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, const String &chemical_unit)
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.
void	setNMRAtomDataSet (NMRAtomDataSet const &nmr_atom_data_set)
	Set the NMRAtomDataSet.
bool	setNMRAtomDataSetByName (String const &chemical_unit_name)
	Set the NMRAtomDataSet by chemical unit name.
const NMRAtomDataSet *	getNMRAtomDataSet () const
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	getNumberOfGaps ()
	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_
const NMRAtomDataSet *	nmr_atom_data_set_
Position	nmr_atom_data_set_index_
int	num_mismatches_
int	num_gaps_
bool	valid_
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 449 of file NMRStarFile.h.

Member Typedef Documentation

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

Definition at line 461 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 460 of file NMRStarFile.h.

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

Definition at line 462 of file NMRStarFile.h.

Constructor & Destructor Documentation

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

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

Detailed constructor

Parameters:

	chain	the chain to be mapped to a shift reference set
	nmr_data	the NMRStarFile provinding the chemical shifts for chain
	chemical_unit	the name of the molecular system (chemical unit) storing the atom shifts

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

Destructor.

Definition at line 481 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 molecular system named chemical_unit of the given 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 gaps.

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 517 of file NMRStarFile.h.

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

Return the mapping.

Definition at line 514 of file NMRStarFile.h.

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

Return the mapping.

Definition at line 523 of file NMRStarFile.h.

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

Return the mapping.

Definition at line 520 of file NMRStarFile.h.

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

Get the chain.

Definition at line 489 of file NMRStarFile.h.

const NMRAtomDataSet* BALL::NMRStarFile::BALLToBMRBMapper::getNMRAtomDataSet ( ) const [inline]

Definition at line 511 of file NMRStarFile.h.

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

Get the NMRStar file.

Definition at line 502 of file NMRStarFile.h.

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

Return the number of mismatches in the current mapping.

Definition at line 529 of file NMRStarFile.h.

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

Return the number of mismatches in the current mapping.

Definition at line 526 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 492 of file NMRStarFile.h.

void BALL::NMRStarFile::BALLToBMRBMapper::setNMRAtomDataSet ( NMRAtomDataSet const & nmr_atom_data_set ) [inline]

Set the NMRAtomDataSet.

Definition at line 505 of file NMRStarFile.h.

bool BALL::NMRStarFile::BALLToBMRBMapper::setNMRAtomDataSetByName ( String const & chemical_unit_name )

Set the NMRAtomDataSet by chemical unit name.

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

Set the NMRStar file.

Definition at line 497 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 585 of file NMRStarFile.h.

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

map NMR atom data to BALL atoms

Definition at line 588 of file NMRStarFile.h.

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

Definition at line 591 of file NMRStarFile.h.

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

Definition at line 578 of file NMRStarFile.h.

const NMRAtomDataSet* BALL::NMRStarFile::BALLToBMRBMapper::nmr_atom_data_set_ [protected]

Definition at line 593 of file NMRStarFile.h.

Position BALL::NMRStarFile::BALLToBMRBMapper::nmr_atom_data_set_index_ [protected]

Definition at line 594 of file NMRStarFile.h.

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

Definition at line 592 of file NMRStarFile.h.

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

Definition at line 596 of file NMRStarFile.h.

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

Definition at line 595 of file NMRStarFile.h.

bool BALL::NMRStarFile::BALLToBMRBMapper::valid_ [protected]

Definition at line 597 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