This class provides methods for reading and assigning chemical shifts. More...

#include <BALL/FORMAT/NMRStarFile.h>

Inheritance diagram for BALL::NMRStarFile:

Classes
class	BALLToBMRBMapper

class	EntryInformation

class	MolecularSystem

class	MonomericPolymer

class	NMRAtomData

class	NMRAtomDataSet

class	NMRSpectrometer

class	Sample

class	SampleCondition

class	ShiftReferenceElement

class	ShiftReferenceSet

Public Member Functions
Constructors and Destructors
	NMRStarFile ()

	NMRStarFile (const String &file_name, File::OpenMode open_mode=std::ios::in)

	~NMRStarFile ()
	Destructor. More...

Access methods
bool	read ()

bool	read (AtomContainer &ac)

bool	assignShifts (BALLToBMRBMapper &ball_to_bmrb_mapping)

bool	assignShifts (AtomContainer &ac, const String &chemical_unit, const String &aligned_ball_sequence, const String &aligned_nmrstar_sequence)

Size	getNumberOfAtoms () const

Size	getNumberOfShiftsAssigned () const

const std::vector < NMRAtomDataSet > &	getNMRData () const

const EntryInformation &	getEntryInformation () const

const MolecularSystem &	getMolecularInformation () const

MolecularSystem &	getMolecularInformation ()

const MolecularSystem::ChemicalUnit &	getChemicalUnitByLabel (String const &label) const

MolecularSystem::ChemicalUnit &	getChemicalUnitByLabel (String const &label)

bool	hasSampleCondition (String name)

bool	hasSampleCondition (String name) const

SampleCondition &	getSampleConditionByName (String name)

const SampleCondition &	getSampleConditionByName (String name) const

SampleCondition &	getSampleCondition (Position i)
	Get the i-th SampleCondition. More...

const SampleCondition &	getSampleCondition (Position i) const
	Get the i-th SampleCondition. More...

Size	getNumberOfSampleConditions () const
	Get the number of sample conditions. More...

const std::vector < SampleCondition > &	getSampleConditions () const
	Get the sample conditions. More...

std::vector< SampleCondition > &	getSampleConditions ()
	Get the sample conditions. More...

std::vector< Sample >	getSamples () const
	Get the samples. More...

Size	getNumberOfSamples () const
	Get the number of samples. More...

bool	hasSample (String label) const
	Return true if the file contains a sample named label, false otherwise. More...

Sample	getSample (Position i) const

Sample	getSample (String label) const

std::vector< ShiftReferenceSet > &	getShiftReferenceSets ()
	Get the shift reference sets. More...

const std::vector < ShiftReferenceSet > &	getShiftReferenceSets () const
	Get the shift reference sets. More...

Size	getNumberOfShiftReferenceSets () const
	Get the number of shift reference sets. More...

bool	hasShiftReferenceSet (String name)
	Check if there is a ShiftReferenceSet named name. More...

ShiftReferenceSet &	getShiftReferenceSet (Position i)
	Get the i-th shift reference set. More...

const ShiftReferenceSet &	getShiftReferenceSet (Position i) const
	Get the i-th shift reference set. More...

const ShiftReferenceSet &	getShiftReferenceSetByName (String name) const
	Get a ShiftReferenceSet by its SaveFrame name. More...

ShiftReferenceSet &	getShiftReferenceSetByName (String name)
	Get a ShiftReferenceSet by its SaveFrame name. More...

std::vector< NMRSpectrometer > &	getNMRSpectrometers ()
	Get the spectrometers. More...

const std::vector < NMRSpectrometer > &	getNMRSpectrometers () const
	Get the spectrometers. More...

Size	getNumberOfNMRSpectrometers () const
	Get the number of nmr spectrometers. More...

NMRSpectrometer &	getNMRSpectrometer (Position i)
	Get the i-th spectrometer. More...

const NMRSpectrometer &	getNMRSpectrometer (Position i) const
	Get the i-th spectrometer. More...

NMRSpectrometer &	getNMRSpectrometerByName (String name)
	Get the spectrometer by its SaveFrame name. More...

const NMRSpectrometer &	getNMRSpectrometerByName (String name) const
	Get the spectrometer by its SaveFrame name. More...

