syndirella.slipper.flatness
===========================

.. py:module:: syndirella.slipper.flatness

.. autoapi-nested-parse::

   slipper/flatness.py

   This module was directly sourced from the PoseBusters repository, which is open source code under the BSD-3-Clause license.
   The original code is found at: https://github.com/maabuu/posebusters/blob/3c467ab82bdbae5b71f80a286bb49ecc011be529/posebusters/modules/flatness.py

   It is used to check flatness of aromatic rings and double bonds of ligand conformations.



Attributes
----------

.. autoapisummary::

   syndirella.slipper.flatness._flat
   syndirella.slipper.flatness._empty_results


Functions
---------

.. autoapisummary::

   syndirella.slipper.flatness.check_flatness
   syndirella.slipper.flatness._get_distances_to_plane
   syndirella.slipper.flatness._get_coords


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

.. py:data:: _flat

.. py:data:: _empty_results

.. py:function:: check_flatness(mol_pred: rdkit.Chem.rdchem.Mol, threshold_flatness: float = 0.1, flat_systems: dict[str, str] = _flat) -> dict[str, Any]

   Check whether substructures of molecule are flat.

   :param mol_pred: Molecule with exactly one conformer.
   :param threshold_flatness: Maximum distance from shared plane used as cutoff. Defaults to 0.1.
   :param flat_systems: Patterns of flat systems provided as SMARTS. Defaults to 5 and 6 membered
                        aromatic rings and carbon sigma bonds.

   :returns: PoseBusters results dictionary.


.. py:function:: _get_distances_to_plane(X: numpy.ndarray) -> numpy.ndarray

   Get distances of points X to their common plane.


.. py:function:: _get_coords(mol: rdkit.Chem.rdchem.Mol, indices: Iterable[int]) -> numpy.ndarray