picometer.atom
==============

.. py:module:: picometer.atom


Attributes
----------

.. autoapisummary::

   picometer.atom.logger
   picometer.atom.group_registry


Classes
-------

.. autoapisummary::

   picometer.atom.Locator
   picometer.atom.AtomSet


Module Contents
---------------

.. py:data:: logger

.. py:class:: Locator

   Bases: :py:obj:`NamedTuple`


   .. py:attribute:: label
      :type:  str


   .. py:attribute:: symm
      :type:  str
      :value: 'x,y,z'



   .. py:attribute:: at
      :type:  Sequence[Locator]
      :value: None



   .. py:method:: from_dict(d: dict) -> Locator
      :classmethod:



   .. py:method:: __bool__()


.. py:data:: group_registry
   :type:  Dict[str, List[Locator]]

.. py:class:: AtomSet(bf: hikari.dataframes.BaseFrame = None, table: pandas.DataFrame = None)

   Bases: :py:obj:`picometer.shapes.Shape`


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


   .. py:attribute:: kind


   .. py:attribute:: base
      :value: None



   .. py:attribute:: table
      :value: None



   .. py:method:: __len__() -> int


   .. py:method:: __add__(other) -> AtomSet


   .. py:method:: __getitem__(item) -> AtomSet


   .. py:method:: from_cif(cif_path: str, block_name: str = None) -> AtomSet
      :classmethod:


      Initialize from cif file using hikari's `BaseFrame` and `CifFrame`



   .. py:property:: fract_xyz
      :type: numpy.ndarray



   .. py:property:: cart_xyz
      :type: numpy.ndarray



   .. py:property:: fract_uij
      :type: numpy.ndarray


      Return a 3D array i.e. stack of 3x3 fract. displacement tensors.


   .. py:method:: fractionalise(cart_xyz: numpy.ndarray) -> numpy.ndarray

      Multiply 3xN vector by crystallographic matrix to get fract coord



   .. py:method:: orthogonalise(fract_xyz: numpy.ndarray) -> numpy.ndarray

      Multiply 3xN vector by crystallographic matrix to get Cart. coord



   .. py:method:: locate(locators: Sequence[Locator]) -> AtomSet

      Convenience method to select multiple fragments from locators
      while interpreting and extending groups if necessary



   .. py:method:: select_atom(label_regex: str) -> AtomSet


   .. py:method:: transform(symm_op_code: str) -> AtomSet


   .. py:property:: u_cartesian_eigenvalues


   .. py:property:: centroid
      :type: numpy.ndarray


      A 3-vector with average atom position.


   .. py:property:: direction
      :type: picometer.shapes.Vector3



   .. py:property:: line
      :type: picometer.shapes.Line


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


   .. py:property:: plane
      :type: picometer.shapes.Plane


      A 3-vector normal to plane that best fits atoms' cartesian coords.
      Based on https://gist.github.com/amroamroamro/1db8d69b4b65e8bc66a6


   .. py:property:: origin
      :type: picometer.shapes.Vector3



   .. py:method:: _angle(*others: picometer.shapes.Shape) -> float


   .. py:method:: _distance(other: picometer.shapes.Shape) -> float


   .. py:method:: dihedral(*others: AtomSet) -> float