Data Structures Module

class beautifuljason.data.Image(h5_group)

Bases: IDedObject

Represents an image data object /JasonDocument/General/Pixmaps/<N>

The image is stored in HDF5 format and can be accessed as a numpy array.

class List(h5_group)

Bases: GroupList

Represents a list of image data objects

property class_: bytes

Returns:: The image class attribute.
Return type:: bytes

property depth: int

Returns:: The image depth. 24 for RGB and 32 for RGBA
Return type:: int

property height: int

Returns:: The image height.
Return type:: int

property interlace_mode: bytes

Returns:: The image interlace mode attribute.
Return type:: bytes

property min_max_range: ndarray[uint8]

Returns:: The image min max range attribute.
Return type:: np.ndarray of np.uint8

property pixmap: ndarray[uint8]

New in version 1.1.0.

The image data.

Returns:: The image data as a numpy array.
Return type:: np.ndarray of np.uint8

property subclass: bytes

Returns:: The image subclass attribute.
Return type:: bytes

property version: bytes

Returns:: The image version attribute.
Return type:: bytes

property width: int

Returns:: The image width.
Return type:: int

class beautifuljason.data.Molecule(h5_group)

Bases: IDedObject

Represents a molecule data object from /JasonDocument/Molecules/Molecules/<N> groups.

class Atom(h5_group)

Bases: H5Group

Represents an atom.

class List(h5_group)

Bases: GroupList

Represents a list of atoms.

class NuclType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Nuclide types enumeration.

Ag107 = 60

Ag109 = 61

Al27 = 18

As75 = 43

Au197 = 111

B10 = 8

B11 = 9

Ba135 = 77

Ba137 = 78

Be9 = 7

Bi209 = 117

Br79 = 45

Br81 = 46

C13 = 10

Ca43 = 26

Cd111 = 62

Cd113 = 63

Cl35 = 22

Cl37 = 23

Co59 = 35

Cr53 = 32

Cs133 = 76

Cu63 = 37

Cu65 = 38

Dy161 = 91

Dy163 = 92

Er167 = 94

Eu151 = 86

Eu153 = 87

F19 = 14

Fe57 = 34

Ga69 = 40

Ga71 = 41

Gd155 = 88

Gd157 = 89

Ge73 = 42

H1 = 1

H2 = 2

H3 = 3

He3 = 4

Hf177 = 100

Hf179 = 101

Hg199 = 112

Hg201 = 113

Ho165 = 93

I127 = 73

In113 = 64

In115 = 65

Ir191 = 108

Ir193 = 109

K39 = 24

K41 = 25

Kr83 = 47

La138 = 79

La139 = 80

Li6 = 5

Li7 = 6

Lu175 = 98

Lu176 = 99

Mg25 = 17

Mn55 = 33

Mo95 = 54

Mo97 = 55

N14 = 11

N15 = 12

Na23 = 16

Nb93 = 53

Nd143 = 82

Nd145 = 83

Ne21 = 15

Ni61 = 36

O17 = 13

Os187 = 106

Os189 = 107

P31 = 20

Pb207 = 116

Pd105 = 59

Pr141 = 81

Pt195 = 110

Rb85 = 48

Rb87 = 49

Re185 = 104

Re187 = 105

Rh103 = 58

Ru101 = 57

Ru99 = 56

S33 = 21

Sb121 = 69

Sb123 = 70

Sc45 = 27

Se77 = 44

Si29 = 19

Sm147 = 84

Sm149 = 85

Sn115 = 66

Sn117 = 67

Sn119 = 68

Sr87 = 50

Ta181 = 102

Tb159 = 90

Te123 = 71

Te125 = 72

Ti47 = 28

Ti49 = 29

Tl203 = 114

Tl205 = 115

Tm169 = 95

U235 = 118

Undef = 0

V50 = 30

V51 = 31

W183 = 103

Xe129 = 74

Xe131 = 75

Y89 = 51

Yb171 = 96

Yb173 = 97

Zn67 = 39

Zr91 = 52

class Type(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Atom elements enumeration.

