narupatools.mdanalysis.utils

Utility methods for dealing with MDAnalysis.

Functions

guess_atomic_number	Get the list of atomic numbers from an MDAnalysis object.
guess_elements	Get the list of atomic symbols from a MDAnalysis object.

narupatools.mdanalysis.utils.guess_atomic_number(group: MDAnalysis.core.groups.AtomGroup) → numpy.ndarray

Get the list of atomic numbers from an MDAnalysis object.

In order, this will try to convert elements, atom names and masses to a list of atomic numbers, skipping if that field is not available.

Parameters

group – AtomGroup to extract atomic numbers from.

Raises

NoDataError – AtomGroup has no elements, atom names or atom masses.

narupatools.mdanalysis.utils.guess_elements(group: MDAnalysis.core.groups.AtomGroup) → numpy.ndarray

Get the list of atomic symbols from a MDAnalysis object.

If the group does not have element information, try converting atom names if present. If these are also not present, try using the atomic masses if available.

Parameters

group – AtomGroup to extract elements from.

Raises

NoDataError – AtomGroup has no elements, atom names or atom masses.