String	getNMRSpectrometerManufacturer (Position i) const
	Get the spectrometer manufacturer. More...

float	getNMRSpectrometerFieldStrength (Position i) const
	Get the spectrometer field strength. More...

NMRStarFile::MonomericPolymer &	getMonomericPolymer (Position i)

const NMRStarFile::MonomericPolymer &	getMonomericPolymer (Position i) const

NMRStarFile::MonomericPolymer &	getMonomericPolymer (const String &name)

const NMRStarFile::MonomericPolymer &	getMonomericPolymer (const String &name) const

Size	getNumberOfMonomericPolymers () const
	Get the number of monomeric polymers in the file. More...

vector< MonomericPolymer >	getMonomericPolymers () const
	Get all Monomeric Polymers. More...

bool	hasMonomericPolymer (String name) const
	Check if polymer name is already stored is a monomeric polymer. More...

bool	isMonomericPolymer (String chemical_unit_label)

void	addMonomericPolymer (MonomericPolymer mp)

String	getResidueSequence (Position i=0) const

bool	hasHshifts () const
	Check, whether this NMRFile provides hydrogen shifts. More...

bool	hasCshifts () const
	Check, whether this NMRFile provides carbon shifts. More...

bool	hasNshifts () const
	Check, whether this NMRFile provides nitrogen shifts. More...

Equality
bool	operator== (const NMRStarFile &f)

bool	operator!= (const NMRStarFile &f)

void	clear ()

Public Member Functions inherited from BALL::CIFFile
	CIFFile ()

	CIFFile (const String &filename, File::OpenMode open_mode=std::ios::in)

virtual	~CIFFile ()

virtual bool	write ()

void	inSafeframe (const char *name)

void	inItem (const char *name)

void	inDatablock (const char *name)

void	insertDatablock (const Datablock &datablock)

const Datablock &	getDatablock (const String &name) const

Datablock &	getDatablock (const String &name)

bool	hasDatablock (const String &name) const

void	setMolecule (Molecule *molecule)

void	clearParameters ()

Public Member Functions inherited from BALL::File
	File ()

	File (const String &name, OpenMode open_mode=std::ios::in)

virtual	~File ()

bool	isValid () const

bool	open (const String &name, File::OpenMode open_mode=std::ios::in)

bool	reopen ()

bool	reopen (File::OpenMode open_mode)

void	close ()

const String &	getName () const

void	setName (const String &name)

const String &	getOriginalName () const

Size	getSize ()

File::OpenMode	getOpenMode () const

Type	getType (bool trace_link) const

bool	copyTo (const String &destination_name, Size buffer_size=4096)

bool	moveTo (const String &destination_name)

bool	remove ()

bool	renameTo (const String &new_path)

bool	truncate (Size size=0)

std::fstream &	getFileStream ()

TransformationManager &	getTransformationManager ()

const TransformationManager &	getTransformationManager () const

bool	operator== (const File &file) const

bool	operator!= (const File &file) const

bool	isOpen () const

bool	isClosed () const

bool	isAccessible () const

bool	isCanonized () const

bool	isReadable () const

bool	isWritable () const

bool	isExecutable () const

Static Public Attributes
static const float	FLOAT_VALUE_NA

static const int	INT_VALUE_NA

static const Position	POSITION_VALUE_NA

Static Public Attributes inherited from BALL::CIFFile
static State	state

Static Public Attributes inherited from BALL::File
static const OpenMode	MODE_IN
	Open for input (default) More...

static const OpenMode	MODE_OUT
	Open for output. More...

static const OpenMode	MODE_APP
	Append. Seek to end before each write operation. More...

static const OpenMode	MODE_BINARY
	Binary mode. More...

static const OpenMode	MODE_ATE
	Seek to end directly after opening. More...

static const OpenMode	MODE_TRUNC
	Truncate an existing file. More...

static const String	TRANSFORMATION_EXEC_PREFIX
	Prefix for filenames that are created through the execution of commands "exec:". More...

static const String	TRANSFORMATION_FILE_PREFIX
	Prefix for files (to mimick URL-like behavior) "file:". More...

static const String	TRANSFORMATION_FTP_PREFIX
	Prefix for FTP-transfers "ftp://". More...

static const String	TRANSFORMATION_HTTP_PREFIX
	Prefix for HTTP-transfer "http://". More...

