Global dictionary for the lookup of meta-data associated with the residues in biological macromolecules. More...

#include <ResidueDictionary.hpp>

Classes
class	Entry
	A single residue dictionary entry. More...

Public Types
typedef std::shared_ptr< ResidueDictionary >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `ResidueDictionary` instances. More...

typedef boost::transform_iterator< std::function< const Entry &(const EntryLookupTable::value_type &)>, EntryLookupTable::const_iterator >	ConstEntryIterator
	A constant iterator over the entries of the dictionary. More...

Public Member Functions
void	addEntry (const Entry &entry)
	Adds (or overwrites) the dictionary entry entry. More...

void	addEntry (Entry &&entry)
	Adds (or overwrites) the dictionary entry entry by moving its data. More...

bool	containsEntry (const std::string &code) const
	Tells whether the dictionary contains an entry for the residue with three-letter code code. More...

void	removeEntry (const std::string &code)
	Removes the dictionary entry for the residue with three-letter code code. More...

const Entry &	getEntry (const std::string &code) const
	Returns the dictionary entry for the residue with three-letter code code. More...

void	clear ()
	Removes all entries from the dictionary. More...

std::size_t	getNumEntries () const
	Returns the number of entries in the dictionary. More...

ConstEntryIterator	getEntriesBegin () const
	Returns a constant iterator pointing to the beginning of the entry list. More...

ConstEntryIterator	getEntriesEnd () const
	Returns a constant iterator pointing one past the last entry. More...

ConstEntryIterator	begin () const
	Returns a constant iterator pointing to the beginning of the entry list (alias of getEntriesBegin()). More...

ConstEntryIterator	end () const
	Returns a constant iterator pointing one past the last entry (alias of getEntriesEnd()). More...

const std::string &	getReplacedCode (const std::string &code) const
	Returns the TLC of the residue replaced by the residue with three-letter code code. More...

const std::string &	getReplacedByCode (const std::string &code) const
	Returns the TLC of the residue that replaces the residue with three-letter code code. More...

const std::string &	getParentCode (const std::string &code) const
	Returns the TLC of the parent residue of the residue with three-letter code code. More...

const std::string &	getOneLetterCode (const std::string &code) const
	Returns the one-letter code of the residue with three-letter code code. More...

bool	isObsolete (const std::string &code) const
	Tells whether the residue type with three-letter code code is obsolete. More...

const std::string &	getName (const std::string &code) const
	Returns the full name of the residue with three-letter code code. More...

unsigned int	getType (const std::string &code) const
	Returns the residue type (see Biomol::ResidueType) of the residue with three-letter code code. More...

Chem::MolecularGraph::SharedPointer	getStructure (const std::string &code) const
	Retrieves the structure of the residue with three-letter code code. More...

void	loadDefaults ()
	Loads the built-in default residue dictionary entries. More...

Static Public Member Functions
static bool	isStdResidue (const std::string &code)
	Tells whether the residue with three-letter code code is a standard biopolymer residue (amino acid or nucleotide). More...

static void	set (const SharedPointer &dict)
	Replaces the process-wide default dictionary by dict. More...

static const SharedPointer &	get ()
	Returns the process-wide default dictionary (lazily initialized on first call). More...

Detailed Description

Global dictionary for the lookup of meta-data associated with the residues in biological macromolecules.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<ResidueDictionary> CDPL::Biomol::ResidueDictionary::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated ResidueDictionary instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const EntryLookupTable::value_type&)>, EntryLookupTable::const_iterator> CDPL::Biomol::ResidueDictionary::ConstEntryIterator

A constant iterator over the entries of the dictionary.

Member Function Documentation

◆ isStdResidue()

static bool CDPL::Biomol::ResidueDictionary::isStdResidue ( const std::string & code )

static

Tells whether the residue with three-letter code code is a standard biopolymer residue (amino acid or nucleotide).

Parameters

code	The residue three-letter code.

Returns: true if the residue is a standard biopolymer residue, and false otherwise.

◆ addEntry() [1/2]

void CDPL::Biomol::ResidueDictionary::addEntry ( const Entry & entry )

Adds (or overwrites) the dictionary entry entry.

Parameters

entry The entry to add.

◆ addEntry() [2/2]

void CDPL::Biomol::ResidueDictionary::addEntry ( Entry && entry )

Adds (or overwrites) the dictionary entry entry by moving its data.

Parameters

entry The entry to add.

Since: 1.2

◆ containsEntry()

bool CDPL::Biomol::ResidueDictionary::containsEntry ( const std::string & code ) const

Tells whether the dictionary contains an entry for the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: true if a matching entry exists, and false otherwise.

◆ removeEntry()

void CDPL::Biomol::ResidueDictionary::removeEntry ( const std::string & code )

Removes the dictionary entry for the residue with three-letter code code.

Parameters

code	The residue three-letter code.