A = 152

Ac = 89

Ag = 47

Al = 13

Am = 95

Ar = 18

As = 33

At = 85

Au = 79

B = 5

Ba = 56

Be = 4

Bh = 107

Bi = 83

Bk = 97

Br = 35

C = 6

Ca = 20

Cd = 48

Ce = 58

Cf = 98

Cl = 17

Cm = 96

Cn = 112

Co = 27

Cr = 24

Cs = 55

Cu = 29

Db = 105

Ds = 110

Dy = 66

El119 = 119

El120 = 120

El121 = 121

El122 = 122

El123 = 123

El124 = 124

El125 = 125

El126 = 126

El127 = 127

El128 = 128

El129 = 129

El130 = 130

El131 = 131

El132 = 132

El133 = 133

El134 = 134

El135 = 135

El136 = 136

El137 = 137

El138 = 138

El139 = 139

El140 = 140

El141 = 141

El142 = 142

El143 = 143

El144 = 144

El145 = 145

El146 = 146

El147 = 147

El148 = 148

El149 = 149

El150 = 150

Er = 68

Es = 99

Eu = 63

F = 9

FV = 151

Fe = 26

Fl = 114

Fm = 100

Fr = 87

Ga = 31

Gd = 64

Ge = 32

H = 1

He = 2

Hf = 72

Hg = 80

Ho = 67

Hs = 108

I = 53

In = 49

Ir = 77

K = 19

Kr = 36

L = 154

La = 57

Li = 3

Lr = 103

Lu = 71

Lv = 116

Mc = 115

Md = 101

Mg = 12

Mn = 25

Mo = 42

Mt = 109

N = 7

NL = 155

NONE = 0

Na = 11

Nb = 41

Nd = 60

Ne = 10

Nh = 113

Ni = 28

No = 102

Np = 93

O = 8

Og = 118

Os = 76

P = 15

Pa = 91

Pb = 82

Pd = 46

Pm = 61

Po = 84

Pr = 59

Pt = 78

Pu = 94

Q = 153

Ra = 88

Rb = 37

Re = 75

Rf = 104

Rg = 111

Rh = 45

Rn = 86

Ru = 44

S = 16

Sb = 51

Sc = 21

Se = 34

Sg = 106

Si = 14

Sm = 62

Sn = 50

Sr = 38

Ta = 73

Tb = 65

Tc = 43

Te = 52

Th = 90

Ti = 22

Tl = 81

Tm = 69

Ts = 117

U = 92

V = 23

W = 74

Xe = 54

Y = 39

Yb = 70

Zn = 30

Zr = 40

property bonded_atom_numbers: ndarray[uint32]

Returns:: The bonded atom numbers of the atom.
Return type:: np.ndarray of np.uint32

property bonded_atoms: list[Atom]

Returns:: The bonded atoms of the atom.
Return type:: list of Molecule.Atom

property bonds: ndarray[uint32]

Returns:: The bonds of the atom.
Return type:: np.ndarray of np.uint32

property charge: int | None

Returns:: The charge of the atom.
Return type:: int | None

property isotope: int | None

Returns:: The isotope of the atom.
Return type:: int | None

property nh: int

Returns:: The number of hydrogen atoms attached to the atom.
Return type:: int

property type: Type

Returns:: The type of the atom.
Return type:: Type

property valence: int | None

Returns:: The valence of the atom.
Return type:: int | None

property x: float

Returns:: The X coordinate of the atom.
Return type:: float

property y: float

Returns:: The Y coordinate of the atom.
Return type:: float

property z: float | None

Returns:: The Z coordinate of the atom if present.
Return type:: float | None

class Coupling(h5_group)

Bases: H5Group

Represents a j-coupling.

class List(h5_group)

Bases: GroupList

Represents a list of j-couplings.

property acount1: int

Returns:: The number of identical atoms of the first coupling partner.
Return type:: int

property acount2: int

Returns:: The number of identical atoms of the second coupling partner.
Return type:: int

property error_spheres: int

Returns:: The error spheres of the coupling.
Return type:: int

property ignored_auto: bool

Returns:: Whether the coupling is ignored automatically.
Return type:: bool

property ignored_user: bool

Returns:: Whether the coupling is ignored by the user.
Return type:: bool

property is_exchangeable1: bool

Returns:: Whether the first coupling partner is exchangeable.
Return type:: bool

property is_exchangeable2: bool

Returns:: Whether the second coupling partner is exchangeable.
Return type:: bool

