AtomGroup not found

[Pallavi Banerjee]

Hi everyone,

I need to use an old version of MDAnalysis, that is, v-1.1.1. However, I get the following error: 

AttributeError: 'module' object has no attribute 'AtomGroup'

Could someone tell me which was the earliest version of MDAnalysis to include 'AtomGroup' ?

Thanks!

Best,

Pallavi

[Irfan Alibay]

Hi,

v1.1.1 definitely uses AtomGroup objects. It's hard to tell what is happening here, could you paste the code you are trying to use?

Many thanks,

Irfan

[Pallavi Banerjee]

Hi Irfan, 

Thanks for the clarification! Here is a snippet of the code that the error points to :

def ReadInTrajectory(nucleotides, universe, PARMS):

    TimeTable = {}

    for nuc in nucleotides:

        segid = nuc.get_segid().strip()

        resname = nuc.get_resname().strip()

        rnum = str(nuc.get_id()[1])

        for at in nuc:

            atname = at.get_id()

            full_id = at.get_full_id()

            desc = exact_description(at, rnum, segid, resname, atname)

            atoms = universe.select_atoms(desc)

            if len(atoms) == 0:

                desc = "resid "+rnum

                tmp = [n for n in universe.select_atoms(desc)

                       if (n.name == atname) and (n.resname == resname)]

                atoms = MDAnalysis.core.AtomGroup.AtomGroup(tmp)

Thanks in advance!

Best,

Pallavi

[Irfan Alibay]

Hi Pallavi,

It looks like the import orders changed a bit for 2.0.0, can you try "MDAnalysis.core.groups.AtomGroup(tmp)" instead of "MDAnalysis.core.AtomGroup.AtomGroup(tmp)"?

Best,

Irfan

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[Pallavi Banerjee]

Hi Irfan, 

That worked perfectly.. Thanks a lot!

Best,

Pallavi