version(), read_residue_type(), and report_residue_type().

The documentation for this class was generated from the following files:
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