property jvalue: int

Returns:: Number of bonds between the coupling partners.
Return type:: int

property mark1: str | None

Returns:: The mark of the first coupling partner if present.
Return type:: str | None

property mark2: str | None

Returns:: The mark of the second coupling partner if present.
Return type:: str | None

property n1: uint32

Returns:: The first atom number of the coupling.
Return type:: np.uint32

property n2: uint32

Returns:: The second atom number of the coupling.
Return type:: np.uint32

property nucl1: NuclType

Returns:: The nuclide type of the first coupling partner.
Return type:: Molecule.Atom.NuclType

property nucl2: NuclType

Returns:: The nuclide type of the second coupling partner.
Return type:: Molecule.Atom.NuclType

property value: ndarray[float64]

Returns:: array of experimental and calculated J values of the coupling. The value at index 0 is the experimental J value.
Return type:: np.ndarray of np.float64

property value_error: ndarray[float64]

Returns:: array of calculated J value errors of the coupling. The value at index 0, corresponding to the experimental J value, is -1.
Return type:: np.ndarray of np.float64

property value_method: ndarray[int32]

Returns:: array of value calculation methods of the coupling.
Return type:: np.ndarray of np.int32

property value_spheres: int

Returns:: The value spheres of the coupling.
Return type:: int

class List(h5_group)

Bases: GroupList

New in version 1.1.0.

Represents a list of molecules.

class Ring(h5_group)

Bases: H5Group

Represents a ring.

class List(h5_group)

Bases: GroupList

Represents a list of rings.

Parameters:: h5_group (h5py.Group) – The H5 group.

property atoms: ndarray[uint32]

Returns:: The atoms of the ring.
Return type:: np.ndarray of np.uint32

property is_aromatic: bool

Returns:: Whether the ring is aromatic.
Return type:: bool

class Spectrum(h5_group)

Bases: H5Group

Represents a prediction spectrum.

class List(h5_group)

Bases: GroupList

Represents a list of prediction spectra.

class Shift(h5_group)

Bases: H5Group

Represents a chemical shift.

class List(h5_group)

Bases: GroupList

Represents a list of chemical shifts.

property acount: int

Returns:: The number of identical atoms of the chemical shift.
Return type:: int

property error_spheres: int

Returns:: The error spheres of the chemical shift.
Return type:: int

property ignored_auto: bool

Returns:: Whether the chemical shift is ignored automatically.
Return type:: bool

property ignored_user: bool

Returns:: Whether the chemical shift is ignored by the user.
Return type:: bool

property is_exchangeable: bool

Returns:: Whether the chemical shift is exchangeable.
Return type:: bool

property mark: str | None

Returns:: The mark of the chemical shift if present.
Return type:: str | None

property nh: int

Returns:: The number of hydrogen atoms attached to the atom.
Return type:: int

property nums: ndarray[uint32]

Returns:: The atom numbers of the chemical shift.
Return type:: np.ndarray of np.uint32

property value: ndarray[float64]

Returns:: The experimental and calculated chemical shift values. The value at index 0 is the experimental chemical shift.
Return type:: np.ndarray of np.float64

property value_error: ndarray[float64]

Returns:: The calculated chemical shift errors. The value at index 0, corresponding to the experimental chemical shift, is -1.
Return type:: np.ndarray of np.float64

property value_method: ndarray[int32]

Returns:: The value calculation methods of the chemical shift.
Return type:: np.ndarray of np.int32

property value_spheres: int

Returns:: The value spheres of the chemical shift.
Return type:: int

class Type(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Spectrum types enumeration.

ADEQUATE = 16

APT = 4

All = 28

C13 = 27

COLOC = 14

COSY = 5

Chrom = 23

DEPT135 = 3

DEPT45 = 24

DEPT90 = 2

H1 = 26

H2BC = 15

HETCOR = 12

HMBC = 13

HMQC = 10

HSQC = 9

HSQC_DEPT135 = 25

HSQC_TOCSY = 11

INADEQUATE = 17

IR = 21

Long_2D = 19

Mass = 20

NOESY = 7

Near_2D = 18

ROESY = 8

STD = 1

TOCSY = 6

UV = 22

Undef = 0

property nucleus: NuclType

Returns:: The nucleus of the spectrum.
Return type:: Molecule.Atom.NuclType

property origin: int

Returns:: The origin of the spectrum.
Return type:: int

property shifts: List

Returns:: The chemical shifts of the spectrum.
Return type:: Shift.List of Molecule.Spectrum.Shift

