polyply_1.0
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Error message for undefined atom/bead types
Not a bug but possible enhancement.
This is the error one gets if the [ atoms ] contains a atom/bead type S4
that is not defined in the [atomtypes]
section:
Traceback (most recent call last):
File "/Users/alessandri/miniconda3/envs/polyply/bin/polyply", line 258, in <module>
main()
File "/Users/alessandri/miniconda3/envs/polyply/bin/polyply", line 254, in main
subprogram(**args_dict)
File "/Users/alessandri/miniconda3/envs/polyply/lib/python3.10/site-packages/polyply/src/gen_coords.py", line 246, in gen_coords
GenerateTemplates(topology=topology, max_opt=10).run_system(topology)
File "/Users/alessandri/miniconda3/envs/polyply/lib/python3.10/site-packages/polyply/src/processor.py", line 31, in run_system
mols.append(self.run_molecule(molecule))
File "/Users/alessandri/miniconda3/envs/polyply/lib/python3.10/site-packages/polyply/src/generate_templates.py", line 366, in run_molecule
self.gen_templates(meta_molecule)
File "/Users/alessandri/miniconda3/envs/polyply/lib/python3.10/site-packages/polyply/src/generate_templates.py", line 353, in gen_templates
self.volumes[resname] = compute_volume(block,
File "/Users/alessandri/miniconda3/envs/polyply/lib/python3.10/site-packages/polyply/src/generate_templates.py", line 180, in compute_volume
rad = float(nonbond_params[frozenset([atom_key, atom_key])]["nb1"])
KeyError: frozenset({'S4'})
This error message for this could be improved. Opening this issue to hear your opinion and in case I can try to add an error message.
(P.S. Sorry I need to catch up with a couple of PRs but I'm planning to schedule some closing-open-PRs hackathon soon :))