polymerist.rdutils.rdcoords.piercing

Methods for detecting ring piercing in molecular conformers

Attributes

N

ring_piercing_idxs

Functions

PINPRICS(→ tuple[tuple[int, int]])

Implements the PINPRICS algorithm (Planar Intersection Nomography for Pierced Ring Identification via Cut Sets)

detect_ring_is_pierced(→ tuple[tuple[int, int]])

Detects and returns all bonded pairs of atoms which pierce a particular ring in a molecule

summarize_ring_piercing(→ dict[tuple[int], ...)

Apply PINPRICS algorithm to all ring detected in a molecule and

Module Contents

polymerist.rdutils.rdcoords.piercing.N
polymerist.rdutils.rdcoords.piercing.PINPRICS(positions: numpy.ndarray[tuple[N, 3], float], bonded_atom_idxs: Sequence[tuple[int, int]], ring_atom_idxs: list[int]) → tuple[tuple[int, int]][source]

Implements the PINPRICS algorithm (Planar Intersection Nomography for Pierced Ring Identification via Cut Sets) Assumes rings is oblate, i.e. faces along the minor axis and is “wider than it is tall”

Parameters:

  • positions (Array[[N, 3], float]) – An array of the 3D coordinates of all atoms in a molecule

  • bonded_atom_idxs (Sequence[tuple[int, int]]) – A sequence of pairs of indices of all bonded atoms in the molecule This represents the topology on the molecules graph

  • ring_atom_idxs (list[int]) – List of indices of the atoms which make up the ring to be tested for piercing Requirement of specifically a list (i.e. not just a Sequence etc.) is to allow for “smart” indexing in numpy

Returns:

piercing_idxs – A tuple of all pairs of atom indices which were perceived to pierce the ring

Return type:

tuple[tuple[int, int]]

polymerist.rdutils.rdcoords.piercing.ring_piercing_idxs
polymerist.rdutils.rdcoords.piercing.detect_ring_is_pierced(mol: rdkit.Chem.Mol, ring_atom_idxs: list[int], conformer_idx: int = 0) → tuple[tuple[int, int]][source]

Detects and returns all bonded pairs of atoms which pierce a particular ring in a molecule

Parameters:

  • mol (Mol) – An RDKit Mol instance assumed to have at least one conformer

  • ring_atom_idxs (list[int]) – List of indices of the atoms which make up the ring to be tested for piercing

  • conformer_idx (int, default 0) – The index of the conformer to draw coordinates from By default, will just take the first conformer

Returns:

piercing_idxs – A tuple of all pairs of atom indices which were perceived to pierce the ring

Return type:

tuple[tuple[int, int]]

polymerist.rdutils.rdcoords.piercing.summarize_ring_piercing(mol: rdkit.Chem.Mol, conformer_idx: int = 0) → dict[tuple[int], tuple[tuple[int, int]]][source]

Apply PINPRICS algorithm to all ring detected in a molecule and provide a summary of which bonds (if any) were detected to be piercing each ring

Parameters:

  • mol (Mol) – An RDKit Mol instance assumed to have at least one conformer

  • conformer_idx (int, default 0) – The index of the conformer to draw coordinates from By default, will just take the first conformer

Returns:

piercing_summary – A dict mapping the indices of the atoms in each ring to a tuple of all pairs of atom indices which were perceived to pierce the ring

Return type:

dict[tuple[int], tuple[tuple[int, int]]]