Example Usage:

import beautifuljason as bjason

# It is assumed that the 'example.jjh5' document contains a molecule.
with bjason.Document('example.jjh5', mode='r') as doc:
    for pred_spec in doc.mol_data[0].spectra:
        print(f'Nucleus: {pred_spec.nucleus.name}')
        for shift in pred_spec.shifts:
            print(f'  Atoms: {shift.nums}, Shift: {shift.value[0]} ppm')

property spec_type: Type

Returns:: The type of the spectrum.
Return type:: Type

class Symmetry(h5_group)

Bases: H5Group

Represents atom symmetry.

property items: Iterable[int]

Returns:: The symmetry items.
Return type:: Iterable of int

property atoms: List

Returns:: The atoms of the molecule.
Return type:: Atom.List of Molecule.Atom

property couplings: List

Returns:: The j-couplings of the molecule.
Return type:: Coupling.List of Molecule.Coupling

property rings: List

Returns:: The rings of the molecule.
Return type:: Ring.List of Molecule.Ring

property spectra: List

Returns:: The prediction spectra of the molecule.
Return type:: Spectrum.List of Molecule.Spectrum

Example Usage:

import beautifuljason as bjason

# It is assumed that the 'example.jjh5' document contains a molecule.
with bjason.Document('example.jjh5', mode='r') as doc:
    for pred_spec in doc.mol_data[0].spectra:
        print(f'Nucleus: {pred_spec.nucleus.name}')
        for shift in pred_spec.shifts:
            print(f'  Atoms: {shift.nums}, Shift: {shift.value[0]} ppm')

property symmetry: Symmetry

Returns:: The symmetry of the molecule.
Return type:: Symmetry

class beautifuljason.data.NMREntry(h5_group)

Bases: H5Group

Represents an NMR entry encapsulated within an HDF5 group.

Parameters:: h5_group (h5py.Group) – The actual HDF5 group object.

property ndim

Retrieve the number of dimensions for the NMR data. Provided for convenience, as the value is not directly available in the HDF5 group.

Returns:: Number of dimensions for the NMR data.
Return type:: int

class beautifuljason.data.NMRMultiplet(h5_group)

Bases: IDedObject

Represents an NMR multiplet stored within an HDF5 group.

Parameters:: h5_group (h5py.Group) – The actual HDF5 group object.

class List(h5_group)

Bases: IDedObject, GroupList

Represents a list of NMR multiplets.

Parameters:: h5_group (h5py.Group) – The actual HDF5 group object.

property auto_baseline

Returns:: True if the baseline is automatically calculated, otherwise False.
Return type:: bool

property integral_lvl

Returns:: integral level of the multiplets.
Return type:: float

property integral_scale

Returns:: integral scale of the multiplets.
Return type:: float

property integral_scale_scoped

Returns:: array of scoped integral scales of the multiplets.
Return type:: numpy.ndarray of numpy.float64 or None

property integral_tlt

Returns:: integral tilt of the multiplets.
Return type:: float

property integral_total

Returns:: total integral of the multiplets.
Return type:: float

property integral_vscale

Returns:: integral vertical scale of the multiplets.
Return type:: float

property integral_vshift

Returns:: integral vertical shift of the multiplets.
Return type:: float

property pos_units

Returns:: A tuple of position units.
Return type:: tuple of Units

class ShowType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Enumeration representing the types of display for the multiplet.

