BALL::NMRStarFile Class Reference

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

#include <BALL/FORMAT/NMRStarFile.h>

Inheritance diagram for BALL::NMRStarFile:
Inheritance graph
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List of all members.

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.
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.
const SampleCondition & getSampleCondition (Position i) const
 Get the i-th SampleCondition.
Size getNumberOfSampleConditions () const
 Get the number of sample conditions.
const std::vector
< SampleCondition > & 		getSampleConditions () const
 Get the sample conditions.
std::vector< SampleCondition > & getSampleConditions ()
 Get the sample conditions.
std::vector< Sample > getSamples () const
 Get the samples.
Size getNumberOfSamples () const
 Get the number of samples.
bool hasSample (String label) const
 Return true if the file contains a sample named label, false otherwise.
Sample getSample (Position i) const
Sample getSample (String label) const
std::vector< ShiftReferenceSet > & getShiftReferenceSets ()
 Get the shift reference sets.
const std::vector
< ShiftReferenceSet > & 		getShiftReferenceSets () const
 Get the shift reference sets.
Size getNumberOfShiftReferenceSets () const
 Get the number of shift reference sets.
bool hasShiftReferenceSet (String name)
 Check if there is a ShiftReferenceSet named name.
ShiftReferenceSet & getShiftReferenceSet (Position i)
 Get the i-th shift reference set.
const ShiftReferenceSet & getShiftReferenceSet (Position i) const
 Get the i-th shift reference set.
const ShiftReferenceSet & getShiftReferenceSetByName (String name) const
 Get a ShiftReferenceSet by its SaveFrame name.
ShiftReferenceSet & getShiftReferenceSetByName (String name)
 Get a ShiftReferenceSet by its SaveFrame name.
std::vector< NMRSpectrometer > & getNMRSpectrometers ()
 Get the spectrometers.
const std::vector
< NMRSpectrometer > & 		getNMRSpectrometers () const
 Get the spectrometers.
Size getNumberOfNMRSpectrometers () const
 Get the number of nmr spectrometers.
NMRSpectrometer & getNMRSpectrometer (Position i)
 Get the i-th spectrometer.
const NMRSpectrometer & getNMRSpectrometer (Position i) const
 Get the i-th spectrometer.
NMRSpectrometer & getNMRSpectrometerByName (String name)
 Get the spectrometer by its SaveFrame name.
const NMRSpectrometer & getNMRSpectrometerByName (String name) const
 Get the spectrometer by its SaveFrame name.
String getNMRSpectrometerManufacturer (Position i) const
 Get the spectrometer manufacturer.
float getNMRSpectrometerFieldStrength (Position i) const
 Get the spectrometer field strength.
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.
vector< MonomericPolymer > getMonomericPolymers () const
 Get all Monomeric Polymers.
bool hasMonomericPolymer (String name) const
 Check if polymer name is already stored is a monomeric polymer.
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.
bool hasCshifts () const
 Check, whether this NMRFile provides carbon shifts.
bool hasNshifts () const
 Check, whether this NMRFile provides nitrogen shifts.
Equality

bool operator== (const NMRStarFile &f)
bool operator!= (const NMRStarFile &f)
void clear ()

Static Public Attributes

static const float FLOAT_VALUE_NA
static const int INT_VALUE_NA
static const Position POSITION_VALUE_NA

Private Member Functions

void readEntryInformation_ ()
 reads the number of chemical shifts
void readMolSystem_ ()
 reads the molecular system name
void readMonomericPolymers_ ()
 read the MonomericPolymers
void readSampleConditions_ ()
 reads the sample conditions
void readShiftReferences_ ()
 reads the shift references
void readShifts_ ()
 reads the shift datas
void readSamples_ ()
 read the samples
void readNMRSpectrometer_ ()
 reads the NMR spectrometer data
void findDependiencies_ ()
 find dependencies for the ChemicalUnits
void setSpecialCharacters_ (String characters)
 set the characters denoting single non-available values
bool isValidSingleValue_ (String value)
 check whether the given String denotes a non-available value
float valueToFloat_ (String value)
 returns the value as float, if it is a valid one, or FLOAT_VALUE_NA
int valueToInt_ (String value)
 returns the value as int, if it is a valid one, or INT_VALUE_NA
bool assignShifts_ (BALLToBMRBMapper &pdb_to_bmrb_mapping)

