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AutoMapper failing if first bonding atoms is not already bonded to other atoms #10

@AlZocc84

Description

@AlZocc84

Mr/Ms/Mx,

I would like to report a minor issue to your attention.
I have recently tried to use AutoMapper to generate a map to bond a single atom to a molecule. The unbound atom was the first one in the pre-reacted lammps data file, as well as the first atom in the post reacted lammps data file.
Operation of AutoMapper results in the error message

Traceback (most recent call last):
File "/home/alberto_z/sw/AutoMapper/AutoMapper.py", line 92, in
map_processor(directory, args.data_files[0], args.data_files[1], args.save_name[0], args.save_name[1], args.ba[:2], args.ba[2:], args.da, args.ebt, args.ca, args.debug)
File "/home/alberto_z/sw/AutoMapper/MapProcessor.py", line 74, in map_processor
prePreservedAtomIDs = is_cyclic(preAtomObjectDict, preBondingAtoms, 'Pre-bond')
File "/home/alberto_z/sw/AutoMapper/MapProcessor.py", line 286, in is_cyclic
if cyclicPath is not None:
UnboundLocalError: local variable 'cyclicPath' referenced before assignment

Similar attempts for the casein which the single atom to connect is not the first one in the data file seem to be successful.

I would be happy to provide you the files generating the issue.
Thank you for your time,

Best regards,

A. Zoccante, Ph.D.

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