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Static Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
core::io::NomenclatureManager Class Reference

#include <NomenclatureManager.hh>

Inheritance diagram for core::io::NomenclatureManager:
Inheritance graph
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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::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
 
std::string find_alternate_codes_file (std::string const &filename)
 

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

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

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

References achiral_set_.

Referenced by decide_is_known_achiral().

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().

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

References core::pack::dunbrack::c, 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().

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

References d_aa_set_.

Referenced by decide_is_d_aa().

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

References d_aa_set().

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

References achiral_set().

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

References l_aa_set().

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().

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

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

Referenced by NomenclatureManager().

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().

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

References metal_set().

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

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

References na_set().

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().

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().

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

References sugar_set().

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

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().

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

References l_aa_set_.

Referenced by decide_is_l_aa().

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

References metal_set_.

Referenced by is_metal().

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().

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

References is_NA_.

Referenced by is_NA().

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

References is_old_DNA_.

Referenced by is_old_DNA().

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

References is_old_RNA_.

Referenced by is_old_RNA().

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().

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().

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

References sugar_set_.

Referenced by is_sugar().

Friends And Related Function Documentation

friend class utility::SingletonBase< NomenclatureManager >
friend

Member Data Documentation

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

Referenced by achiral_set(), and NomenclatureManager().

AltCodeMap core::io::NomenclatureManager::alt_codes_
private

Referenced by get_alternate_3_letter_code_map(), and NomenclatureManager().

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

Referenced by iupac_map(), and NomenclatureManager().

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

Referenced by modomics_map(), and NomenclatureManager().

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

Referenced by d_aa_set(), and NomenclatureManager().

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

Referenced by na_set(), and NomenclatureManager().

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

Referenced by NomenclatureManager(), and old_dna_set().

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

Referenced by NomenclatureManager(), and old_rna_set().

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

Referenced by l_aa_set(), and NomenclatureManager().

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

Referenced by metal_set(), and NomenclatureManager().

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:
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