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guess_bonds which guessing types #2143

PicoCentauri opened this Issue Nov 18, 2018 · 0 comments


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PicoCentauri commented Nov 18, 2018

When you create a universe i.e with

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD
u = mda.Universe(PSF,DCD, guess_bonds=True)

this will fail with an ValueError that the vdw radii for types are not defined. To resolve this one can first guess the types and then run bond guesser again. Maybe an option would be to add an option that the bond guesser can also try to guess the types and/or an option like: u = mda.Universe(PSF,DCD, guess_bonds=True, guess_types=True).

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