Integral = 1

Multiplet = 0

_get_peaks(attr_name) → list[NMRPeak]

Parameters:: attr_name (str) – The name of the attribute to retrieve the peaks from.
Returns:: The peaks associated with the attribute.
Return type:: list of NMRPeak

property all_peaks: list[NMRPeak]

Returns:: All peaks found within the multiplet region, including those not associated with the multiplet.
Return type:: list of NMRPeak

property curve: ndarray[float64]

Returns:: The curve data for the multiplet.
Return type:: numpy.ndarray with dtype numpy.float64

property flags: int32

Returns:: The flags associated with the multiplet.
Return type:: int

property integral_scope: int32

Returns:: The scope for the integral. Defaults to 0 if not specified in the HDF5 group.
Return type:: numpy.int32

property js: ndarray[float64]

Returns:: The J values for the multiplet. If not present, returns an empty array.
Return type:: numpy.ndarray with dtype numpy.float64

property jtree

Returns:: The J coupling tree data, represented as a list of dictionaries with ‘groups’ and ‘positions’ as keys.
Return type:: list of dict with keys ‘groups’ and ‘positions’

property moments: ndarray[float64]

Returns:: The moments associated with the multiplet.
Return type:: numpy.ndarray with dtype numpy.float64

property multiplets

Returns:: The associated list of multiplets.
Return type:: NMRMultiplet.List or None if not present.

property multiplicities: ndarray[int32]

Returns:: The multiplicities for the multiplet. If not present, returns an empty array.
Return type:: numpy.ndarray with dtype numpy.int32

property multiplicities_str: str | None

Returns:: The multiplicities for the multiplet as a string.
Return type:: str or None if not present.

property normalized_value

Returns:: The normalized value of the multiplet.
Return type:: numpy.float64

property peaks: list[NMRPeak]

Returns:: The peaks associated with the multiplet.
Return type:: list of NMRPeak

Example Usage:

import beautifuljason as bjason

# It is assumed that the 'example.jjh5' document contains a spectrum with multiplets.
with bjason.Document('example.jjh5', mode='r') as doc:
    for multiplet in doc.nmr_data[0].multiplets:
        print(f'Pos: {multiplet.pos[0]}, Sum Integral: {multiplet.value_hz}')
        for peak in multiplet.peaks:
            print(f'  Peak Pos: {peak.pos[0]}, Area: {peak.area}')

property pos: ndarray[float64]

Returns:: The position of the multiplet.
Return type:: numpy.ndarray of shape (3,) with dtype numpy.float64

property range: tuple[ndarray, ndarray, ndarray]

Returns:: The multiplet range as a tuple of np.array objects.
Return type:: tuple of shape (3,) of numpy.ndarray with dtype numpy.float64

property show_type: ShowType

Returns:: The display type of the multiplet.
Return type:: ShowType

property value

Returns:: The value of the multiplet.
Return type:: numpy.float64

property value_hz

Returns:: The value in Hertz (Hz) of the multiplet.
Return type:: numpy.float64

property value_hz_factor

Returns:: The factor to convert the value to Hertz (Hz). Defaults to 1.0 if not specified in the HDF5 group.
Return type:: numpy.float64

class beautifuljason.data.NMRPeak(h5_group)

Bases: IDedObject

Represents an NMR peak stored within an HDF5 group.

Parameters:: h5_group (h5py.Group) – The actual HDF5 group object.

class List(h5_group)

Bases: IDedObject, GroupList

Represents a list of NMR peaks.

Parameters:: h5_group (h5py.Group) – The actual HDF5 group object.

property pos_units: tuple[Units, Units, Units]

Returns the position units of the peaks.

Returns:: A tuple of position units.
Return type:: tuple of base.Units

class PeakClassification(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Enumeration representing the classifications of peaks.

C13Satellite = 4

Compound = 0

Contaminant = 1

NMRSolvent = 2

ReactionSolvent = 3

SSSideband = 5

class PeakType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Enumeration representing the types of peaks.

GenLorentz = 1

PseudoVoigt = 0

property area: float64

New in version 1.0.4.

Returns:: The area of the peak.
Return type:: numpy.float64

Note

Requires JASON 4.1 or later.

property area_sigma: float64

New in version 1.0.4.

Returns:: The area sigma of the peak.
Return type:: numpy.float64

Note

Requires JASON 4.1 or later.

property classification: PeakClassification

The classification of the peak.

Getter:: Returns the classification of the peak.
Return type:: PeakClassification
Setter:: Sets the classification of the peak.
Parameters:: new_classification (PeakClassification) – The new classification of the peak.

property height: float64

Returns:: The height of the peak.
Return type:: numpy.float64

property label

The label of the peak.

