picometer.atom

Attributes

`logger`
`group_registry`

Classes

`Locator`
`AtomSet`	Container class w/ atoms stored in pd.Dataframe & convenience methods

Module Contents

picometer.atom.logger

class picometer.atom.Locator[source]

Bases: NamedTuple

label: str

symm: str = 'x,y,z'

at: Sequence[Locator] = None

classmethod from_dict(d: dict) → Locator[source]

__bool__()[source]

picometer.atom.group_registry: Dict[str, List[Locator]]

class picometer.atom.AtomSet(bf: hikari.dataframes.BaseFrame = None, table: pandas.DataFrame = None)[source]

Bases: picometer.shapes.Shape

Container class w/ atoms stored in pd.Dataframe & convenience methods

kind

base = None

table = None

__len__() → int[source]

__add__(other) → AtomSet[source]

__getitem__(item) → AtomSet[source]

classmethod from_cif(cif_path: str, block_name: str = None) → AtomSet[source]: Initialize from cif file using hikari’s BaseFrame and CifFrame

property fract_xyz: numpy.ndarray

property cart_xyz: numpy.ndarray

property fract_uij: numpy.ndarray: Return a 3D array i.e. stack of 3x3 fract. displacement tensors.

fractionalise(cart_xyz: numpy.ndarray) → numpy.ndarray[source]: Multiply 3xN vector by crystallographic matrix to get fract coord

orthogonalise(fract_xyz: numpy.ndarray) → numpy.ndarray[source]: Multiply 3xN vector by crystallographic matrix to get Cart. coord

locate(locators: Sequence[Locator]) → AtomSet[source]: Convenience method to select multiple fragments from locators while interpreting and extending groups if necessary

select_atom(label_regex: str) → AtomSet[source]

transform(symm_op_code: str) → AtomSet[source]

property u_cartesian_eigenvalues

property centroid: numpy.ndarray: A 3-vector with average atom position.

property direction: picometer.shapes.Vector3

property line: picometer.shapes.Line: A 3-vector describing line that best fits the cartesian coordinates of atoms. Based on https://stackoverflow.com/q/2298390/

property plane: picometer.shapes.Plane: A 3-vector normal to plane that best fits atoms’ cartesian coords. Based on https://gist.github.com/amroamroamro/1db8d69b4b65e8bc66a6

property origin: picometer.shapes.Vector3

_angle(*others: picometer.shapes.Shape) → float[source]

_distance(other: picometer.shapes.Shape) → float[source]

dihedral(*others: AtomSet) → float[source]