Data structure for the storage of data records found in PDB formatted data [PDB]. More...

#include <PDBData.hpp>

Public Types
enum	RecordType { HEADER , OBSLTE , TITLE , SPLIT , CAVEAT , COMPND , SOURCE , KEYWDS , EXPDTA , AUTHOR , REVDAT , SPRSDE , JRNL , REMARK , DBREF , DBREF1 , DBREF2 , SEQADV , SEQRES , MODRES , HET , FORMUL , HETNAM , HETSYN , HELIX , SHEET , TURN , SSBOND , LINK , CISPEP , SITE , CRYST1 , MTRIX1 , MTRIX2 , MTRIX3 , ORIGX1 , ORIGX2 , ORIGX3 , SCALE1 , SCALE2 , SCALE3 , STRUCTURE_ID , DEPOSITION_DATE , RESOLUTION }
	Identifies the type of PDB data record. More...

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

typedef TypeToDataMap::value_type	Record
	The type of a stored (record-type, record-data) pair. More...

typedef TypeToDataMap::const_iterator	ConstRecordIterator
	A constant iterator over the stored records. More...

typedef TypeToDataMap::iterator	RecordIterator
	A mutable iterator over the stored records. More...

Public Member Functions
	PDBData ()
	Constructs an empty `PDBData` instance. More...

	PDBData (const PDBData &other)
	Constructs a copy of the `PDBData` instance other. More...

void	clear ()
	Removes all stored records. More...

std::size_t	getNumRecords () const
	Returns the number of stored records. More...

bool	isEmpty () const
	Tells whether no records are stored. More...

bool	containsRecord (const RecordType &type) const
	Tells whether a record of the given type is stored. More...

RecordIterator	getRecord (const RecordType &type)
	Returns an iterator to the record of the given type. More...

ConstRecordIterator	getRecord (const RecordType &type) const
	Returns a constant iterator to the record of the given type. More...

std::string &	getData (const RecordType &type)
	Returns the data string associated with the given record type. More...

const std::string &	getData (const RecordType &type) const
	Returns the data string associated with the given record type. More...

void	removeRecord (const RecordIterator &it)
	Removes the record referenced by the given iterator. More...

bool	removeRecord (const RecordType &type)
	Removes the record of the given type. More...

RecordIterator	setRecord (const Record &rec)
	Stores the given record. Any pre-existing record of the same type is replaced. More...

RecordIterator	setRecord (const RecordType &type, const std::string &data)
	Stores a record built from type and data. Any pre-existing record of the same type is replaced. More...

ConstRecordIterator	getRecordsBegin () const
	Returns a constant iterator pointing to the first stored record. More...

RecordIterator	getRecordsBegin ()
	Returns a mutable iterator pointing to the first stored record. More...

ConstRecordIterator	getRecordsEnd () const
	Returns a constant iterator pointing one past the last stored record. More...

RecordIterator	getRecordsEnd ()
	Returns a mutable iterator pointing one past the last stored record. More...

ConstRecordIterator	begin () const
	Returns a constant iterator pointing to the first stored record (range-based for support). More...

RecordIterator	begin ()
	Returns a mutable iterator pointing to the first stored record (range-based for support). More...

ConstRecordIterator	end () const
	Returns a constant iterator pointing one past the last stored record (range-based for support). More...

RecordIterator	end ()
	Returns a mutable iterator pointing one past the last stored record (range-based for support). More...

Detailed Description

Data structure for the storage of data records found in PDB formatted data [PDB].

Member Typedef Documentation

◆ SharedPointer

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

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

◆ Record

typedef TypeToDataMap::value_type CDPL::Biomol::PDBData::Record

The type of a stored (record-type, record-data) pair.

◆ ConstRecordIterator

typedef TypeToDataMap::const_iterator CDPL::Biomol::PDBData::ConstRecordIterator

A constant iterator over the stored records.

◆ RecordIterator

typedef TypeToDataMap::iterator CDPL::Biomol::PDBData::RecordIterator

A mutable iterator over the stored records.

Member Enumeration Documentation

◆ RecordType

enum CDPL::Biomol::PDBData::RecordType

Identifies the type of PDB data record.

