a single carbon atom error

[gry-613]

Hello，I would like to ask whether the fragment connection module is unable to handle elements such as S, F, Cl, etc. Look forward to your reply. If so, is there any way to make it capable of handling structures containing these elements? Here is my error message:
Traceback (most recent call last):
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/bin/reinvent", line 8, in
sys.exit(main_script())
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/Reinvent.py", line 195, in main_script
main(args)
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/Reinvent.py", line 164, in main
runner(
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/run_staged_learning.py", line 364, in run_staged_learning
terminate = optimize(package.terminator)
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/learning.py", line 129, in optimize
self.sampled = self.sampling_model.sample(self.seed_smilies)
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/samplers/linkinvent.py", line 45, in sample
dataset = Dataset(clean_warheads, self.model.get_vocabulary().input)
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/models/linkinvent/dataset/dataset.py", line 28, in init
enc = self._model_vocabulary.encode(smi)
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/models/linkinvent/model_vocabulary/model_vocabulary.py", line 26, in encode
return self.vocabulary.encode(self.tokenizer.tokenize(smiles_str))
File "/disk2/gry/anaconda_install_pack/install_path/envs/reinvent4/lib/python3.10/site-packages/reinvent/models/linkinvent/model_vocabulary/vocabulary.py", line 105, in encode
raise KeyError(f"{token} is not supported! Supported tokens are {self.tokens()}.")
KeyError: "[C] is not supported! Supported tokens are ['', '$', '^', '#', '(', ')', '*', '-', '1', '2', '3', '4', '5', '6', '=', 'Br', 'C', 'Cl', 'F', 'N', 'O', 'S', '[N+]', '[O-]', '[O]', '[S+]', '[n+]', '[nH]', '[s+]', 'c', 'n', 'o', 's', '|']."

[halx]

This really comes from REINVENT. The error message tells you that the SMILES token [C] is not supported by the prior. The notation is not typical and denotes a single carbon atom. If this comes from you input then you will need to clean your input data.

[gry-613]

Thank you for your answer, I'll try.