AttributeError: Atom has no attribute indices. Do you mean index

[Dan-Burns]

Trying to parallelize the Hole Analysis calculation assuming that I can have n slices of the trajectory being processed simultaneously with a function like

def hole_calc(atomgroup,ts):
    
    PDB_HOLE = f'hole_frame_{ts.frame}.pdb'
    # write the frame to pdb
    atomgroup.write(PDB_HOLE)
    hole_u = mda.Universe(PDB_HOLE)
  
    # Get the pore Center Atoms
    center_resis = hole_u.select_atoms('resnum 675 and name CA')
    
    center_coords = np.mean(center_resis.positions,axis=0)
    
    profiles = hole2.hole(PDB_HOLE, executable=hole_exe,
                          cpoint=center_coords,
                          cvect=[0,0,1],
                          keep_files=False)
    os.remove(PDB_HOLE)
    
    return {'rxn_coord':profiles[0]['rxn_coord'], 
            'radius': profiles[0]['radius'], 
            'cen_line_D':profiles[0]['cen_line_D']
            }

Using this as the function inside of:

NewAnalysis(ParallelAnalysisBase)

def _single_frame(self, ts, agroups):
        # REQUIRED
        # called for every frame. ``ts`` contains the current time step
        # and ``agroups`` a tuple of atomgroups that are updated to the
        # current frame. Return result of `some_function` for a single
        # frame
        
        return {ts.frame: hole_calc(agroups[0], ts)}

and calling it with:

test = HoleParallel(u.select_atoms('all'),None).run()

I get the following error:

test = HoleParallel(u.select_atoms('protein'),None).run()
Traceback (most recent call last):
File "", line 1, in
File "HoleParallel.py", line 57, in init
super(HoleParallel, self).init(atomgroup.universe,
File "conda_environments/miniconda3/envs/mdanalysis/lib/python3.9/site-packages/pmda/parallel.py", line 213, in init
self._indices = [ag.indices for ag in atomgroups]
File "conda_environments/miniconda3/envs/mdanalysis/lib/python3.9/site-packages/pmda/parallel.py", line 213, in
self._indices = [ag.indices for ag in atomgroups]
File "conda_environments/miniconda3/envs/mdanalysis/lib/python3.9/site-packages/MDAnalysis/core/groups.py", line 4142, in getattr
return super(Atom, self).getattr(attr)
File "conda_environments/miniconda3/envs/mdanalysis/lib/python3.9/site-packages/MDAnalysis/core/groups.py", line 4016, in getattr
raise AttributeError(err.format(selfcls=selfcls, attr=attr,
AttributeError: Atom has no attribute indices. Do you mean index
....
'''

Currently version of MDAnalysis: 2.2

[Dan-Burns]

changing line 216 in parallel.py to
self._indices = [list(atomgroups.indices)]
made it run but lots of errors followed.

raise ApplicationError(proc.returncode,
MDAnalysis.exceptions.ApplicationError: [Errno 2] HOLE failure (/work/LAS/potoyan-lab/Dan/SOFTWARE/hole2/exe/hole). Check output hole.out

Probably going to be faster running it without parallel implementation in the short term.

[orbeckst]

We haven't updated PMDA to work with MDA 2.0 yet #148 so that's probably creating problems.