Enumerator
HEADER	PDB `HEADER` record (structure classification, deposition date, PDB ID).
OBSLTE	PDB `OBSLTE` record (PDB IDs that have replaced this entry).
TITLE	PDB `TITLE` record (title of the entry).
SPLIT	PDB `SPLIT` record (list of entries that together form the complete structure).
CAVEAT	PDB `CAVEAT` record (caveats about the structure).
COMPND	PDB `COMPND` record (description of macromolecular contents).
SOURCE	PDB `SOURCE` record (source organism information).
KEYWDS	PDB `KEYWDS` record (keywords describing the entry).
EXPDTA	PDB `EXPDTA` record (experimental technique).
AUTHOR	PDB `AUTHOR` record (authors of the entry).
REVDAT	PDB `REVDAT` record (revision history of the entry).
SPRSDE	PDB `SPRSDE` record (PDB IDs that this entry supersedes).
JRNL	PDB `JRNL` record (literature citation associated with the entry).
REMARK	PDB `REMARK` record (free-text annotations).
DBREF	PDB `DBREF` record (cross-references to external sequence databases).
DBREF1	PDB `DBREF1` record (first part of a two-line database cross-reference).
DBREF2	PDB `DBREF2` record (second part of a two-line database cross-reference).
SEQADV	PDB `SEQADV` record (sequence differences relative to the reference database).
SEQRES	PDB `SEQRES` record (residue sequence of biopolymer chains).
MODRES	PDB `MODRES` record (modified residues).
HET	PDB `HET` record (non-standard residue identification).
FORMUL	PDB `FORMUL` record (chemical formula of non-standard residues).
HETNAM	PDB `HETNAM` record (chemical name of non-standard residues).
HETSYN	PDB `HETSYN` record (synonyms for non-standard residues).
HELIX	PDB `HELIX` record (helix secondary-structure annotations).
SHEET	PDB `SHEET` record (sheet secondary-structure annotations).
TURN	PDB `TURN` record (turn secondary-structure annotations).
SSBOND	PDB `SSBOND` record (disulfide bond annotations).
LINK	PDB `LINK` record (covalent links between non-standard residues).
CISPEP	PDB `CISPEP` record (cis peptide bond annotations).
SITE	PDB `SITE` record (groups of residues describing an active or binding site).
CRYST1	PDB `CRYST1` record (unit cell parameters and space group).
MTRIX1	PDB `MTRIX1` record (first row of a non-crystallographic-symmetry transformation matrix).
MTRIX2	PDB `MTRIX2` record (second row of a non-crystallographic-symmetry transformation matrix).
MTRIX3	PDB `MTRIX3` record (third row of a non-crystallographic-symmetry transformation matrix).
ORIGX1	PDB `ORIGX1` record (first row of the orthogonal-to-submitted-coordinates transformation).
ORIGX2	PDB `ORIGX2` record (second row of the orthogonal-to-submitted-coordinates transformation).
ORIGX3	PDB `ORIGX3` record (third row of the orthogonal-to-submitted-coordinates transformation).
SCALE1	PDB `SCALE1` record (first row of the orthogonal-to-fractional-coordinates transformation).
SCALE2	PDB `SCALE2` record (second row of the orthogonal-to-fractional-coordinates transformation).
SCALE3	PDB `SCALE3` record (third row of the orthogonal-to-fractional-coordinates transformation).
STRUCTURE_ID	Derived: the 4-character PDB identifier extracted from the `HEADER` record.
DEPOSITION_DATE	Derived: the deposition date extracted from the `HEADER` record.
RESOLUTION	Derived: the experimental resolution extracted from `REMARK` records.

Constructor & Destructor Documentation

◆ PDBData() [1/2]

CDPL::Biomol::PDBData::PDBData ( )

inline

Constructs an empty PDBData instance.

◆ PDBData() [2/2]

CDPL::Biomol::PDBData::PDBData ( const PDBData & other )

inline

Constructs a copy of the PDBData instance other.

Parameters

other The PDBData to copy.

Member Function Documentation

◆ clear()

void CDPL::Biomol::PDBData::clear ( )

Removes all stored records.

◆ getNumRecords()

std::size_t CDPL::Biomol::PDBData::getNumRecords ( ) const

Returns the number of stored records.

Returns: The number of records.

◆ isEmpty()

bool CDPL::Biomol::PDBData::isEmpty ( ) const

Tells whether no records are stored.

Returns: true if no records are stored, and false otherwise.

◆ containsRecord()

bool CDPL::Biomol::PDBData::containsRecord ( const RecordType & type ) const

Tells whether a record of the given type is stored.

Parameters

type	The queried record type.

Returns: true if a record of the given type is stored, and false otherwise.

◆ getRecord() [1/2]

RecordIterator CDPL::Biomol::PDBData::getRecord ( const RecordType & type )

Returns an iterator to the record of the given type.

Parameters

type	The record type to look up.

Returns: An iterator pointing to the matching record, or to getRecordsEnd() if no matching record exists.

◆ getRecord() [2/2]

ConstRecordIterator CDPL::Biomol::PDBData::getRecord ( const RecordType & type ) const

Returns a constant iterator to the record of the given type.