Private Member Functions
void	readEntryInformation_ ()
	reads the number of chemical shifts More...

void	readMolSystem_ ()
	reads the molecular system name More...

void	readMonomericPolymers_ ()
	read the MonomericPolymers More...

void	readSampleConditions_ ()
	reads the sample conditions More...

void	readShiftReferences_ ()
	reads the shift references More...

void	readShifts_ ()
	reads the shift datas More...

void	readSamples_ ()
	read the samples More...

void	readNMRSpectrometer_ ()
	reads the NMR spectrometer data More...

void	findDependiencies_ ()
	find dependencies for the ChemicalUnits More...

void	setSpecialCharacters_ (String characters)
	set the characters denoting single non-available values More...

bool	isValidSingleValue_ (String value)
	check whether the given String denotes a non-available value More...

float	valueToFloat_ (String value)
	returns the value as float, if it is a valid one, or FLOAT_VALUE_NA More...

int	valueToInt_ (String value)
	returns the value as int, if it is a valid one, or INT_VALUE_NA More...

bool	assignShifts_ (BALLToBMRBMapper &pdb_to_bmrb_mapping)

Private Attributes
bool	valid_

Size	number_of_shift_sets_
	the number of shift data sets More...

Size	number_of_assigned_shifts_
	the number of assigned shifts during the last call of assignShifts() More...

EntryInformation	entry_information_
	the general entry data More...

MolecularSystem	molecular_system_
	the system information More...

std::vector< NMRAtomDataSet >	atom_data_sets_
	the data for the atoms is stored here More...

std::vector< SampleCondition >	sample_conditions_
	the data for different sample sets More...

std::vector< Sample >	samples_
	the samples More...

std::vector< ShiftReferenceSet >	shift_references_
	the data for shift references More...

std::vector< NMRSpectrometer >	nmr_spectrometers_
	the data of nmr spectrometers More...

vector< MonomericPolymer >	monomeric_polymers_
	Monomeric Polymer information. More...

bool	has_H_shifts_
	stores, which shifts are given in the file More...

bool	has_C_shifts_

bool	has_N_shifts_

SaveFrame	dummy_saveframe_

SampleCondition	dummy_sample_condition_

Sample	dummy_sample_

ShiftReferenceSet	dummy_shift_reference_set_

NMRSpectrometer	dummy_NMR_spectrometer_

MonomericPolymer	dummy_monomeric_polymer_

String	special_characters_
	characters, that denote non-available values More...

Additional Inherited Members
Public Types inherited from BALL::File
typedef std::ios::openmode	OpenMode

enum	Transformation { TRANSFORMATION__EXEC = 1, TRANSFORMATION__FILTER = 2, TRANSFORMATION__URL = 3 }

enum	Type { TYPE__UNKNOWN = 0, TYPE__DIRECTORY = 1, TYPE__CHAR_SPECIAL_FILE = 2, TYPE__BLOCK_SPECIAL_FILE = 3, TYPE__REGULAR_FILE = 4, TYPE__SYMBOLIC_LINK = 5, TYPE__SOCKET = 6, TYPE__FIFO_SPECIAL_FILE = 7 }

Static Public Member Functions inherited from BALL::File
static Size	getSize (String name)

static Type	getType (String name, bool trace_link)

static bool	copy (String source_name, String destination_name, Size buffer_size=4096)

static bool	move (const String &source_name, const String &destination_name)

static bool	remove (String name)

static bool	rename (String old_path, String new_path)

static bool	truncate (String path, Size size=0)

static bool	createTemporaryFilename (String &temporary, const String &suffix=".TMP")

static void	enableTransformation (Transformation transformation)

static void	disableTransformation (Transformation transformation)

static bool	isTransformationEnabled (Transformation transformation)

static void	registerTransformation (const String &pattern, const String &exec)

static void	unregisterTransformation (const String &pattern)

static bool	isAccessible (String name)

static bool	isReadable (String name)

static bool	isWritable (String name)

static bool	isExecutable (String name)

