core::chemical::ResidueDatabaseIO Class Reference

#include <ResidueDatabaseIO.hh>

Inheritance diagram for core::chemical::ResidueDatabaseIO:

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

)

Referenced by core::chemical::GlobalResidueTypeSet::load_residue_types_from_sql_database().

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

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

(

)

References version_.

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

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

this needs to get called after read_residue_type_atom

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::aa(), get_atom_name_from_database_atom_index(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::chemical::name_from_aa(), core::chemical::MutableResidueType::nbr_atom(), core::chemical::MutableResidueType::nbr_radius(), core::chemical::ResidueTypeBase::rotamer_library_specification(), core::chemical::MutableResidueType::set_lower_connect_atom(), core::chemical::MutableResidueType::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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::chemical::MutableResidueType::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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::chemical::MutableResidueType::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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::chemical::MutableResidueType::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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::chemical::MutableResidueType::add_chi_rotamer(), and core::simple_metrics::metrics::mean.

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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::chemical::MutableResidueType::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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::kinematics::distance(), core::chemical::fill_ideal_xyz_from_icoor(), core::chemical::MutableResidueType::graph(), and core::chemical::MutableResidueType::set_icoor().

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::MutableResidueType &  res_type, utility::sql_database::sessionOP  db_session  )

private

References core::chemical::ResidueTypeBase::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::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

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

Referenced by read_residuetype_from_database().

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
	)

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::GlobalResidueTypeSet::load_residue_types_from_sql_database().

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::ResidueType::lower_connect_atom(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueTypeBase::rotamer_library_specification(), 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

References core::chemical::ResidueType::atom_charge(), core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::AtomType::atom_type_name(), core::chemical::ResidueType::mm_name(), core::chemical::ResidueTypeBase::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

References core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::bonded_neighbor_types(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), and protocols::sic_dock::scores::nbr.

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

References core::chemical::ResidueType::chi_atoms(), core::chemical::ResidueTypeBase::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

References core::chemical::ResidueType::chi_rotamers(), core::chemical::ResidueTypeBase::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

References core::chemical::ResidueType::cut_bond_neighbor(), core::chemical::ResidueTypeBase::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

References core::chemical::ResidueType::atom_name(), core::chemical::CONNECT, core::chemical::ResidueType::icoor(), core::chemical::INTERNAL, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), and core::chemical::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

References core::chemical::ResidueProperties::get_list_of_properties(), core::chemical::ResidueTypeBase::name(), and core::chemical::ResidueTypeBase::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

References core::chemical::ResidueType::n_proton_chi(), core::chemical::ResidueTypeBase::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

References core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueTypeBase::name(), and core::chemical::ResidueTypeBase::properties().

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

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
	)

References core::chemical::ResidueTypeBase::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

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

Referenced by get_atom_name_from_database_atom_index().

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

private

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

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

• src/core/chemical/ResidueDatabaseIO.hh
• src/core/chemical/ResidueDatabaseIO.cc