Getter:: Returns the label of the peak.
Return type:: str
Setter:: Sets the label of the peak.
Parameters:: new_label (str) – The new label of the peak.

property offset: float64

Returns:: The offset of the peak.
Return type:: numpy.float64

property pos: ndarray[float64]

Returns:: The position of the peak.
Return type:: numpy.ndarray of shape (3,) with dtype numpy.float64

property shape_par: ndarray[float64]

Returns:: The shape parameter of the peak.
Return type:: numpy.ndarray of shape (3,) with dtype numpy.float64

property type

Returns:: The type of the peak.
Return type:: PeakType

property width: ndarray[float64]

Returns:: The width of the peak.
Return type:: numpy.ndarray of shape (3,) with dtype numpy.float64

class beautifuljason.data.NMRProcessing(h5_group)

Bases: IDedObject

Represents an NMR processing step stored within an HDF5 group.

Parameters:: h5_group – The actual HDF5 group object.

class List(h5_group)

Bases: GroupList

Represents a list of NMR processing steps.

Parameters:: h5_group – The actual HDF5 group object.

class EndType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Enumeration representing the types of endpoints.

Full = 0

Orig = 1

postFT = 3

preFT = 2

property end_point_dim: int32

Returns:: The dimension of the endpoint.
Return type:: numpy.int32

property end_point_type: EndType

Returns:: The type of endpoint.
Return type:: EndType

class Parameter(h5_group)

Bases: H5Group

Represents a parameter for an NMR processing step.

class List(h5_group)

Bases: GroupList

Represents a list of parameters for an NMR processing step.

property current_index: int32 | None

Returns:: The current index for the parameter.
Return type:: numpy.int32 or None if not present.

property decimals: int32 | None

Returns:: The number of decimals for the parameter.
Return type:: numpy.int32 or None if not present.

property max_value: Any | None

Returns:: The maximum value for the parameter.
Return type:: Any or None if not present.

property min_value: Any | None

Returns:: The minimum value for the parameter.
Return type:: Any or None if not present.

property name: str

Returns:: The name of the parameter.
Return type:: str

property step: float64 | None

Returns:: The step size for the parameter.
Return type:: numpy.float64 or None if not present.

property tip: str

Returns:: The tip for the parameter.
Return type:: str

property units: Units

Returns:: The units for the parameter.
Return type:: base.Units

property value: Any

Returns:: The value of the parameter.
Return type:: Any

property value_type: QMetaType_Type

Returns:: The type of the parameter.
Return type:: base.QMetaType_Type

class Type(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: IntEnum

Enumeration representing the types of processing steps.

ATD = 33

Abs = 8

Apodize = 2

CSSF = 19

Compress = 37

Cov = 41

Custom = 39

DC = 26

DOSY = 24

DTA = 25

DcFID = 40

DownSample = 45

External = 14

FT = 4

Fiddle = 38

Filter = 32

Flatten = 12

Lp = 3

NUS = 15

NextDim = 9

NoiseGen = 34

Normalize = 42

PeakRef = 29

Phase = 6

PhaseFID = 23

PolyBC = 11

PrepIndir = 5

ROSY = 36

ReSample = 35

Real = 13

Reverse = 7

Rot = 21

Round = 44

SGFilter2D = 18

SGSmooth = 10

Scale = 27

Shear = 46

Sim = 20

Sub = 17

Sum = 28

Sym = 16

T1Sup = 30

Tilt = 47

Unknown = 0

ZF = 1

bLP = 43

fLP = 31

iFT = 22

property active: bool

Returns:: True if the processing step is active, otherwise False.
Return type:: bool

property name: str

Returns:: The name of the processing step.
Return type:: str

property parameters: List

New in version 1.1.0.

Returns:: The list of parameters for the processing step.
Return type:: Parameter.List

property type: Type

Returns:: The type of the processing step.
Return type:: Type

class beautifuljason.data.NMRSpecInfo(h5_group, ndim)

Bases: H5Group

Represents spectral information for an NMR dataset encapsulated within an HDF5 group.

Parameters:

h5_group (h5py.Group) – The actual HDF5 group object.
ndim (int) – The number of dimensions for the NMR data.

get_orig_param(group_name, param_name)

Retrieve an original parameter value from a specified group within the OriginalParameters section of the HDF5 group. Original parameters are values imported directly from the original dataset without modification. For some vendors, parameters may include attributes written using the syntax param_name.attr_name. For example, the JEOL Delta X_FREQ parameter also includes X_FREQ.unts and X_FREQ.unts.str attributes.

