shnitsel.core.geom

This module will contain two types of closely-related functionality: - generic geometry functions - functions that use RDKit to identify internal coordinates, and then the above to calculate the values Currently, the first category of function is found under postprocess

Functions

bond_type_to_symbols(e1, e2)

identify_bonds(mol[, symbols])

get_bond_lengths(atXYZ[, bond_types, mol])

identify_angles(mol)

get_bond_angles(atXYZ[, angle_types, mol, deg])

identify_torsions(mol)

Finds sets of four contiguous atoms that form a torsion

get_bond_torsions(atXYZ[, quadruple_types, mol, ...])

get_bats(atXYZ[, mol, signed, deg])

Get bond lengths, angles and torsions.

center_geoms(atXYZ[, by_mass])

kabsch(atXYZ[, reference_or_indexers])

Module Contents

bond_type_to_symbols(e1, e2)
identify_bonds(mol, symbols=True)
get_bond_lengths(atXYZ, bond_types=None, mol=None)
identify_angles(mol)
Parameters:

mol (rdkit.Chem.Mol)

get_bond_angles(atXYZ, angle_types=None, mol=None, deg=False)
identify_torsions(mol)

Finds sets of four contiguous atoms that form a torsion

Parameters:

mol (rdkit.Chem.Mol)

Return type:

xarray.Dataset

get_bond_torsions(atXYZ, quadruple_types=None, mol=None, signed=False, deg=False)
get_bats(atXYZ, mol=None, signed=False, deg=False)

Get bond lengths, angles and torsions.

Parameters:

  • atXYZ – The coordinates to use.

  • mol – An rdkit Mol object used to determine connectivity; by default this is determined automatically based on the first frame of atXYZ.

  • optional – An rdkit Mol object used to determine connectivity; by default this is determined automatically based on the first frame of atXYZ.

Return type:

An xarray.DataArray containing bond lengths, angles and tensions.

Examples

>>> import shnitsel as st
>>> from shnitsel.core import geom
>>> frames = st.open_frames('/tmp/A03_filtered.nc')
>>> geom.get_bats(frames['atXYZ'])
center_geoms(atXYZ, by_mass=False)
Parameters:

by_mass (Literal[False])

kabsch(atXYZ, reference_or_indexers=None, **indexers_kwargs)
Parameters:

reference_or_indexers (xarray.DataArray | dict | None)