#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. More...

Access methods
const Chain *	getChain () const
	Get the chain. More...

void	setChain (Chain const &chain)
	Set the chain. More...

void	setNMRStarFile (NMRStarFile const &nmrfile)
	Set the NMRStar file. More...

const NMRStarFile *	getNMRStarFile () const
	Get the NMRStar file. More...

void	setNMRAtomDataSet (NMRAtomDataSet const &nmr_atom_data_set)
	Set the NMRAtomDataSet. More...

bool	setNMRAtomDataSetByName (String const &chemical_unit_name)
	Set the NMRAtomDataSet by chemical unit name. More...

const NMRAtomDataSet *	getNMRAtomDataSet () const

BALLToBMRBMapping &	getBALLToBMRBMapping ()
	Return the mapping. More...

const BALLToBMRBMapping &	getBALLToBMRBMapping () const
	Return the mapping. More...

BMRBToBALLMapping &	getBMRBToBALLMapping ()
	Return the mapping. More...

const BMRBToBALLMapping &	getBMRBToBALLMapping () const
	Return the mapping. More...

int	getNumberOfMismatches ()
	Return the number of mismatches in the current mapping. More...

int	getNumberOfGaps ()
	Return the number of mismatches in the current mapping. More...

bool	isMapped (const NMRAtomData &nmr_atom) const
	Test whether the given nmr atom data is mapped to a structure atom. More...

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. More...

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 More...

BMRBToBALLMapping	bmrb_to_ball_map_
	map NMR atom data to BALL atoms More...

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_

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 445 of file NMRStarFile.h.

Member Typedef Documentation

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

Definition at line 457 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 456 of file NMRStarFile.h.

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

Definition at line 458 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 ( )

inlinevirtual

Destructor.

Definition at line 477 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::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.

BALLToBMRBMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBALLToBMRBMapping ( )

inline

Return the mapping.

Definition at line 510 of file NMRStarFile.h.

const BALLToBMRBMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBALLToBMRBMapping ( ) const

inline

Return the mapping.

Definition at line 513 of file NMRStarFile.h.

BMRBToBALLMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBMRBToBALLMapping ( )

inline

Return the mapping.

Definition at line 516 of file NMRStarFile.h.

const BMRBToBALLMapping& BALL::NMRStarFile::BALLToBMRBMapper::getBMRBToBALLMapping ( ) const

inline

Return the mapping.

Definition at line 519 of file NMRStarFile.h.

const Chain* BALL::NMRStarFile::BALLToBMRBMapper::getChain ( ) const

inline

Get the chain.

Definition at line 485 of file NMRStarFile.h.

const NMRAtomDataSet* BALL::NMRStarFile::BALLToBMRBMapper::getNMRAtomDataSet ( ) const

inline

Definition at line 507 of file NMRStarFile.h.

const NMRStarFile* BALL::NMRStarFile::BALLToBMRBMapper::getNMRStarFile ( ) const

inline

Get the NMRStar file.

Definition at line 498 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::getNumberOfGaps ( )

inline

Return the number of mismatches in the current mapping.

Definition at line 525 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::getNumberOfMismatches ( )

inline

Return the number of mismatches in the current mapping.

Definition at line 522 of file NMRStarFile.h.

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

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

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

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 488 of file NMRStarFile.h.

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

inline

Set the NMRAtomDataSet.

Definition at line 501 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 493 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 581 of file NMRStarFile.h.

BMRBToBALLMapping BALL::NMRStarFile::BALLToBMRBMapper::bmrb_to_ball_map_

protected

map NMR atom data to BALL atoms

Definition at line 584 of file NMRStarFile.h.

const Chain* BALL::NMRStarFile::BALLToBMRBMapper::chain_

protected

Definition at line 587 of file NMRStarFile.h.

Peptides::NameConverter BALL::NMRStarFile::BALLToBMRBMapper::name_converter_

protected

Definition at line 574 of file NMRStarFile.h.

const NMRAtomDataSet* BALL::NMRStarFile::BALLToBMRBMapper::nmr_atom_data_set_

protected

Definition at line 589 of file NMRStarFile.h.

Position BALL::NMRStarFile::BALLToBMRBMapper::nmr_atom_data_set_index_

protected

Definition at line 590 of file NMRStarFile.h.

const NMRStarFile* BALL::NMRStarFile::BALLToBMRBMapper::nmr_data_

protected

Definition at line 588 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::num_gaps_

protected

Definition at line 592 of file NMRStarFile.h.

int BALL::NMRStarFile::BALLToBMRBMapper::num_mismatches_

protected

Definition at line 591 of file NMRStarFile.h.

bool BALL::NMRStarFile::BALLToBMRBMapper::valid_

protected

Definition at line 593 of file NMRStarFile.h.

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation