#include <NomenclatureManager.hh>

Inheritance diagram for core::io::NomenclatureManager:

Static Public Member Functions
static std::pair< std::string, std::string >	rosetta_names_from_pdb_code (std::string const &pdb_code)
	Return a pair of Rosetta names (3-letter code and base ResidueType name, if available) from the given pdb_code. More...

static char	default_mainchain_connectivity_from_pdb_code (std::string const &pdb_code)
	Return the default main-chain connectivity (if available) from the given pdb_code. More...

static std::string	pdb_code_from_rosetta_name (std::string const &rosetta_name)
	This function returns the pdb code that corresponds to the residue name. More...

static bool	is_NA (std::string const &name3)

static bool	is_old_RNA (std::string const &name3)

static bool	is_old_DNA (std::string const &name3)

static bool	decide_is_d_aa (std::string const &name3)

static bool	decide_is_l_aa (std::string const &name3)

static bool	decide_is_known_achiral (std::string const &name3)

static bool	is_metal (std::string const &name3)

static bool	is_sugar (std::string const &name3)

static std::string	annotated_sequence_from_modomics_oneletter_sequence (std::string const &seq)

static std::string	annotated_sequence_from_IUPAC_sequence (std::string const &seq)

Private Member Functions
	NomenclatureManager ()

AltCodeMap const &	get_alternate_3_letter_code_map () const

std::string	find_alternate_codes_file (std::string const &filename) const

std::set< std::string > const &	na_set () const

std::set< std::string > const &	old_rna_set () const

std::set< std::string > const &	old_dna_set () const

std::set< std::string > const &	d_aa_set () const

std::set< std::string > const &	l_aa_set () const

std::set< std::string > const &	achiral_set () const

std::set< std::string > const &	metal_set () const

std::set< std::string > const &	sugar_set () const

std::map< std::string, std::string > const &	iupac_map () const

std::map< char, std::string > const &	modomics_map () const

Private Attributes
AltCodeMap	alt_codes_

std::set< std::string >	is_NA_

std::set< std::string >	is_old_RNA_

std::set< std::string >	is_old_DNA_

std::set< std::string >	d_aa_set_

std::set< std::string >	l_aa_set_

std::set< std::string >	achiral_set_

std::set< std::string >	metal_set_

std::set< std::string >	sugar_set_

std::map< char, std::string >	annotated_seq_from_modomics_map_

std::map< std::string, std::string >	annotated_seq_from_IUPAC_map_

Friends
class	utility::SingletonBase< NomenclatureManager >

Detailed Description

This class is a singleton and manages AltCodeMap data that should only be read from the database one time and shared among all processes constructing Poses.

Constructor & Destructor Documentation

◆ NomenclatureManager()

core::io::NomenclatureManager::NomenclatureManager ( )

private

References achiral_set_, alt_codes_, annotated_seq_from_IUPAC_map_, annotated_seq_from_modomics_map_, d_aa_set_, protocols::abinitio::filename(), find_alternate_codes_file(), is_NA_, is_old_DNA_, is_old_RNA_, l_aa_set_, metal_set_, core::io::read_alternative_3_letter_codes_from_database_file(), and sugar_set_.

Member Function Documentation

◆ achiral_set()

std::set< std::string > const& core::io::NomenclatureManager::achiral_set ( ) const

inlineprivate

References achiral_set_.

Referenced by decide_is_known_achiral().

◆ annotated_sequence_from_IUPAC_sequence()

std::string core::io::NomenclatureManager::annotated_sequence_from_IUPAC_sequence ( std::string const & seq )

static

References core::sequence::end, iupac_map(), and core::io::TR().

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), and protocols::rna::movers::RNAThreadAndMinimizeMover::set_up_target_sequence().

◆ annotated_sequence_from_modomics_oneletter_sequence()

std::string core::io::NomenclatureManager::annotated_sequence_from_modomics_oneletter_sequence ( std::string const & seq )

static

References core::sequence::end, modomics_map(), and core::io::TR().

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), and protocols::rna::movers::RNAThreadAndMinimizeMover::set_up_target_sequence().

◆ d_aa_set()

std::set< std::string > const& core::io::NomenclatureManager::d_aa_set ( ) const

inlineprivate

References d_aa_set_.

