5 #ifndef BALL_FORMAT_NMRSTARFILE_H 6 #define BALL_FORMAT_NMRSTARFILE_H 8 #ifndef BALL_FORMAT_CIFFILE_H 12 #ifndef BALL_KERNEL_PROTEIN_H 16 #ifndef BALL_STRUCTURE_PEPTIDES_H 489 num_mismatches_ = -1;
494 num_mismatches_ = -1;
504 bool setNMRAtomDataSetByName(
String const& chemical_unit_name);
541 bool isMapped(
Atom const* atom)
const;
544 BMRBIndex operator () (
const Atom* atom);
552 bool createTrivialMapping();
563 bool createMapping(
const String& aligned_ball_sequence,
564 const String& aligned_nmrstar_sequence);
660 const String& chemical_unit,
661 const String& aligned_ball_sequence,
662 const String& aligned_nmrstar_sequence);
666 Size getNumberOfAtoms()
const;
674 const std::vector<NMRAtomDataSet>& getNMRData()
const;
700 bool hasSampleCondition(
String name);
704 bool hasSampleCondition(
String name)
const;
739 bool hasSample(
String label)
const;
760 bool hasShiftReferenceSet(
String name);
795 float getNMRSpectrometerFieldStrength(
Position i)
const;
825 bool hasMonomericPolymer(
String name)
const;
832 bool isMonomericPolymer(
String chemical_unit_label);
890 void readEntryInformation_();
893 void readMolSystem_();
896 void readMonomericPolymers_();
899 void readSampleConditions_();
902 void readShiftReferences_();
911 void readNMRSpectrometer_();
914 void findDependiencies_();
917 void setSpecialCharacters_(
String characters);
920 bool isValidSingleValue_(
String value);
923 float valueToFloat_(
String value);
926 int valueToInt_(
String value);
945 Size number_of_shift_sets_;
948 Size number_of_assigned_shifts_;
957 std::vector<NMRAtomDataSet> atom_data_sets_;
960 std::vector<SampleCondition> sample_conditions_;
963 std::vector<Sample> samples_;
966 std::vector<ShiftReferenceSet> shift_references_;
969 std::vector<NMRSpectrometer> nmr_spectrometers_;
972 vector<MonomericPolymer> monomeric_polymers_;
980 SaveFrame dummy_saveframe_;
998 String special_characters_;
1005 #endif // BALL_FORMAT_NMRSTARFILE_H const BMRBToBALLMapping & getBMRBToBALLMapping() const
Return the mapping.
const NMRAtomDataSet * nmr_atom_data_set_
void setChain(Chain const &chain)
Set the chain.
float seq_to_submitted_percentage
static const int INT_VALUE_NA
StringHashMap< float > errors
SampleCondition & getSampleCondition(Position i)
Get the i-th SampleCondition.
Position residue_seq_code
const MolecularSystem & getMolecularInformation() const
float concentration_value
Peptides::NameConverter name_converter_
std::map< Atom const *, BMRBIndex > BALLToBMRBMapping
StringHashMap< String > residues_by_index
const NMRStarFile * getNMRStarFile() const
Get the NMRStar file.
std::vector< ShiftReferenceElement > elements
BMRBToBALLMapping bmrb_to_ball_map_
map NMR atom data to BALL atoms
int getNumberOfGaps()
Return the number of mismatches in the current mapping.
BMRBToBALLMapping & getBMRBToBALLMapping()
Return the mapping.
const NMRStarFile * nmr_data_
String abbreviation_common
Size getNumberOfShiftReferenceSets() const
Get the number of shift reference sets.
Position nmr_atom_data_set_index_
ShiftReferenceSet & getShiftReferenceSet(Position i)
Get the i-th shift reference set.
vector< RelatedDB > related_database_entries
std::vector< NMRSpectrometer > & getNMRSpectrometers()
Get the spectrometers.
std::istream & operator>>(std::istream &is, TRegularData1D< ValueType > &grid)
Input operator.
BALLToBMRBMapping ball_to_bmrb_map_
map BALL atoms to NMR atom data
void setNMRAtomDataSet(NMRAtomDataSet const &nmr_atom_data_set)
Set the NMRAtomDataSet.
bool hasType(String type)
std::vector< SampleCondition > & getSampleConditions()
Get the sample conditions.
std::vector< ShiftReferenceSet > & getShiftReferenceSets()
Get the shift reference sets.
Size getNumberOfNMRSpectrometers() const
Get the number of nmr spectrometers.
ChemicalUnit const & getChemicalUnit(Position i) const
vector< Component > components
const EntryInformation & getEntryInformation() const
String system_physical_state
static const float FLOAT_VALUE_NA
String system_thiol_state
String system_paramagnetic
int getNumberOfMismatches()
Return the number of mismatches in the current mapping.
const std::vector< ShiftReferenceSet > & getShiftReferenceSets() const
Get the shift reference sets.
vector< MonomericPolymer > getMonomericPolymers() const
Get all Monomeric Polymers.
vector< HomologDB > homolog_database_entries
std::ios::openmode OpenMode
std::map< const NMRAtomData *, Atom const * > BMRBToBALLMapping
bool hasNshifts() const
Check, whether this NMRFile provides nitrogen shifts.
bool hasCshifts() const
Check, whether this NMRFile provides carbon shifts.
Size getNumberOfMonomericPolymers() const
Get the number of monomeric polymers in the file.
String experimental_method
BALLToBMRBMapping & getBALLToBMRBMapping()
Return the mapping.
vector< ChemicalUnit > chemical_units
bool has(const String &key) const
BALL_EXPORT bool operator!=(const String &s1, const String &s2)
bool hasHshifts() const
Check, whether this NMRFile provides hydrogen shifts.
const SampleCondition & getSampleCondition(Position i) const
Get the i-th SampleCondition.
ChemicalUnit & getChemicalUnit(Position i)
const NMRAtomDataSet * getNMRAtomDataSet() const
This class provides methods for reading and assigning chemical shifts.
StringHashMap< String > units
This class provides conversion of atom names between naming schemata.
String system_oligomer_state
std::vector< String > samples
const std::vector< SampleCondition > & getSampleConditions() const
Get the sample conditions.
MonomericPolymer * monomeric_polymer
std::pair< Position, Position > BMRBIndex
std::vector< NMRAtomData > atom_data
BALL_EXPORT bool operator==(const String &s1, const String &s2)
void setNMRStarFile(NMRStarFile const &nmrfile)
Set the NMRStar file.
std::vector< Sample > getSamples() const
Get the samples.
float homology_expectation_value
Size getNumberOfChemicalUnits() const
String BMRB_accession_code
-*- Mode: C++; tab-width: 2; -*-
StringHashMap< float > values
Size getNumberOfSampleConditions() const
Get the number of sample conditions.
Size getNumberOfSamples() const
Get the number of samples.
Database with homolog entries.
float system_molecular_weight
The systems molecular weigth in dalton.
virtual ~BALLToBMRBMapper()
Destructor.
const std::vector< NMRSpectrometer > & getNMRSpectrometers() const
Get the spectrometers.
const Chain * getChain() const
Get the chain.
float indirect_shift_ratio
static const Position POSITION_VALUE_NA
const BALLToBMRBMapping & getBALLToBMRBMapping() const
Return the mapping.
MolecularSystem & getMolecularInformation()
const ShiftReferenceSet & getShiftReferenceSet(Position i) const
Get the i-th shift reference set.
Size getNumberOfShiftsAssigned() const