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Issue with AnalysisFromFunction() when reading Amber .nc trajectory files

Open luponzo86 opened this issue 4 years ago • 3 comments

Expected behaviour

reading frames from a trajectory imported by MDAnalysis from a .nc file

Actual behaviour

TypeError: cannot serialize '_io.BufferedReader' object

Code to reproduce the behaviour

import MDAnalysis as mda
u = mda.Universe("example.pdb", "example.nc") 

def test(ag):
    return len(ag)

from pmda.custom import AnalysisFromFunction

analysis = AnalysisFromFunction(
    calc_PLEC_on_frame,
    u, 
    u.atoms, 
).run(n_jobs=3)

Currently version of MDAnalysis:

import MDAnalysis as mda; print(mda.__version__) 0.20.1

import pmda; print(pmda.__version__) 0.3.0

import dask; print(dask.__version__) 2.9.2

luponzo86 avatar Jun 02 '20 22:06 luponzo86