shnitsel.data.tree.compound
===========================

.. py:module:: shnitsel.data.tree.compound


Attributes
----------

.. autoapisummary::

   shnitsel.data.tree.compound.DataType
   shnitsel.data.tree.compound.ResType
   shnitsel.data.tree.compound.NewChildType


Classes
-------

.. autoapisummary::

   shnitsel.data.tree.compound.CompoundInfo
   shnitsel.data.tree.compound.CompoundGroup


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

.. py:data:: DataType

.. py:data:: ResType

.. py:data:: NewChildType

.. py:class:: CompoundInfo

   Class to hold identifying and auxiliary info of a compound type in ShnitselDB


   .. py:attribute:: compound_name
      :type:  str
      :value: 'unknown'



   .. py:attribute:: compound_smiles
      :type:  str | None
      :value: None



.. py:class:: CompoundGroup(*, name = None, compound_info = None, group_info = None, children = None, level_name = None, attrs = None, **kwargs)

   Bases: :py:obj:`Generic`\ [\ :py:obj:`DataType`\ ], :py:obj:`shnitsel.data.tree.data_group.DataGroup`\ [\ :py:obj:`DataType`\ ]


   DataTree node to keep track of all data associated with a common compound within the datatree


   .. py:attribute:: _compound_info
      :type:  CompoundInfo


   .. py:method:: construct_copy(children: Mapping[Hashable, DataGroup[DataType]|DataLeaf[DataType]] | None = None, dtype: None = None, data: DataType | None = None, **kwargs) -> Self
                  construct_copy(children: None = None, dtype: type[ResType] | types.UnionType | None = None, data: ResType | None = None, **kwargs) -> CompoundGroup[ResType]
                  construct_copy(children: Mapping[Hashable, NewChildType] | None = None, dtype: type[ResType] | types.UnionType | None = None, data: None = None, **kwargs) -> CompoundGroup[ResType]

      Helper function to create a copy of this tree structure, but with potential changes to metadata, data or children

      Parameters:
      -----------
      data: None, optional
          Data setting not supported on this type of node.
      children: Mapping[Hashable, CompoundGroup[ResType]], optional
          The mapping of children with a potentially new `DataType`. If not provided, will be copied from the current node's child nodes.
      dtype: type[ResType] | TypeForm[ResType], optional
          The data type of the data in the copy constructed tree.

      :raises AssertionError: If dtype is provided but children parameter not set and node has children, indicating an issue with a type update without setting the new children
      :raises Returns::
      :raises -----------: Self: A copy of this node with recursively copied children if `children` is not set with an appropriate mapping.



   .. py:property:: compound_info
      :type: CompoundInfo


      Get the stored compound info of this Compound group.

      :returns: The metadata for the compound in this compound group
      :rtype: CompoundInfo


   .. py:method:: add_data_group(group_info, filter_func_data = None, flatten_data=False, **kwargs)

      Function to add trajectories within this compound subtree to a `TrajectoryGroup` of trajectories.

      The `group_name` will be set as the name of the group in the tree.
      If `flatten_trajectories=True` all existing groups will be dissolved before filtering and the children will be turned into an ungrouped list of trajectories.
      The `filter_func_trajectories` will either be applied to only the current groups and trajectories immediately beneath this compound or to the flattened list of all child directories.

      :param group_name: The name to be set for the TrajectoryGroup object
      :type group_name: str
      :param filter_func_Trajectories: A function to return true for Groups and individual trajectories that should be added to the new group. Defaults to None.
      :type filter_func_Trajectories: Callable[[Trajectory|GroupInfo], bool] | None, optional
      :param flatten_trajectories: A flag whether all descendant groups should be dissolved and flattened into a list of trajectories first before applying a group. Defaults to False.
      :type flatten_trajectories: bool, optional

      :returns: The restructured Compound with a new added group if at least one trajectory has satisfied the filter condition.
      :rtype: CompoundGroup