soprano.properties.nmr.isc

Implementation of AtomsProperties that relate to NMR J couplings

Classes

ISCDiagonal([name])	Produces an array containing eigenvalues and eigenvectors for the symmetric part of each J coupling tensor in the system.
JCAnisotropy([name])	Produces a dictionary of J coupling anisotropies for atom pairs in the system.
JCAsymmetry([name])	Produces a dictionary of J coupling asymmetries for atom pairs in the system.
JCDiagonal([name])	Produces a dictionary of diagonalised J coupling tensors for atom pairs in the system.
JCIsotropy([name])	Produces a dictionary of J coupling isotropies for atom pairs in the system.
JCQuaternion([name])	Produces a dictionary of J ase.Quaternion objects expressing the orientation of the J coupling tensors with respect to the cartesian axes for atom pairs in the system.
JCReducedAnisotropy([name])	Produces a dictionary of J coupling reduced anisotropies for atom pairs in the system.
JCSkew([name])	Produces a dictionary of J coupling skews for atom pairs in the system.
JCSpan([name])	Produces a dictionary of J coupling spans for atom pairs in the system.

class soprano.properties.nmr.isc.ISCDiagonal(name=None, **params)

Bases: AtomsProperty

Produces an array containing eigenvalues and eigenvectors for the symmetric part of each J coupling tensor in the system. By default saves them as part of the Atoms’ arrays as well. Requires the Atoms object to have been loaded from a .magres file containing the relevant information.

Parameters:

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• save_info (bool) – if True, save the diagonalised tensors in the Atoms object as info. By default True.

Returns:

dictionary of eigenvalues and eigenvectors by atom

index pairs (lower index first)

Return type:

isc_diag (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCAnisotropy(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J coupling anisotropies for atom pairs in the system. See JCDiagonal for how reduced couplings are transformed into couplings.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair, in Hz.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCAsymmetry(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J coupling asymmetries for atom pairs in the system. See JCDiagonal for how reduced couplings are transformed into couplings.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair, in Hz.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCDiagonal(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of diagonalised J coupling tensors for atom pairs in the system. The J coupling for a pair of nuclei i and j is defined as:

\[J_{ij} = 10^{19}\frac{h\gamma_i\gamma_j}{4\pi^2}K\]

where the gammas represent the gyromagnetic ratios of the nuclei and K is the J coupling reduced tensor found in a .magres file, in \(10^{19} T^2 J^{-1}\).

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCIsotropy(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J coupling isotropies for atom pairs in the system. See JCDiagonal for how reduced couplings are transformed into couplings.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair, in Hz.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCQuaternion(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J ase.Quaternion objects expressing the orientation of the J coupling tensors with respect to the cartesian axes for atom pairs in the system. Requires the Atoms object to have been loaded from a .magres file containing the relevant information.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of coupling quaternions by atomic index pair, in Hz.

Return type:

quat_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCReducedAnisotropy(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J coupling reduced anisotropies for atom pairs in the system. See JCDiagonal for how reduced couplings are transformed into couplings.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair, in Hz.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCSkew(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J coupling skews for atom pairs in the system. See JCDiagonal for how reduced couplings are transformed into couplings.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair, in Hz.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

class soprano.properties.nmr.isc.JCSpan(name=None, **params)

Bases: AtomsProperty

Produces a dictionary of J coupling spans for atom pairs in the system. See JCDiagonal for how reduced couplings are transformed into couplings.

Parameters:

• sel_i (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling. By default is None (= all of them).

• sel_j (AtomSelection or [int]) – Selection or list of indices of atoms for which to return the J coupling with the ones in sel_i. By default is None (= same as sel_i).

• tag (str) – name of the J coupling component to return. Magres files usually contain isc, isc_spin, isc_fc, isc_orbital_p and isc_orbital_d. Default is isc.

• isotopes (dict) – dictionary of specific isotopes to use, by element symbol. If the isotope doesn’t exist an error will be raised.

• isotope_list (list) – list of isotopes, atom-by-atom. To be used if different atoms of the same element are supposed to be of different isotopes. Where a ‘None’ is present will fall back on the previous definitions. Where an isotope is present it overrides everything else.

• self_coupling (bool) – if True, include coupling of a nucleus with itself. Otherwise excluded. Default is False.

• force_recalc (bool) – if True, always diagonalise the tensors even if already present. Default is False.

Returns:

Dictionary of couplings by atomic index pair, in Hz.

Return type:

dip_dict (dict)

Initialize an AtomsProperty and set its parameters. The AtomsProperty instance can then be called with a structure as its only argument to get the property with the given parameters.

Args:

name (str): a name to give to this specific instance of the

property (will be used to store it as array if

requested)

params: named arguments specific to this type of property

__call__(s, store_array=False)

Calling the AtomsProperty returns the value of the property as extracted with the parameters of this specific instance.

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the given name for this instance

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed

static extract(s, *args, **kwargs)

Extract the given property with given parameters from an Atoms object.

Args:

s (ase.Atoms): the structure from which to extract the property

params: named arguments specific to this type of property

Returns:

property: the value of the property for the given structure and

parameters

classmethod get(s, store_array=False, **kwargs)

Extract the given property using the default parameters on an Atoms object s

Args:

s (ase.Atoms or AtomsCollection): the structure or collection

from which to extract the

property

store_array (bool): if s is a collection, whether to store the

resulting data as an array in the collection

using the default name for this property

Returns:

property: the value of the property for the given structure or

a list of values if a collection has been passed