soprano.properties.transform.transform

Implementation of AtomsProperties that transform the instance in some way

Classes

Mirror([name])	Returns an Atoms object with some or all the atoms reflected with either a given center or a given plane.
Rotate([name])	Returns an Atoms object with some or all the atoms rotated by a given quaternion and with a given center.
Translate([name])	Returns an Atoms object with some or all the atoms translated by a given vector.

class soprano.properties.transform.transform.Mirror(name=None, **params)

Bases: AtomsProperty

Returns an Atoms object with some or all the atoms reflected with either a given center or a given plane. Absolute or scaled coordinates may be used.

Parameters:

selection (AtomSelection): selection object defining which atoms to

act on. By default, all of them.

center ([float]*3): center around which the reflection should take

place. By default the origin of the axes. Can’t be

present at the same time as plane.

plane ([float]*4): plane with respect to which the reflection should

take place, in the form [a, b, c, d] parameters of

the plane equation.

By default is not used. Can’t be present at the

same time as center.

scaled (bool): if True, treat the input vector as expressed in scaled,

not absolute, coordinates.

Returns:

reflected (ase.Atoms): Atoms object with the reflection performed.

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, selection=None)

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

selection (str): a selection string to filter the atoms or AtomSelection

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, selection, **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, selection=None, **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

selection (str): a selection string to filter the atoms or AtomSelection

Returns:

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

a list of values if a collection has been passed

mean(s, axis=None, weights=None, **kwargs)

Compute the mean of the property over a list of structures.

The default behaviours are: - For a list of scalars, compute the mean along the specified axis. - For a list of dictionaries, compute the mean for each key across all dictionaries. - For a list of NMRTensor objects, compute the mean using the NMRTensor.mean method. - For a list of arrays, convert to numpy array and then compute the mean along the specified axis.

Parameters:

• s (list[ase.Atoms] | AtomsCollection) – The structure or collection from which to extract the property.

• axis (int | None) – Axis along which the means are computed. If None, compute the mean of scalars.

• weights (np.ndarray | None) – An array of weights associated with the values. If specified, the weighted average will be computed. Must have the same shape as the property values.

• **kwargs – Additional arguments passed to the property’s get method.

Returns:

The mean value of the property for the given structures.

Return type:

dict | float | np.ndarray | NMRTensor

Raises:

• ValueError – If s is not a collection/list, if property values are None, or if there’s an incompatible shape for computing the mean.

• TypeError – If the property values are of a type that cannot be averaged.

class soprano.properties.transform.transform.Rotate(name=None, **params)

Bases: AtomsProperty

Returns an Atoms object with some or all the atoms rotated by a given quaternion and with a given center. Absolute or scaled coordinates may be used.

Parameters:

selection (AtomSelection): selection object defining which atoms to

act on. By default, all of them.

center ([float]*3): center around which the rotation should take

place. By default the origin of the axes.

quaternion (ase.quaternions.Quaternion): quaternion expressing the

rotation that should be

applied.

scaled (bool): if True, treat the input vector as expressed in scaled,

not absolute, coordinates.

periodic (bool): if True, always rotate each atom around the minimum

periodic image of the rotation center.

Returns:

rotated (ase.Atoms): Atoms object with the rotation performed.

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, selection=None)

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

selection (str): a selection string to filter the atoms or AtomSelection

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, selection, **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, selection=None, **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

selection (str): a selection string to filter the atoms or AtomSelection

Returns:

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

a list of values if a collection has been passed

mean(s, axis=None, weights=None, **kwargs)

Compute the mean of the property over a list of structures.

The default behaviours are: - For a list of scalars, compute the mean along the specified axis. - For a list of dictionaries, compute the mean for each key across all dictionaries. - For a list of NMRTensor objects, compute the mean using the NMRTensor.mean method. - For a list of arrays, convert to numpy array and then compute the mean along the specified axis.

Parameters:

• s (list[ase.Atoms] | AtomsCollection) – The structure or collection from which to extract the property.

• axis (int | None) – Axis along which the means are computed. If None, compute the mean of scalars.

• weights (np.ndarray | None) – An array of weights associated with the values. If specified, the weighted average will be computed. Must have the same shape as the property values.

• **kwargs – Additional arguments passed to the property’s get method.

Returns:

The mean value of the property for the given structures.

Return type:

dict | float | np.ndarray | NMRTensor

Raises:

• ValueError – If s is not a collection/list, if property values are None, or if there’s an incompatible shape for computing the mean.

• TypeError – If the property values are of a type that cannot be averaged.

class soprano.properties.transform.transform.Translate(name=None, **params)

Bases: AtomsProperty

Returns an Atoms object with some or all the atoms translated by a given vector. Absolute or scaled coordinates may be used.

Parameters:

selection (AtomSelection): selection object defining which atoms to

act on. By default, all of them.

vector ([float]*3): vector by which to translate the atoms.

scaled (bool): if True, treat the input vector as expressed in scaled,

not absolute, coordinates.

Returns:

translated (ase.Atoms): Atoms object with the translation performed.

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, selection=None)

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

selection (str): a selection string to filter the atoms or AtomSelection

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, selection, **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, selection=None, **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

selection (str): a selection string to filter the atoms or AtomSelection

Returns:

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

a list of values if a collection has been passed

mean(s, axis=None, weights=None, **kwargs)

Compute the mean of the property over a list of structures.

The default behaviours are: - For a list of scalars, compute the mean along the specified axis. - For a list of dictionaries, compute the mean for each key across all dictionaries. - For a list of NMRTensor objects, compute the mean using the NMRTensor.mean method. - For a list of arrays, convert to numpy array and then compute the mean along the specified axis.

Parameters:

• s (list[ase.Atoms] | AtomsCollection) – The structure or collection from which to extract the property.

• axis (int | None) – Axis along which the means are computed. If None, compute the mean of scalars.

• weights (np.ndarray | None) – An array of weights associated with the values. If specified, the weighted average will be computed. Must have the same shape as the property values.

• **kwargs – Additional arguments passed to the property’s get method.

Returns:

The mean value of the property for the given structures.

Return type:

dict | float | np.ndarray | NMRTensor

Raises:

• ValueError – If s is not a collection/list, if property values are None, or if there’s an incompatible shape for computing the mean.

• TypeError – If the property values are of a type that cannot be averaged.