Parameters:

group_name (str) – Name of the group under ‘OriginalParameters’ to search in.
param_name (str) – Name of the parameter to retrieve.

Returns:

Value of the specified parameter if found; None otherwise.

Return type:

Any or None

Example Usage

import beautifuljason as bjason

def extract_metadata(jdf_file: str) -> dict:
    jason = bjason.JASON()
    with jason.create_document(jdf_file) as doc:
        raw_spec_info = doc.nmr_data[0].raw_data.spec_info

        # Extract example metadata
        metadata = {
            "X_SWEEP": raw_spec_info.get_orig_param("parameters", "X_SWEEP"),
            "X_FREQ": raw_spec_info.get_orig_param("parameters", "X_FREQ")
        }

    return metadata

get_param(param_name)

Retrieve a parameter value from the HDF5 group.

Unlike original parameters (see get_orig_param()), these parameters are part of a predefined set that is populated using vendor data.

Parameters:: param_name (str) – Name of the parameter to retrieve.
Returns:: Value of the specified parameter if found; None otherwise.
Return type:: Any or None

Example Usage

import beautifuljason as bjason

def extract_metadata(jdf_file: str) -> dict:
    jason = bjason.JASON()
    with jason.create_document(jdf_file) as doc:
        raw_spec_info = doc.nmr_data[0].raw_data.spec_info

        # Extract example metadata
        metadata = {
            "Title": bjason.utils.ensure_str(raw_spec_info.get_param("Title")),
            "Solvent": bjason.utils.ensure_str(raw_spec_info.get_param("Solvent")),
            "Temperature": raw_spec_info.get_param("Temperature")
        }

    return metadata

property nuclides

Retrieve the nuclide information for each dimension of the NMR data. Provided for convenience, as the value is not readily accessible in the HDF5 group.

Returns:: A tuple of nuclide strings for each dimension.
Return type:: tuple

class beautifuljason.data.NMRSpectrum(h5_group)

Bases: NMREntry, IDedObject

Represents an NMR spectrum stored within an HDF5 group.

Parameters:: h5_group – The actual HDF5 group object.

class List(h5_group)

Bases: GroupList

Represents a list of NMR spectra.

Parameters:: h5_group – The actual HDF5 group object.

property multiplets: List

Returns:: The associated list of multiplets.
Return type:: NMRMultiplet.List of NMRMultiplet.

Example Usage:

import beautifuljason as bjason

# It is assumed that the 'example.jjh5' document contains a spectrum with multiplets.
with bjason.Document('example.jjh5', mode='r') as doc:
    for multiplet in doc.nmr_data[0].multiplets:
        print(f'Pos: {multiplet.pos[0]}, Sum Integral: {multiplet.value_hz}')

property peaks: List

Returns:: The associated list of peaks.
Return type:: NMRPeak.List of NMRPeak.

Example Usage:

import beautifuljason as bjason

# It is assumed that the 'example.jjh5' document contains a spectrum with peaks.
with bjason.Document('example.jjh5', mode='r') as doc:
    for peak in doc.nmr_data[0].peaks:
        print(f'Pos: {peak.pos[0]}, Area: {peak.area}')

property proc_list: List

Returns:: The associated list of processing steps.
Return type:: NMRProcessing.List of NMRProcessing.

Example Usage:

import beautifuljason as bjason

# It is assumed that the 'example.jjh5' document contains a spectrum.
with bjason.Document('example.jjh5', mode='r') as doc:
    for proc in doc.nmr_data[0].proc_list:
        print(f'Name: {proc.name}')
        for param in proc.parameters:
            print(f'  {param.name}({param.tip}): {param.value}')

class beautifuljason.data.Text(h5_group)

Bases: IDedObject

Represents a text data object located at /JasonDocument/General/TextDocuments/<N>.

The text is stored as an HTML string.

class List(h5_group)

Bases: GroupList

Represents a list of text data objects

property html: str

The HTML text.

Getter:: Returns the HTML text.
Return type:: str
Setter:: Sets the HTML text.
Parameters:: new_html (str) – The new HTML text.