Unhandled exceptions and KeyError #6
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Figured it out, need to use selfies==1.2 |
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Thank you for your comment. Looking at the error message, it seems that that previously, selfies version 2.0.0 or higher was being used with JANUS. These versions have a slightly different character set (hence the errors). Version 1.0.2 should work fine, however, we suggest using v1.0.3. Please let me know if there are any further suggestions! :) |
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I tried running JANUS.py but got a number of exceptions. In addition, the script terminated with a KeyError.
Initial population obtained! Forming Fragments! Fragment creation: 0/10000 Fragment creation: 1000/10000 Fragment creation: 2000/10000 Fragment creation: 3000/10000 Fragment creation: 4000/10000 Fragment creation: 5000/10000 Fragment creation: 6000/10000 Fragment creation: 7000/10000 Fragment creation: 8000/10000 Fragment creation: 9000/10000 Process Process-5: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch3_1]' SELFIES: [S][C][=N][N][=C][Branch1][Ring1][C][C][C][Branch1][#Branch1][O][C][Branch1][C][C][=O][C][Branch1][C][C][Branch1][C][C][C][N][N][N][Branch3_1][C][C][=C][=C][Branch1][C][N][C][=C][Ring1][#Branch1][C][#Branch1][N] Process Process-7: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 124, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Expl=Ring3]' SELFIES: [C][Expl=Ring3][=C][Branch2][Ring1][=Branch1][C][=C][C][=C][Branch1][#C][C][=C][Ring1][=Branch1][C][=C][C][=C][C][=C][Ring1][=Branch1][Ring1][=C][F][C][Branch1][C][C][C][C][C][N][Branch1][=Branch2][S][Branch1][C][C][=Branch1][C][=O][=O][C][C][Ring1][#Branch2][C][N][Branch1][Branch1][C][C][C][C][C][C][C][C] Process Process-4: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch1_3]' SELFIES: [C][C][=C][Branch1][=Branch1][C][C][=Ring1][=Branch1][Branch1_3][C][C][=C][C][=C][Branch1][C][C][=C][C][=C][Branch1][C][N][C][=N][Ring1][#Branch1][#Branch2][C][N][C][O][C][C][Ring1][=Branch1][C][Branch1][C][O][=C][C][=C][Ring1][=C][O][Ring1][P] Process Process-6: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch3_2]' SELFIES: [C][C][=Branch1][#C][=C][C][=C][C][=Ring1][=Branch1][C][Branch1][C][F][Branch1][C][F][F][C][C][Branch1][C][C][=N][N][C][=Branch1][C][C][C][N][C][C][C][Branch1][C][N][C][C][Ring1][#Branch1][C][O][=C][C][Branch1][O][C][Branch3_2][C][N][C][C][O][C][C][Ring1][=Branch1][=O] Process Process-8: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch2_1]' SELFIES: [C][=Branch1][C][=O][Branch1][C][O][C][N][C][=Branch1][C][=O][C][Branch2][Ring1][=Branch1][N][C][=Branch1][C][=O][C][Branch1][N][C][=C][C][=C][C][Branch2_1][Ring2][=N][Ring1][=Branch1][N][=N][O][C][Ring2][Ring1][C][S][C][C][=Ring2][Ring1][=Branch1][S][C][S][N][=C][Branch1][Ring2][N][=Ring1][Branch1][S][C][C][N] Process Process-11: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch2_3]' SELFIES: [C][C][=C][C][Branch1][=C][C][N][Branch1][C][C][N][C][=Branch1][C][=O][C][S][C][C][C][Ring1][#Branch1][=C][C][=Ring1][O][C][=C][C][=C][C][=C][Ring1][=Branch1][O][C][=C][Branch2_3][Branch1] Process Process-10: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch3_3]' SELFIES: [F][C][=C][C][=C][Branch2][Ring2][O][C][N][C][Branch2][Ring2][Ring2][C][Branch1][#C][C][C][=C][Branch1][=Branch2][C][=C][C][=C][C][=Branch1][C][=O][N][Branch1][C][C][Branch3_3][C][Branch1][C][F][C][=Ring1][#Branch1][F][=N][C][C][Ring1][C][N][C][C][N][C][C][Ring1][=Branch1][=C][=N][C][=Branch1][Branch1][=N][C][=Ring1][=Branch1][N][Branch1][C][C][C][=O][C][=C][Ring2][Ring1][=N] Process Process-9: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols init_state=binit_state, root_atom=prev_atom, rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch3_3]' SELFIES: [C][C][Branch1][#Branch2][C][=C][C][=Branch1][Ring2][=C][=Branch1][F][=N][C][=C][Branch2][Ring2][Branch1][N][Branch1][Branch2][C][=N][C][Ring1][=Branch1][=Ring1][=C][N][=C][C][=C][C][=C][Branch1][P][C][=Branch1][Ring2][=C][Ring1][=Branch1][C][Branch3_3][C][N][=C][C][=C][C][=Ring1][=Branch1][O][C][O] On generation 0/200 (Explr) Top Fitness: 1.0 (Explr) Top Smile: C=C1N=CC=C(N=CNc2ccc(N)cc2)N=C(C)[SH]1C Process Process-27: Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations) # TODO: TESTING File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in mutated_smiles = [decoder(x) for x in mutated_sf] File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder rings=rings File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols _raise_decoder_error(selfies, symbol) File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error raise DecoderError(err_msg) selfies.exceptions.DecoderError: invalid symbol '[Branch3_2]' SELFIES: [C][O][=C][N][C][N][C][=Branch1][C][=O][N][Branch1][=Branch1][N+1][=Branch1][C][=O][O-1][C][Ring1][=Branch2][N][Ring1][N][O][C][=C][C][C][N][C][N][C][N][C][=C][C][=C][Branch1][C][F][C][Branch1][C][F][=C][Ring1][Branch2][=N][C][Branch1][C][C][Branch3_2][Branch1][=Branch1][C][Branch1][C][C][=O][S][Ring1][=Branch2][=C][C][=Ring1][#Branch1][N][C][N][C][C][=C][C][=C][C][=C][Ring1][=Branch1][C][N][=C][Branch1][=C][SH1][Branch1][C][C][C][=C][C][=C][C][=C][Ring1][=Branch1][=Branch1][C][=C][N][=C][C][=Ring1][#Branch2][C] Traceback (most recent call last): File "./JANUS.py", line 308, in mut_smi_dict_local = mut_smi_dict_local[population[top_idx]] KeyError: 'C=C1N=CC=C(N=CNc2ccc(N)cc2)N=C(C)[SH]1C'The text was updated successfully, but these errors were encountered: