syndirella.slipper.flatness

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

`_flat`
`_empty_results`

Functions

`check_flatness`(→ dict[str, Any])	Check whether substructures of molecule are flat.
`_get_distances_to_plane`(→ numpy.ndarray)	Get distances of points X to their common plane.
`_get_coords`(→ numpy.ndarray)

Module Contents

syndirella.slipper.flatness._flat[source]

syndirella.slipper.flatness._empty_results[source]

syndirella.slipper.flatness.check_flatness(mol_pred: rdkit.Chem.rdchem.Mol, threshold_flatness: float = 0.1, flat_systems: dict[str, str] = _flat) → dict[str, Any][source]

Check whether substructures of molecule are flat.

Parameters:

mol_pred – Molecule with exactly one conformer.
threshold_flatness – Maximum distance from shared plane used as cutoff. Defaults to 0.1.
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.

syndirella.slipper.flatness._get_distances_to_plane(X: numpy.ndarray) → numpy.ndarray[source]: Get distances of points X to their common plane.

syndirella.slipper.flatness._get_coords(mol: rdkit.Chem.rdchem.Mol, indices: Iterable[int]) → numpy.ndarray[source]