Private Attributes

bool valid_
Size number_of_shift_sets_
 the number of shift data sets
Size number_of_assigned_shifts_
 the number of assigned shifts during the last call of assignShifts()
EntryInformation entry_information_
 the general entry data
MolecularSystem molecular_system_
 the system information
std::vector< NMRAtomDataSet > atom_data_sets_
 the data for the atoms is stored here
std::vector< SampleCondition > sample_conditions_
 the data for different sample sets
std::vector< Sample > samples_
 the samples
std::vector< ShiftReferenceSet > shift_references_
 the data for shift references
std::vector< NMRSpectrometer > nmr_spectrometers_
 the data of nmr spectrometers
vector< MonomericPolymer > monomeric_polymers_
 Monomeric Polymer information.
bool has_H_shifts_
 stores, which shifts are given in the file
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

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 117 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 ( 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 &  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_ ( 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

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

Get a chemical unit by name

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

Get a chemical unit by name

const EntryInformation& BALL::NMRStarFile::getEntryInformation (  )  const [inline]

Get the entry information

Definition at line 682 of file NMRStarFile.h.

MolecularSystem& BALL::NMRStarFile::getMolecularInformation (  )  [inline]

Get the molecular information

Definition at line 690 of file NMRStarFile.h.

const MolecularSystem& BALL::NMRStarFile::getMolecularInformation (  )  const [inline]

Get the molecular information

Definition at line 686 of file NMRStarFile.h.

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
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 ( 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 ( 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
vector<MonomericPolymer> BALL::NMRStarFile::getMonomericPolymers (  )  const [inline]

Get all Monomeric Polymers.

Definition at line 826 of file NMRStarFile.h.

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

Get the extracted data for the atoms

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

Get the i-th spectrometer.

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

Get the i-th spectrometer.

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

Get the spectrometer by its SaveFrame name.

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

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.

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

Get the spectrometers.

Definition at line 780 of file NMRStarFile.h.

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

Get the spectrometers.

Definition at line 778 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 823 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfNMRSpectrometers (  )  const [inline]

Get the number of nmr spectrometers.

Definition at line 783 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfSampleConditions (  )  const [inline]

Get the number of sample conditions.

Definition at line 725 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfSamples (  )  const [inline]

Get the number of samples.

Definition at line 740 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfShiftReferenceSets (  )  const [inline]

Get the number of shift reference sets.

Definition at line 761 of file NMRStarFile.h.

Size BALL::NMRStarFile::getNumberOfShiftsAssigned (  )  const [inline]

Return the number of atoms assigned a chemical shift

Definition at line 674 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 ( String  label  )  const

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

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

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

const SampleCondition& BALL::NMRStarFile::getSampleCondition ( Position  i  )  const [inline]

Get the i-th SampleCondition.

Definition at line 722 of file NMRStarFile.h.

SampleCondition& BALL::NMRStarFile::getSampleCondition ( Position  i  )  [inline]

Get the i-th SampleCondition.

Definition at line 719 of file NMRStarFile.h.

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

Get a SampleCondition by its SaveFrame name

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

Get a SampleCondition by its SaveFrame name

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

Get the sample conditions.

Definition at line 731 of file NMRStarFile.h.

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

Get the sample conditions.

Definition at line 728 of file NMRStarFile.h.

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

Get the samples.

Definition at line 736 of file NMRStarFile.h.

const ShiftReferenceSet& BALL::NMRStarFile::getShiftReferenceSet ( Position  i  )  const [inline]

Get the i-th shift reference set.

Definition at line 769 of file NMRStarFile.h.

ShiftReferenceSet& BALL::NMRStarFile::getShiftReferenceSet ( Position  i  )  [inline]

Get the i-th shift reference set.

Definition at line 767 of file NMRStarFile.h.