Referenced by decide_is_d_aa().

◆ decide_is_d_aa()

bool core::io::NomenclatureManager::decide_is_d_aa ( std::string const & name3 )

static

References d_aa_set().

◆ decide_is_known_achiral()

bool core::io::NomenclatureManager::decide_is_known_achiral ( std::string const & name3 )

static

References achiral_set().

◆ decide_is_l_aa()

bool core::io::NomenclatureManager::decide_is_l_aa ( std::string const & name3 )

static

References l_aa_set().

◆ default_mainchain_connectivity_from_pdb_code()

char core::io::NomenclatureManager::default_mainchain_connectivity_from_pdb_code ( std::string const & pdb_code )

static

Return the default main-chain connectivity (if available) from the given pdb_code.

Returns: If a file of alternative 3-letter codes has been provided at the command line, return the default main- chain connectivity (if available) from the given PDB 3-letter code. If no file has been provided, or if there is no default value for the given code, simply return a null character.

References get_alternate_3_letter_code_map().

◆ find_alternate_codes_file()

std::string core::io::NomenclatureManager::find_alternate_codes_file ( std::string const & filename ) const

private

References protocols::abinitio::filename(), and protocols::hybridization::path.

Referenced by NomenclatureManager().

◆ get_alternate_3_letter_code_map()

AltCodeMap const & core::io::NomenclatureManager::get_alternate_3_letter_code_map ( ) const

private

References alt_codes_.

Referenced by default_mainchain_connectivity_from_pdb_code(), pdb_code_from_rosetta_name(), and rosetta_names_from_pdb_code().

◆ is_metal()

bool core::io::NomenclatureManager::is_metal ( std::string const & name3 )

static

References metal_set().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::setup().

◆ is_NA()

bool core::io::NomenclatureManager::is_NA ( std::string const & name3 )

static

References na_set().

◆ is_old_DNA()

bool core::io::NomenclatureManager::is_old_DNA ( std::string const & name3 )

static

References old_dna_set().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard().

◆ is_old_RNA()

bool core::io::NomenclatureManager::is_old_RNA ( std::string const & name3 )

static

References old_rna_set().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard().

◆ is_sugar()

bool core::io::NomenclatureManager::is_sugar ( std::string const & name3 )

static

References sugar_set().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::setup().

◆ iupac_map()

std::map< std::string, std::string > const& core::io::NomenclatureManager::iupac_map ( ) const

inlineprivate

References annotated_seq_from_IUPAC_map_.

Referenced by annotated_sequence_from_IUPAC_sequence().

◆ l_aa_set()

std::set< std::string > const& core::io::NomenclatureManager::l_aa_set ( ) const

inlineprivate

References l_aa_set_.

Referenced by decide_is_l_aa().

◆ metal_set()

std::set< std::string > const& core::io::NomenclatureManager::metal_set ( ) const

inlineprivate

References metal_set_.

Referenced by is_metal().

◆ modomics_map()

std::map< char, std::string > const& core::io::NomenclatureManager::modomics_map ( ) const

inlineprivate

References annotated_seq_from_modomics_map_.

Referenced by annotated_sequence_from_modomics_oneletter_sequence().

◆ na_set()

std::set< std::string > const& core::io::NomenclatureManager::na_set ( ) const

inlineprivate

References is_NA_.

Referenced by is_NA().

◆ old_dna_set()

std::set< std::string > const& core::io::NomenclatureManager::old_dna_set ( ) const

inlineprivate

References is_old_DNA_.

Referenced by is_old_DNA().

◆ old_rna_set()

std::set< std::string > const& core::io::NomenclatureManager::old_rna_set ( ) const

inlineprivate

References is_old_RNA_.

Referenced by is_old_RNA().

◆ pdb_code_from_rosetta_name()

std::string core::io::NomenclatureManager::pdb_code_from_rosetta_name ( std::string const & rosetta_name )

static

This function returns the pdb code that corresponds to the residue name.

Returns: The unique PDB 3-letter code that corresponds to the give ResidueType name or an empty string if no match is found.

Author: Brandon Frenz; Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References protocols::vip::base_name(), get_alternate_3_letter_code_map(), and core::io::TR().