Protected Member Functions inherited from BALL::CIFFile
virtual void	initRead_ ()

Protected Attributes inherited from BALL::CIFFile
Molecule *	molecule_

String	current_datablock_

String	current_saveframe_

String	current_item_

StringHashMap< Index >	datablocks_hash_

vector< Datablock >	datablocks_

Static Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

This class provides methods for reading and assigning chemical shifts.

NMRStarFile class.

This class provides methods for reading and assigning experimental chemical shifts from NMRStar files to peptides. The nested class BALLToBMRBMapper creates a mapping between NMRStar file atoms and atoms of a chain either based on a trivial mapping

See Also: createTrivialMapping() or based on a given alignment; createMapping(). Access to information other than the shifts is provided as well.

Example code:

System system;
pdb_file >> system;
Chain& chain = *(system.beginChain());
NMRStarFile nmr_file("NMRStarFile_test.bmr");
cout << "File contains "      << nmr_file.getNumberOfAtoms()   << " chemical shifts" << endl;
cout << "Number of samples: " << nmr_file.getNumberOfSamples() << endl;
NMRStarFile::MolecularSystem nmr_mol_sys = nmr_file.getMolecularInformation();
cout << "Molecular systems name: " <<  nmr_mol_sys.system_name << endl;
cout << "Number of possible chemical units: " <<  nmr_mol_sys.getNumberOfChemicalUnits() << endl;
// the chemical units of this file
for (Size k=0; k <  nmr_mol_sys.getNumberOfChemicalUnits(); k++)
{
   NMRStarFile::MolecularSystem::ChemicalUnit cu = nmr_mol_sys.getChemicalUnit(k);
   cout << " " << k << " : " <<  cu.component_name 
        << " " <<  cu.label << endl;
}
// get the shift data   
// NOTE: nmr_file.atom_data_sets_ equals  nmr_data !
std::vector<NMRStarFile::NMRAtomDataSet> const& nmr_data = nmr_file.getNMRData();
cout << "Number of shift sets: " <<  nmr_data.size() << endl;
for (Size k=0; k < nmr_data.size(); k++)
{
   cout << " " << k << " shift set name: " << nmr_data[k].name << "   -- condition name: " << nmr_data[k].condition << endl;
}
// decide for a chemical unit 
NMRStarFile::MolecularSystem::ChemicalUnit cu = nmr_mol_sys.getChemicalUnit(0);
String chemical_unit_label = cu.label;
cout << Peptides::GetSequence(chain)  << endl;
cout << nmr_file.getResidueSequence() << endl;
// create a mapping based on an alignment
cout << "Create a mapping... " ;
NMRStarFile::BALLToBMRBMapper mapper(chain, nmr_file, chemical_unit_label);
mapper.createMapping("MKSTGIVRKVDELGR-VVIPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMT", 
                     "MKSTGIVRKVDELGRVV-IPIELRRTLGIAEKDALEIYVDDEKIILKKYKPNMT");
cout << "Number of mismatches: " << mapper.getNumberOfMismatches() << endl;
cout << "Number of gaps: "       << mapper.getNumberOfGaps() << endl;
// assign the shifts
nmr_file.assignShifts(mapper);
cout << "Assigned "      << nmr_file.getNumberOfShiftsAssigned() 
     << " shifts given " << nmr_file.getNumberOfAtoms() << " chemical shifts." << endl << endl;
...
   cout << atom->getProperty(ShiftModule::PROPERTY__EXPERIMENTAL__SHIFT).getFloat() << endl;
...
// get the ChemicalUnit by label
NMRStarFile::MolecularSystem::ChemicalUnit chemical_unit = getChemicalUnitByLabel(chemical_unit_label); 
// find the corresponding SampleCondition
if (chemical_unit.shifts && nmr_file.hasSampleCondition(chemical_unit.shifts->condition))
{
  NMRStarFile::SampleCondition& condition = nmr_file.getSampleConditionByName(chemical_unit.shifts->condition);     
  if (condition.hasType("pH"))
    pH = condition.values["pH"];  
  if (condition.hasType("pH*"))
    pH = condition.values["pH*"]; 
  if (condition.hasType("temperature"))
    temperature  = condition.values["temperature"];
  if (condition.hasType("pressure"))
    pressure  = condition.values["pressure"];
  cout << "NMR conditions: " << pH << ", " << temperature << ", " << pressure << endl; 
}

Definition at line 113 of file NMRStarFile.h.

