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core::chemical::ResidueDatabaseIO Class Reference

#include <ResidueDatabaseIO.hh>

Inheritance diagram for core::chemical::ResidueDatabaseIO:
Inheritance graph
[legend]

Public Member Functions

 ResidueDatabaseIO ()
 
 ~ResidueDatabaseIO () override
 
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::MutableResidueTypeOP read_residuetype_from_database (chemical::AtomTypeSetCOP atom_types, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types, chemical::orbitals::OrbitalTypeSetCOP 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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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::MutableResidueType &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_
 

Constructor & Destructor Documentation

core::chemical::ResidueDatabaseIO::ResidueDatabaseIO ( )
core::chemical::ResidueDatabaseIO::~ResidueDatabaseIO ( )
overridedefault

Member Function Documentation

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

write the schema

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::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_atom ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_bond ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_chi ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_chi_rotamer ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_cut_bond ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_icoor ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_properties ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_proton_chi ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
void core::chemical::ResidueDatabaseIO::read_residue_type_variant ( std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
core::chemical::MutableResidueType res_type,
utility::sql_database::sessionOP  db_session 
)
private
core::chemical::MutableResidueTypeOP core::chemical::ResidueDatabaseIO::read_residuetype_from_database ( chemical::AtomTypeSetCOP  atom_types,
chemical::ElementSetCOP  elements,
chemical::MMAtomTypeSetCOP  mm_atom_types,
chemical::orbitals::OrbitalTypeSetCOP  orbital_atom_types,
std::string const &  residue_type_set_name,
std::string const &  residue_type_name,
utility::sql_database::sessionOP  db_session 
)
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
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
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
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
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
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
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
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
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
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
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

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

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

References core::simple_metrics::metrics::mean.

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

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

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

References core::kinematics::distance().

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

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

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

References protocols::cluster::calibur::aa.

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

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

Member Data Documentation

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

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