BALL::NMRStarFile::BALLToBMRBMapper Class Reference

#include <BALL/FORMAT/NMRStarFile.h>

Public Types
Type definitions

typedef std::pair< Position, Position >	BMRBIndex
typedef std::map< Atom const *, BMRBIndex >	BALLToBMRBMapping
typedef std::map< const NMRAtomData , Atom const >	BMRBToBALLMapping
Public Member Functions
Constructors and Destructors

	BALLToBMRBMapper ()
	BALLToBMRBMapper (Chain const &chain, const NMRStarFile &nmr_data)
	Detailed constructor.
virtual	~BALLToBMRBMapper ()
	Destructor.
Access methods

const Chain *	getChain () const
	Get the chain.
void	setChain (Chain const &chain)
	Set the chain.
void	setNMRStarFile (NMRStarFile const &nmrfile)
	Set the NMRStar file.
const NMRStarFile *	getNMRStarFile () const
	Get the NMRStar file.
BALLToBMRBMapping &	getBALLToBMRBMapping ()
	Return the mapping.
const BALLToBMRBMapping &	getBALLToBMRBMapping () const
	Return the mapping.
BMRBToBALLMapping &	getBMRBToBALLMapping ()
	Return the mapping.
const BMRBToBALLMapping &	getBMRBToBALLMapping () const
	Return the mapping.
int	getNumberOfMismatches ()
	Return the number of mismatches in the current mapping.
int	getNumberOfGabs ()
	Return the number of mismatches in the current mapping.
bool	isMapped (const NMRAtomData &nmr_atom) const
	Test whether the given nmr atom data is mapped to a structure atom.
const Atom *	getBALLAtom (const NMRAtomData &nmr_atom) const
bool	isMapped (Atom const *atom) const
BMRBIndex	operator() (const Atom *atom)
	Return the mapping of the given atom.
bool	createTrivialMapping ()
bool	createMapping (const String &aligned_ball_sequence, const String &aligned_nmrstar_sequence)
void	clear ()
Protected Attributes
Peptides::NameConverter	name_converter_
Atributes

BALLToBMRBMapping	ball_to_bmrb_map_
	map BALL atoms to NMR atom data
BMRBToBALLMapping	bmrb_to_ball_map_
	map NMR atom data to BALL atoms
const Chain *	chain_
const NMRStarFile *	nmr_data_
int	num_mismatches_
int	num_gabs_
Private Member Functions
const Atom *	findNMRAtom_ (const NMRAtomData &atom) const

Detailed Description

Mapper class between BALL atoms and NMRStar file atom entries.

The main reason for the existence of this class (instead of maps to atompointer,position,position) is the python interface, which is greatly simplified.

Definition at line 388 of file NMRStarFile.h.

Member Typedef Documentation

typedef std::map<Atom const* , BMRBIndex> BALL::NMRStarFile::BALLToBMRBMapper::BALLToBMRBMapping

Definition at line 400 of file NMRStarFile.h.

typedef std::pair<Position, Position> BALL::NMRStarFile::BALLToBMRBMapper::BMRBIndex

BMRMIndex stores the savaframe id and the index of the atom in the NMRAtomDataSet.

Definition at line 399 of file NMRStarFile.h.

typedef std::map<const NMRAtomData*, Atom const*> BALL::NMRStarFile::BALLToBMRBMapper::BMRBToBALLMapping

Definition at line 401 of file NMRStarFile.h.

Constructor & Destructor Documentation

BALL::NMRStarFile::BALLToBMRBMapper::BALLToBMRBMapper ( )

BALL::NMRStarFile::BALLToBMRBMapper::BALLToBMRBMapper	(	Chain const &	chain,
		const NMRStarFile &	nmr_data
	)

Detailed constructor.

virtual BALL::NMRStarFile::BALLToBMRBMapper::~BALLToBMRBMapper ( ) [inline, virtual]

Destructor.

Definition at line 415 of file NMRStarFile.h.

Member Function Documentation

void BALL::NMRStarFile::BALLToBMRBMapper::clear ( )

Clear the object.

bool BALL::NMRStarFile::BALLToBMRBMapper::createMapping	(	const String &	aligned_ball_sequence,
		const String &	aligned_nmrstar_sequence
	)

Create a mapping between the given chain and the NMRStar file atoms based on the given alignment. The alignmed sequences should be given in OneLetterCode, where '-' denotes a gap.