Constructor & Destructor Documentation

BALL::NMRStarFile::NMRStarFile ( )

Standard constructor

BALL::NMRStarFile::NMRStarFile	(	const String &	file_name,
		File::OpenMode	open_mode = `std::ios::in`
	)

Detailed constuctor. Opens the given file and extracts all usefull data (Calls read ).

Exceptions

Exception::FileNotFound if the file could not be opened

BALL::NMRStarFile::~NMRStarFile ( )

Destructor.

Member Function Documentation

void BALL::NMRStarFile::addMonomericPolymer ( MonomericPolymer mp )

Add a Monomeric Polymer NOTE: if a poymer with the same name already exists, it will be overwritten!

bool BALL::NMRStarFile::assignShifts ( BALLToBMRBMapper & ball_to_bmrb_mapping )

Assign the shifts to the given AtomContainer as denoted in the given {BALLToBMRBMapper}.

Returns: bool - true if reading the file was successful

See Also: NMRStarFile::BALLToBMRBMapper

bool BALL::NMRStarFile::assignShifts	(	AtomContainer &	ac,
		const String &	chemical_unit,
		const String &	aligned_ball_sequence,
		const String &	aligned_nmrstar_sequence
	)

Assign the shifts to the given AtomContainer as pointed out in the alignment. The alignmed sequences should be given in OneLetterCode, where '-' denotes a gap.

Parameters

ac	AtomContainer to which the NMRStarfile's shift should be assigned.
chemical_unit	the name of the molecular system (chemical unit) storing the atom shifts
aligned_ball_sequence	the aligned AtomContainers aminoacid sequence
aligned_nmrstar_sequence	the aligned aminoacid sequence of the NMRStar file atoms

Returns: bool - true if reading the file was successful

bool BALL::NMRStarFile::assignShifts_ ( BALLToBMRBMapper & pdb_to_bmrb_mapping )

private

Apply the shifts read into the AtomContainer as denoted in the mapping. We assume, that the file was already read! The shifts are stored as a property under the key {BALL::ShiftModule::PROPERTY__EXPERIMENTAL__SHIFT}

void BALL::NMRStarFile::clear ( )

virtual

Clear the object.

Reimplemented from BALL::File.

void BALL::NMRStarFile::findDependiencies_ ( )

private

find dependencies for the ChemicalUnits

const MolecularSystem::ChemicalUnit& BALL::NMRStarFile::getChemicalUnitByLabel ( String const & label ) const

Get a chemical unit by name

MolecularSystem::ChemicalUnit& BALL::NMRStarFile::getChemicalUnitByLabel ( String const & label )

Get a chemical unit by name

const EntryInformation& BALL::NMRStarFile::getEntryInformation ( ) const

inline

Get the entry information

Definition at line 678 of file NMRStarFile.h.

const MolecularSystem& BALL::NMRStarFile::getMolecularInformation ( ) const

inline

Get the molecular information

Definition at line 682 of file NMRStarFile.h.

MolecularSystem& BALL::NMRStarFile::getMolecularInformation ( )

inline

Get the molecular information

Definition at line 686 of file NMRStarFile.h.