◆ getEntry()

const Entry& CDPL::Biomol::ResidueDictionary::getEntry ( const std::string & code ) const

Returns the dictionary entry for the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A const reference to the matching entry (or to an empty default-constructed entry if no matching entry exists).

◆ clear()

void CDPL::Biomol::ResidueDictionary::clear ( )

Removes all entries from the dictionary.

◆ getNumEntries()

std::size_t CDPL::Biomol::ResidueDictionary::getNumEntries ( ) const

Returns the number of entries in the dictionary.

Returns: The entry count.

◆ getEntriesBegin()

ConstEntryIterator CDPL::Biomol::ResidueDictionary::getEntriesBegin ( ) const

Returns a constant iterator pointing to the beginning of the entry list.

Returns: A constant iterator to the first entry.

◆ getEntriesEnd()

ConstEntryIterator CDPL::Biomol::ResidueDictionary::getEntriesEnd ( ) const

Returns a constant iterator pointing one past the last entry.

Returns: A constant iterator to the end of the entry list.

◆ begin()

ConstEntryIterator CDPL::Biomol::ResidueDictionary::begin ( ) const

Returns a constant iterator pointing to the beginning of the entry list (alias of getEntriesBegin()).

Returns: A constant iterator to the first entry.

◆ end()

ConstEntryIterator CDPL::Biomol::ResidueDictionary::end ( ) const

Returns a constant iterator pointing one past the last entry (alias of getEntriesEnd()).

Returns: A constant iterator to the end of the entry list.

◆ getReplacedCode()

const std::string& CDPL::Biomol::ResidueDictionary::getReplacedCode ( const std::string & code ) const

Returns the TLC of the residue replaced by the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A const reference to the replaced-residue code (or an empty string if no matching entry exists or the entry does not replace any other residue).

◆ getReplacedByCode()

const std::string& CDPL::Biomol::ResidueDictionary::getReplacedByCode ( const std::string & code ) const

Returns the TLC of the residue that replaces the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A const reference to the replacing-residue code (or an empty string if no matching entry exists or the entry has not been replaced).

◆ getParentCode()

const std::string& CDPL::Biomol::ResidueDictionary::getParentCode ( const std::string & code ) const

Returns the TLC of the parent residue of the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A const reference to the parent-residue code (or an empty string if no matching entry exists or the residue has no parent).

Since: 1.2

◆ getOneLetterCode()

const std::string& CDPL::Biomol::ResidueDictionary::getOneLetterCode ( const std::string & code ) const

Returns the one-letter code of the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A const reference to the one-letter residue code (or an empty string if not defined or no matching entry exists).

Since: 1.2

◆ isObsolete()

bool CDPL::Biomol::ResidueDictionary::isObsolete ( const std::string & code ) const

Tells whether the residue type with three-letter code code is obsolete.

Parameters

code	The residue three-letter code.

Returns: true if the residue type is obsolete, and false otherwise (also if no matching entry exists).

◆ getName()

const std::string& CDPL::Biomol::ResidueDictionary::getName ( const std::string & code ) const

Returns the full name of the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A const reference to the residue name (or an empty string if no matching entry exists).

◆ getType()

unsigned int CDPL::Biomol::ResidueDictionary::getType ( const std::string & code ) const

Returns the residue type (see Biomol::ResidueType) of the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: The residue type identifier (or Biomol::ResidueType::UNKNOWN if no matching entry exists).

◆ getStructure()

Chem::MolecularGraph::SharedPointer CDPL::Biomol::ResidueDictionary::getStructure ( const std::string & code ) const

Retrieves the structure of the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns: A shared pointer to the residue structure (or an empty pointer if the structure could not be retrieved).

◆ loadDefaults()

void CDPL::Biomol::ResidueDictionary::loadDefaults ( )

Loads the built-in default residue dictionary entries.

◆ set()

static void CDPL::Biomol::ResidueDictionary::set ( const SharedPointer & dict )

static

Replaces the process-wide default dictionary by dict.

Parameters

dict	The new default dictionary (a `nullptr` resets to the built-in default).

◆ get()

static const SharedPointer& CDPL::Biomol::ResidueDictionary::get ( )

static

Returns the process-wide default dictionary (lazily initialized on first call).

Returns: A const reference to the default-dictionary shared pointer.

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

ResidueDictionary.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

Member Function Documentation

◆ isStdResidue()

◆ addEntry() [1/2]

◆ addEntry() [2/2]

◆ containsEntry()

◆ removeEntry()

◆ getEntry()

◆ clear()

◆ getNumEntries()

◆ getEntriesBegin()

◆ getEntriesEnd()

◆ begin()

◆ end()

◆ getReplacedCode()

◆ getReplacedByCode()

◆ getParentCode()

◆ getOneLetterCode()

◆ isObsolete()

◆ getName()

◆ getType()

◆ getStructure()

◆ loadDefaults()

◆ set()

◆ get()