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

Get a ShiftReferenceSet by its SaveFrame name.

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

Get a ShiftReferenceSet by its SaveFrame name.

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

Get the shift reference sets.

Definition at line 758 of file NMRStarFile.h.

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

Get the shift reference sets.

Definition at line 756 of file NMRStarFile.h.

bool BALL::NMRStarFile::hasCshifts (  )  const [inline]

Check, whether this NMRFile provides carbon shifts.

Definition at line 859 of file NMRStarFile.h.

bool BALL::NMRStarFile::hasHshifts (  )  const [inline]

Check, whether this NMRFile provides hydrogen shifts.

Definition at line 856 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 862 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  )  const

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

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

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 ( AtomContainer &  ac  ) 
bool BALL::NMRStarFile::read (  )  [virtual]

Read an NMRStarFile.

Exceptions:
Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::CIFFile.

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 961 of file NMRStarFile.h.

MonomericPolymer BALL::NMRStarFile::dummy_monomeric_polymer_ [private]

Definition at line 999 of file NMRStarFile.h.

NMRSpectrometer BALL::NMRStarFile::dummy_NMR_spectrometer_ [private]

Definition at line 996 of file NMRStarFile.h.

Sample BALL::NMRStarFile::dummy_sample_ [private]

Definition at line 990 of file NMRStarFile.h.

SampleCondition BALL::NMRStarFile::dummy_sample_condition_ [private]

Definition at line 987 of file NMRStarFile.h.

SaveFrame BALL::NMRStarFile::dummy_saveframe_ [private]

Definition at line 984 of file NMRStarFile.h.

ShiftReferenceSet BALL::NMRStarFile::dummy_shift_reference_set_ [private]

Definition at line 993 of file NMRStarFile.h.

EntryInformation BALL::NMRStarFile::entry_information_ [private]

the general entry data

Definition at line 955 of file NMRStarFile.h.

const float BALL::NMRStarFile::FLOAT_VALUE_NA [static]

Definition at line 123 of file NMRStarFile.h.

bool BALL::NMRStarFile::has_C_shifts_ [private]

Definition at line 980 of file NMRStarFile.h.

bool BALL::NMRStarFile::has_H_shifts_ [private]

stores, which shifts are given in the file

Definition at line 979 of file NMRStarFile.h.

bool BALL::NMRStarFile::has_N_shifts_ [private]

Definition at line 981 of file NMRStarFile.h.

const int BALL::NMRStarFile::INT_VALUE_NA [static]

Definition at line 124 of file NMRStarFile.h.

MolecularSystem BALL::NMRStarFile::molecular_system_ [private]

the system information

Definition at line 958 of file NMRStarFile.h.

vector<MonomericPolymer> BALL::NMRStarFile::monomeric_polymers_ [private]

Monomeric Polymer information.

Definition at line 976 of file NMRStarFile.h.

std::vector<NMRSpectrometer> BALL::NMRStarFile::nmr_spectrometers_ [private]

the data of nmr spectrometers

Definition at line 973 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 952 of file NMRStarFile.h.

Size BALL::NMRStarFile::number_of_shift_sets_ [private]

the number of shift data sets

Definition at line 949 of file NMRStarFile.h.

const Position BALL::NMRStarFile::POSITION_VALUE_NA [static]

Definition at line 126 of file NMRStarFile.h.

std::vector<SampleCondition> BALL::NMRStarFile::sample_conditions_ [private]

the data for different sample sets

Definition at line 964 of file NMRStarFile.h.

std::vector<Sample> BALL::NMRStarFile::samples_ [private]

the samples

Definition at line 967 of file NMRStarFile.h.

std::vector<ShiftReferenceSet> BALL::NMRStarFile::shift_references_ [private]

the data for shift references

Definition at line 970 of file NMRStarFile.h.

String BALL::NMRStarFile::special_characters_ [private]

characters, that denote non-available values

Definition at line 1002 of file NMRStarFile.h.

bool BALL::NMRStarFile::valid_ [private]

Definition at line 946 of file NMRStarFile.h.

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