NMRStarFile::MonomericPolymer& BALL::NMRStarFile::getMonomericPolymer ( Position i )

Get a mutable reference to the MonomericPolymer-information by index

Exceptions

Exception::OutOfRange if a polymer with this index could not be found

const NMRStarFile::MonomericPolymer& BALL::NMRStarFile::getMonomericPolymer ( Position i ) const

Get the MonomericPolymer-information by index

Exceptions

Exception::OutOfRange if a polymer with this index could not be found

NMRStarFile::MonomericPolymer& BALL::NMRStarFile::getMonomericPolymer ( const String & name )

Get a mutable reference to the MonomericPolymer-information by name

Exceptions

Exception::OutOfRange if a polymer with this name could not be found

const NMRStarFile::MonomericPolymer& BALL::NMRStarFile::getMonomericPolymer ( const String & name ) const

Get the MonomericPolymer-information by name

Exceptions

Exception::OutOfRange if a polymer with this name could not be found

vector<MonomericPolymer> BALL::NMRStarFile::getMonomericPolymers ( ) const

inline

Get all Monomeric Polymers.

Definition at line 822 of file NMRStarFile.h.

const std::vector<NMRAtomDataSet>& BALL::NMRStarFile::getNMRData ( ) const

Get the extracted data for the atoms

NMRSpectrometer& BALL::NMRStarFile::getNMRSpectrometer ( Position i )

Get the i-th spectrometer.

const NMRSpectrometer& BALL::NMRStarFile::getNMRSpectrometer ( Position i ) const

Get the i-th spectrometer.

NMRSpectrometer& BALL::NMRStarFile::getNMRSpectrometerByName ( String name )

Get the spectrometer by its SaveFrame name.

const NMRSpectrometer& BALL::NMRStarFile::getNMRSpectrometerByName ( String name ) const

Get the spectrometer by its SaveFrame name.

float BALL::NMRStarFile::getNMRSpectrometerFieldStrength ( Position i ) const

Get the spectrometer field strength.

String BALL::NMRStarFile::getNMRSpectrometerManufacturer ( Position i ) const

Get the spectrometer manufacturer.

std::vector<NMRSpectrometer>& BALL::NMRStarFile::getNMRSpectrometers ( )

inline

Get the spectrometers.

Definition at line 774 of file NMRStarFile.h.

const std::vector<NMRSpectrometer>& BALL::NMRStarFile::getNMRSpectrometers ( ) const

inline

Get the spectrometers.

Definition at line 776 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfAtoms ( ) const

Return the maximum number of atoms in all shift sets

Size BALL::NMRStarFile::getNumberOfMonomericPolymers ( ) const

inline

Get the number of monomeric polymers in the file.

Definition at line 819 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfNMRSpectrometers ( ) const

inline

Get the number of nmr spectrometers.

Definition at line 779 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfSampleConditions ( ) const

inline

Get the number of sample conditions.

Definition at line 721 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfSamples ( ) const

inline

Get the number of samples.

Definition at line 736 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfShiftReferenceSets ( ) const

inline

Get the number of shift reference sets.

Definition at line 757 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfShiftsAssigned ( ) const

inline

Return the number of atoms assigned a chemical shift

Definition at line 670 of file NMRStarFile.h.

String BALL::NMRStarFile::getResidueSequence ( Position i = 0 ) const

Get the sequence of residues of the i-th monomeric polymer in the file.

This method automatically compares the i-th monomeric_polymers' residue sequence with the actual stored NMR shift data. If there is a mismatch, a warning is given! If there is a mismatch or there is no monomeric_polymers residue sequence an empty.

Returns: String amino acid sequence

Sample BALL::NMRStarFile::getSample ( Position i ) const

Get the i-th sample. If i is out of size a dummy sample is returned.

Sample BALL::NMRStarFile::getSample ( String label ) const

Get the sample with name label. If no sample with name label exist a dummy sample is returned.

SampleCondition& BALL::NMRStarFile::getSampleCondition ( Position i )

inline

Get the i-th SampleCondition.

Definition at line 715 of file NMRStarFile.h.

const SampleCondition& BALL::NMRStarFile::getSampleCondition ( Position i ) const

inline

Get the i-th SampleCondition.

Definition at line 718 of file NMRStarFile.h.

SampleCondition& BALL::NMRStarFile::getSampleConditionByName ( String name )

Get a SampleCondition by its SaveFrame name

const SampleCondition& BALL::NMRStarFile::getSampleConditionByName ( String name ) const

Get a SampleCondition by its SaveFrame name

const std::vector<SampleCondition>& BALL::NMRStarFile::getSampleConditions ( ) const

inline

Get the sample conditions.

