[AMBER] Making ParmEd play nice with OpenEye?

From: Brian Radak <brian.radak.gmail.com>
Date: Mon, 11 Nov 2019 10:52:58 -0500

Is there a way (or has anyone tried) to make ParmEd interoperate with
OpenEye Python objects? The two packages are written very differently, so I
wouldn't be surprised if the answer is simple "no" or "not really".

My current workflow starts with a ParmEd AmberParm object:

>>> import parmed as pmd
>>> mol = pmd.load_file(<prmtop>, xyz=<NetCDF file>)

and I would like an OpenEye object for some specific operations (e.g. build
AmberMasks based on some cheminformatics-y calculations). The current hack
is to just write/read a pdb:

>>> mol.save('tmp.pdb') # can preface this with mol.strip() to make the
files small/fast
>>> # read object from file with OpenEye <blah blah>

Can anyone imagine something faster or more elegant here?


Brian Radak, PhD
Senior Investigator
Silicon Therapeutics
AMBER mailing list
Received on Mon Nov 11 2019 - 08:00:03 PST
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