Parameters

type	The record type to look up.

Returns: A constant iterator pointing to the matching record, or to getRecordsEnd() if no matching record exists.

◆ getData() [1/2]

std::string& CDPL::Biomol::PDBData::getData ( const RecordType & type )

Returns the data string associated with the given record type.

Parameters

type	The record type whose data is requested.

Returns: A reference to the data string.

Exceptions

Base::ItemNotFound if no record of the given type is stored.

◆ getData() [2/2]

const std::string& CDPL::Biomol::PDBData::getData ( const RecordType & type ) const

Returns the data string associated with the given record type.

Parameters

type	The record type whose data is requested.

Returns: A const reference to the data string.

Exceptions

Base::ItemNotFound if no record of the given type is stored.

◆ removeRecord() [1/2]

void CDPL::Biomol::PDBData::removeRecord ( const RecordIterator & it )

Removes the record referenced by the given iterator.

Parameters

it	Iterator referencing the record to remove.

◆ removeRecord() [2/2]

bool CDPL::Biomol::PDBData::removeRecord ( const RecordType & type )

Removes the record of the given type.

Parameters

type	The type of the record to remove.

Returns: true if the record was removed, and false if no matching record existed.

◆ setRecord() [1/2]

RecordIterator CDPL::Biomol::PDBData::setRecord ( const Record & rec )

Stores the given record. Any pre-existing record of the same type is replaced.

Parameters

rec	The record to store.

Returns: An iterator referencing the stored record.

◆ setRecord() [2/2]

RecordIterator CDPL::Biomol::PDBData::setRecord	(	const RecordType &	type,
		const std::string &	data
	)

Stores a record built from type and data. Any pre-existing record of the same type is replaced.

Parameters

type	The record type.
data	The record data string.

Returns: An iterator referencing the stored record.

◆ getRecordsBegin() [1/2]

ConstRecordIterator CDPL::Biomol::PDBData::getRecordsBegin ( ) const

Returns a constant iterator pointing to the first stored record.

Returns: A constant iterator pointing to the first record.

◆ getRecordsBegin() [2/2]

RecordIterator CDPL::Biomol::PDBData::getRecordsBegin ( )

Returns a mutable iterator pointing to the first stored record.

Returns: A mutable iterator pointing to the first record.

◆ getRecordsEnd() [1/2]

ConstRecordIterator CDPL::Biomol::PDBData::getRecordsEnd ( ) const

Returns a constant iterator pointing one past the last stored record.

Returns: A constant iterator pointing one past the last record.

◆ getRecordsEnd() [2/2]

RecordIterator CDPL::Biomol::PDBData::getRecordsEnd ( )

Returns a mutable iterator pointing one past the last stored record.

Returns: A mutable iterator pointing one past the last record.

◆ begin() [1/2]

ConstRecordIterator CDPL::Biomol::PDBData::begin ( ) const

Returns a constant iterator pointing to the first stored record (range-based for support).

Returns: A constant iterator pointing to the first record.

◆ begin() [2/2]

RecordIterator CDPL::Biomol::PDBData::begin ( )

Returns a mutable iterator pointing to the first stored record (range-based for support).

Returns: A mutable iterator pointing to the first record.

◆ end() [1/2]

ConstRecordIterator CDPL::Biomol::PDBData::end ( ) const

Returns a constant iterator pointing one past the last stored record (range-based for support).

Returns: A constant iterator pointing one past the last record.

◆ end() [2/2]

RecordIterator CDPL::Biomol::PDBData::end ( )

Returns a mutable iterator pointing one past the last stored record (range-based for support).

Returns: A mutable iterator pointing one past the last record.

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

PDBData.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ Record

◆ ConstRecordIterator

◆ RecordIterator

Member Enumeration Documentation

◆ RecordType

Constructor & Destructor Documentation

◆ PDBData() [1/2]

◆ PDBData() [2/2]

Member Function Documentation

◆ clear()

◆ getNumRecords()

◆ isEmpty()

◆ containsRecord()

◆ getRecord() [1/2]

◆ getRecord() [2/2]

◆ getData() [1/2]

◆ getData() [2/2]

◆ removeRecord() [1/2]

◆ removeRecord() [2/2]

◆ setRecord() [1/2]

◆ setRecord() [2/2]

◆ getRecordsBegin() [1/2]

◆ getRecordsBegin() [2/2]

◆ getRecordsEnd() [1/2]

◆ getRecordsEnd() [2/2]

◆ begin() [1/2]

◆ begin() [2/2]

◆ end() [1/2]

◆ end() [2/2]