MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
https://mdanalysis.org
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Can no longer create dummy universe with new guesser #4750

Closed IAlibay closed 4 weeks ago

IAlibay commented 1 month ago

Related to #4748

The following worked before we introduced the new guesser API:

import MDAnalysis as mda
import numpy as np

a = np.array([
    [0., 0., 150.], [0., 0., 150.], [200., 0., 150.],
    [0., 0., 150.], [100., 100., 150.], [200., 100., 150.],
    [0., 200., 150.], [100., 200., 150.], [200., 200., 150.]
])

u = mda.Universe(a, n_atoms=9)

However, as of the new guesser API, this will fail with due to a lack of atom names.