Definition at line 724 of file NMRStarFile.h.

std::vector<SampleCondition>& BALL::NMRStarFile::getSampleConditions ( )

inline

Get the sample conditions.

Definition at line 727 of file NMRStarFile.h.

std::vector<Sample> BALL::NMRStarFile::getSamples ( ) const

inline

Get the samples.

Definition at line 732 of file NMRStarFile.h.

ShiftReferenceSet& BALL::NMRStarFile::getShiftReferenceSet ( Position i )

inline

Get the i-th shift reference set.

Definition at line 763 of file NMRStarFile.h.

const ShiftReferenceSet& BALL::NMRStarFile::getShiftReferenceSet ( Position i ) const

inline

Get the i-th shift reference set.

Definition at line 765 of file NMRStarFile.h.

const ShiftReferenceSet& BALL::NMRStarFile::getShiftReferenceSetByName ( String name ) const

Get a ShiftReferenceSet by its SaveFrame name.

ShiftReferenceSet& BALL::NMRStarFile::getShiftReferenceSetByName ( String name )

Get a ShiftReferenceSet by its SaveFrame name.

std::vector<ShiftReferenceSet>& BALL::NMRStarFile::getShiftReferenceSets ( )

inline

Get the shift reference sets.

Definition at line 752 of file NMRStarFile.h.

const std::vector<ShiftReferenceSet>& BALL::NMRStarFile::getShiftReferenceSets ( ) const

inline

Get the shift reference sets.

Definition at line 754 of file NMRStarFile.h.

bool BALL::NMRStarFile::hasCshifts ( ) const

inline

Check, whether this NMRFile provides carbon shifts.

Definition at line 855 of file NMRStarFile.h.

bool BALL::NMRStarFile::hasHshifts ( ) const

inline

Check, whether this NMRFile provides hydrogen shifts.

Definition at line 852 of file NMRStarFile.h.

bool BALL::NMRStarFile::hasMonomericPolymer ( String name ) const

Check if polymer name is already stored is a monomeric polymer.

bool BALL::NMRStarFile::hasNshifts ( ) const

inline

Check, whether this NMRFile provides nitrogen shifts.

Definition at line 858 of file NMRStarFile.h.

bool BALL::NMRStarFile::hasSample ( String label ) const

Return true if the file contains a sample named label, false otherwise.

bool BALL::NMRStarFile::hasSampleCondition ( String name )

Return true if the file contains a SampleCondition named name, false otherwise

bool BALL::NMRStarFile::hasSampleCondition ( String name ) const

Return true if the file contains a SampleCondition named name, false otherwise

bool BALL::NMRStarFile::hasShiftReferenceSet ( String name )

Check if there is a ShiftReferenceSet named name.

bool BALL::NMRStarFile::isMonomericPolymer ( String chemical_unit_label )

Check if label is a monomeric polymer.

Returns true if a monomer with name chemical_unit_label exists, false otherwise.

bool BALL::NMRStarFile::isValidSingleValue_ ( String value )

private

check whether the given String denotes a non-available value

bool BALL::NMRStarFile::operator!= ( const NMRStarFile & f )

Inequality operator Test if both instances point to different files.

bool BALL::NMRStarFile::operator== ( const NMRStarFile & f )

Equality operator. Test if both instances point to the same file.

bool BALL::NMRStarFile::read ( )

virtual

Read an NMRStarFile.