◆ rosetta_names_from_pdb_code()

std::pair< std::string, std::string > core::io::NomenclatureManager::rosetta_names_from_pdb_code ( std::string const & pdb_code )

static

Return a pair of Rosetta names (3-letter code and base ResidueType name, if available) from the given pdb_code.

Returns: If a file of alternative 3-letter codes has been provided at the command line, return a pair of Rosetta names (3-letter code and base ResidueType name, if available) from the given PDB 3-letter code. If no file has been provided, or if there is no alternative for the given code, simply return the PDB code and an empty string.

References protocols::vip::base_name(), get_alternate_3_letter_code_map(), and core::io::TR().

◆ sugar_set()

std::set< std::string > const& core::io::NomenclatureManager::sugar_set ( ) const

inlineprivate

References sugar_set_.

Referenced by is_sugar().

Friends And Related Function Documentation

◆ utility::SingletonBase< NomenclatureManager >

friend class utility::SingletonBase< NomenclatureManager >

friend

Member Data Documentation

◆ achiral_set_

std::set< std::string > core::io::NomenclatureManager::achiral_set_

private

Referenced by achiral_set(), and NomenclatureManager().

◆ alt_codes_

AltCodeMap core::io::NomenclatureManager::alt_codes_

private

Referenced by get_alternate_3_letter_code_map(), and NomenclatureManager().

◆ annotated_seq_from_IUPAC_map_

std::map< std::string, std::string > core::io::NomenclatureManager::annotated_seq_from_IUPAC_map_

private

Referenced by iupac_map(), and NomenclatureManager().

◆ annotated_seq_from_modomics_map_

std::map< char, std::string > core::io::NomenclatureManager::annotated_seq_from_modomics_map_

private

Referenced by modomics_map(), and NomenclatureManager().

◆ d_aa_set_

std::set< std::string > core::io::NomenclatureManager::d_aa_set_

private

Referenced by d_aa_set(), and NomenclatureManager().

◆ is_NA_

std::set< std::string > core::io::NomenclatureManager::is_NA_

private

Referenced by na_set(), and NomenclatureManager().

◆ is_old_DNA_

std::set< std::string > core::io::NomenclatureManager::is_old_DNA_

private

Referenced by NomenclatureManager(), and old_dna_set().

◆ is_old_RNA_

std::set< std::string > core::io::NomenclatureManager::is_old_RNA_

private

Referenced by NomenclatureManager(), and old_rna_set().

◆ l_aa_set_

std::set< std::string > core::io::NomenclatureManager::l_aa_set_

private

Referenced by l_aa_set(), and NomenclatureManager().

◆ metal_set_

std::set< std::string > core::io::NomenclatureManager::metal_set_

private

Referenced by metal_set(), and NomenclatureManager().

◆ sugar_set_

std::set< std::string > core::io::NomenclatureManager::sugar_set_

private

Referenced by NomenclatureManager(), and sugar_set().

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

src/core/io/NomenclatureManager.hh
src/core/io/NomenclatureManager.cc

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ NomenclatureManager()

Member Function Documentation

◆ achiral_set()

◆ annotated_sequence_from_IUPAC_sequence()

◆ annotated_sequence_from_modomics_oneletter_sequence()

◆ d_aa_set()

◆ decide_is_d_aa()

◆ decide_is_known_achiral()

◆ decide_is_l_aa()

◆ default_mainchain_connectivity_from_pdb_code()

◆ find_alternate_codes_file()

◆ get_alternate_3_letter_code_map()

◆ is_metal()

◆ is_NA()

◆ is_old_DNA()

◆ is_old_RNA()

◆ is_sugar()

◆ iupac_map()

◆ l_aa_set()

◆ metal_set()

◆ modomics_map()

◆ na_set()

◆ old_dna_set()

◆ old_rna_set()

◆ pdb_code_from_rosetta_name()

◆ rosetta_names_from_pdb_code()

◆ sugar_set()

Friends And Related Function Documentation

◆ utility::SingletonBase< NomenclatureManager >

Member Data Documentation

◆ achiral_set_

◆ alt_codes_

◆ annotated_seq_from_IUPAC_map_

◆ annotated_seq_from_modomics_map_

◆ d_aa_set_

◆ is_NA_

◆ is_old_DNA_

◆ is_old_RNA_

◆ l_aa_set_

◆ metal_set_

◆ sugar_set_