Parameters:

	aligned_ball_sequence	the aligned protein or chain aminoacid sequence
	aligned_nmrstar_sequence	the aligned aminoacid sequence of the NMRStar atoms

Returns:: bool - true if creating the mapping was possible

bool BALL::NMRStarFile::BALLToBMRBMapper::createTrivialMapping ( )

Create a trivial mapping between the given chain and the NMRStar file atoms.

NOTE: this mapping only works for very simple cases as we assume no gabs.

Returns:: bool - true if creating the mapping was possible

const Atom* BALL::NMRStarFile::BALLToBMRBMapper::findNMRAtom_ ( const NMRAtomData & atom ) const [private]

const Atom* BALL::NMRStarFile::BALLToBMRBMapper::getBALLAtom ( const NMRAtomData & nmr_atom ) const

Return the atom mapped to the given NMRAtom.

Parameters:

atom

the NMRAtom

Returns:: the mapped BALL atom. If no atom can be matched a NULL pointer is returned.

const BALLToBMRBMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBALLToBMRBMapping ( ) const [inline]

Return the mapping.

Definition at line 442 of file NMRStarFile.h.

BALLToBMRBMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBALLToBMRBMapping ( ) [inline]

Return the mapping.

Definition at line 439 of file NMRStarFile.h.

const BMRBToBALLMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBMRBToBALLMapping ( ) const [inline]

Return the mapping.

Definition at line 448 of file NMRStarFile.h.

BMRBToBALLMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBMRBToBALLMapping ( ) [inline]

Return the mapping.

Definition at line 445 of file NMRStarFile.h.

const Chain* BALL::NMRStarFile::BALLToBMRBMapper::getChain ( ) const [inline]

Get the chain.

Definition at line 423 of file NMRStarFile.h.

const NMRStarFile* BALL::NMRStarFile::BALLToBMRBMapper::getNMRStarFile ( ) const [inline]

Get the NMRStar file.

Definition at line 436 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::getNumberOfGabs ( ) [inline]

Return the number of mismatches in the current mapping.

Definition at line 454 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::getNumberOfMismatches ( ) [inline]

Return the number of mismatches in the current mapping.

Definition at line 451 of file NMRStarFile.h.

bool BALL::NMRStarFile::BALLToBMRBMapper::isMapped ( Atom const * atom ) const

Test, whether an atom is matched to NMRAtom data entry

Returns:: true if the given atom is mapped to an atom in the NMRStar file,else otherwise

bool BALL::NMRStarFile::BALLToBMRBMapper::isMapped ( const NMRAtomData & nmr_atom ) const

Test whether the given nmr atom data is mapped to a structure atom.

BMRBIndex BALL::NMRStarFile::BALLToBMRBMapper::operator() ( const Atom * atom )

Return the mapping of the given atom.

void BALL::NMRStarFile::BALLToBMRBMapper::setChain ( Chain const & chain ) [inline]

Set the chain.

Definition at line 426 of file NMRStarFile.h.

void BALL::NMRStarFile::BALLToBMRBMapper::setNMRStarFile ( NMRStarFile const & nmrfile ) [inline]

Set the NMRStar file.

Definition at line 431 of file NMRStarFile.h.

Member Data Documentation

BALLToBMRBMapping BALL::NMRStarFile::BALLToBMRBMapper::ball_to_bmrb_map_ [protected]

map BALL atoms to NMR atom data

Definition at line 509 of file NMRStarFile.h.

BMRBToBALLMapping BALL::NMRStarFile::BALLToBMRBMapper::bmrb_to_ball_map_ [protected]

map NMR atom data to BALL atoms

Definition at line 512 of file NMRStarFile.h.

const Chain* BALL::NMRStarFile::BALLToBMRBMapper::chain_ [protected]

Definition at line 515 of file NMRStarFile.h.

Peptides::NameConverter BALL::NMRStarFile::BALLToBMRBMapper::name_converter_ [protected]

Definition at line 502 of file NMRStarFile.h.

const NMRStarFile* BALL::NMRStarFile::BALLToBMRBMapper::nmr_data_ [protected]

Definition at line 516 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::num_gabs_ [protected]

Definition at line 518 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::num_mismatches_ [protected]

Definition at line 517 of file NMRStarFile.h.

BALL::NMRStarFile::BALLToBMRBMapper Class Reference

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation