Data Structures Module

Module contents

class beautifuljason.data.Image(h5_group)

Bases: IDedObject

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

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 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

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

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

property couplings: List

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

property rings: List

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

property spectra: List

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

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

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

property all_peaks: list[NMRPeak]

Returns:: All peaks 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

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

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

New in version 1.0.4.

Note

Requires JASON 4.1 or later.

property area_sigma: float64

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

New in version 1.0.4.

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.

Abs = 8

Apodize = 2

CSSF = 19

DC = 26

DOSY = 24

DTA = 25

External = 14

FT = 4

Flatten = 12

Lp = 3

NUS = 15

NextDim = 9

PeakRef = 29

Phase = 6

PhaseFID = 23

PolyBC = 11

PrepIndir = 5

Real = 13

Reverse = 7

Rot = 21

SGFilter2D = 18

SGSmooth = 10

Scale = 27

Sim = 20

Sub = 17

Sum = 28

Sym = 16

T1Sup = 30

Unknown = 0

ZF = 1

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 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.

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

get_param(param_name)

Retrieve a parameter value from the HDF5 group.

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

property nuclides

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.

property peaks: List

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

property proc_list: List

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

class beautifuljason.data.Text(h5_group)

Bases: IDedObject

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

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.