CDPL::Biomol::PDBData Class Reference

Data structure for the storage of preprocessed Brookhaven Protein Data Bank (PDB) data. 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 }
	Specifies the type of a stored 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 the stored record type and data pairs. 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 preprocessed Brookhaven Protein Data Bank (PDB) data.

See also

[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 the stored record type and data pairs.

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

Specifies the type of a stored PDB data record.

Enumerator
HEADER	HEADER record (structure classification, deposition date, PDB ID).
OBSLTE	OBSLTE record (PDB IDs that have replaced this entry).
TITLE	TITLE record (title of the entry).
SPLIT	SPLIT record (list of entries that together form the complete structure).
CAVEAT	CAVEAT record (warns of errors and unresolved issues of the entry).
COMPND	COMPND record (description of the macromolecular contents).
SOURCE	SOURCE record (specifies the biological and/or chemical source of each biological molecule).
KEYWDS	KEYWDS record (a set of terms relevant to the entry).
EXPDTA	EXPDTA record (information about the experiment).
AUTHOR	AUTHOR record (contains the names of the people responsible for the contents of the entry).
REVDAT	REVDAT record (revision history of the entry).
SPRSDE	SPRSDE record (PDB IDs that this entry supersedes).
JRNL	JRNL record (literature citation associated with the entry).
REMARK	REMARK record (experimental details, annotations, comments, and information not included in other records).
DBREF	DBREF record (cross-reference links between PDB sequences and a corresponding database sequence).
DBREF1	DBREF1 record (first part of a two-line database cross-reference).
DBREF2	DBREF2 record (second part of a two-line database cross-reference).
SEQADV	SEQADV record (differences between sequence information in the SEQRES record and the sequence database entry given in DBREF).
SEQRES	SEQRES record (residue sequence of biopolymer chains).
MODRES	MODRES record (descriptions of modifications to protein and nucleic acid residues).
HET	HET record (describes non-standard residues for which coordinates are supplied).
FORMUL	FORMUL record (chemical formula of non-standard residues).
HETNAM	HETNAM record (chemical names of non-standard residues).
HETSYN	HETSYN record (synonyms for non-standard residues).
HELIX	HELIX record (helix secondary structure annotations).
SHEET	SHEET record (sheet secondary structure annotations).
TURN	TURN record (locations of short loop turns that connect standard secondary structure segments).
SSBOND	SSBOND record (identifies disulfide bonds in protein and polypeptide structures).
LINK	LINK record (bonds between residues that are not implied by the primary structure).
CISPEP	CISPEP record (specifies prolines and other peptides found to be in the cis conformation).
SITE	SITE record (specifies residues of an active or binding site).
CRYST1	CRYST1 record (unit cell parameters, space group, and Z value).
MTRIX1	MTRIX1 record (first row of a non-crystallographic symmetry transformation matrix).
MTRIX2	MTRIX2 record (second row of a non-crystallographic symmetry transformation matrix).
MTRIX3	MTRIX3 record (third row of a non-crystallographic symmetry transformation matrix).
ORIGX1	ORIGX1 record (first row of the orthogonal to submitted coordinates transformation).
ORIGX2	ORIGX2 record (second row of the orthogonal to submitted coordinates transformation).
ORIGX3	ORIGX3 record (third row of the orthogonal to submitted coordinates transformation).
SCALE1	SCALE1 record (first row of the orthogonal to fractional coordinates transformation).
SCALE2	SCALE2 record (second row of the orthogonal to fractional coordinates transformation).
SCALE3	SCALE3 record (third row of the orthogonal to fractional coordinates transformation).
STRUCTURE_ID	The 4 character PDB identifier extracted from the HEADER record.
DEPOSITION_DATE	The deposition date extracted from the HEADER record.
RESOLUTION	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 instance 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 has been found, 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 pointing to 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 pointing to 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 pointing to 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