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::CIFFile.

bool BALL::NMRStarFile::read ( AtomContainer & ac )

void BALL::NMRStarFile::readEntryInformation_ ( )

private

reads the number of chemical shifts

void BALL::NMRStarFile::readMolSystem_ ( )

private

reads the molecular system name

void BALL::NMRStarFile::readMonomericPolymers_ ( )

private

read the MonomericPolymers

void BALL::NMRStarFile::readNMRSpectrometer_ ( )

private

reads the NMR spectrometer data

void BALL::NMRStarFile::readSampleConditions_ ( )

private

reads the sample conditions

void BALL::NMRStarFile::readSamples_ ( )

private

read the samples

void BALL::NMRStarFile::readShiftReferences_ ( )

private

reads the shift references

void BALL::NMRStarFile::readShifts_ ( )

private

reads the shift datas

void BALL::NMRStarFile::setSpecialCharacters_ ( String characters )

private

set the characters denoting single non-available values

float BALL::NMRStarFile::valueToFloat_ ( String value )

private

returns the value as float, if it is a valid one, or FLOAT_VALUE_NA

int BALL::NMRStarFile::valueToInt_ ( String value )

private

returns the value as int, if it is a valid one, or INT_VALUE_NA

Member Data Documentation

std::vector<NMRAtomDataSet> BALL::NMRStarFile::atom_data_sets_

private

the data for the atoms is stored here

Definition at line 957 of file NMRStarFile.h.

MonomericPolymer BALL::NMRStarFile::dummy_monomeric_polymer_

private

Definition at line 995 of file NMRStarFile.h.

NMRSpectrometer BALL::NMRStarFile::dummy_NMR_spectrometer_

private

Definition at line 992 of file NMRStarFile.h.

Sample BALL::NMRStarFile::dummy_sample_

private

Definition at line 986 of file NMRStarFile.h.

SampleCondition BALL::NMRStarFile::dummy_sample_condition_

private

Definition at line 983 of file NMRStarFile.h.

SaveFrame BALL::NMRStarFile::dummy_saveframe_

private

Definition at line 980 of file NMRStarFile.h.

ShiftReferenceSet BALL::NMRStarFile::dummy_shift_reference_set_

private

Definition at line 989 of file NMRStarFile.h.

EntryInformation BALL::NMRStarFile::entry_information_

private

the general entry data

Definition at line 951 of file NMRStarFile.h.

const float BALL::NMRStarFile::FLOAT_VALUE_NA

static

Definition at line 119 of file NMRStarFile.h.

bool BALL::NMRStarFile::has_C_shifts_

private

Definition at line 976 of file NMRStarFile.h.

bool BALL::NMRStarFile::has_H_shifts_

private

stores, which shifts are given in the file

Definition at line 975 of file NMRStarFile.h.

bool BALL::NMRStarFile::has_N_shifts_

private

Definition at line 977 of file NMRStarFile.h.

const int BALL::NMRStarFile::INT_VALUE_NA

static

Definition at line 120 of file NMRStarFile.h.

MolecularSystem BALL::NMRStarFile::molecular_system_

private

the system information

Definition at line 954 of file NMRStarFile.h.

vector<MonomericPolymer> BALL::NMRStarFile::monomeric_polymers_

private

Monomeric Polymer information.

Definition at line 972 of file NMRStarFile.h.

std::vector<NMRSpectrometer> BALL::NMRStarFile::nmr_spectrometers_

private

the data of nmr spectrometers

Definition at line 969 of file NMRStarFile.h.

Size BALL::NMRStarFile::number_of_assigned_shifts_

private

the number of assigned shifts during the last call of assignShifts()

Definition at line 948 of file NMRStarFile.h.

Size BALL::NMRStarFile::number_of_shift_sets_

private

the number of shift data sets

Definition at line 945 of file NMRStarFile.h.

const Position BALL::NMRStarFile::POSITION_VALUE_NA

static

Definition at line 122 of file NMRStarFile.h.

std::vector<SampleCondition> BALL::NMRStarFile::sample_conditions_

private

the data for different sample sets

Definition at line 960 of file NMRStarFile.h.

std::vector<Sample> BALL::NMRStarFile::samples_

private

the samples

Definition at line 963 of file NMRStarFile.h.

std::vector<ShiftReferenceSet> BALL::NMRStarFile::shift_references_

private

the data for shift references

Definition at line 966 of file NMRStarFile.h.

String BALL::NMRStarFile::special_characters_

private

characters, that denote non-available values

Definition at line 998 of file NMRStarFile.h.

bool BALL::NMRStarFile::valid_

private

Definition at line 942 of file NMRStarFile.h.

Classes

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation