Patrick Walters

I've run into the same error. I tried to wrap this with an exception handler at line 117 in generate.py try: smi = self.tokenizer.untokenize(self.vocab.decode(seq.cpu().numpy())) smi = uc.get_canonical_smile(smi) smiles.append(smi) except KeyError:...

The patterns were taken directly from ChEMBL with a few tweaks to make them work with the RDKit. One day, when I get some time, I'll do some curation. I'd...

Thanks for the comments. There's a lot more that I want to do with these datasets, stay tuned.

Good point, I should have gone into into the stats a bit more. I'm going to revise the post to include an assessment of the impact on precision and recall.

Thanks, Taka! Imbalanced data is an important topic and I plan to talk about it more in future posts. As I mentioned in my reply to Jan, I also need...

Good idea, I'll add this

I agree that the command line interface needs to be revamped. What about something like this? It would do away with the config file and allow users to specify variations...

Updated, I'll create a fork this weekend. Usage: rd_filters [-i INPUT_FILE] [-o OUTPUT_FILE] [-a ALERT_SET][--cfg CONFIG_FILE][--rdalert ALERT_FILE][--np NUM_CORES] [--mw MW_LIMIT][--logp LOGP_LIMIT][--hbd HBD_LIMIT][--hba HBA_LIMIT][--tpsa TPSA_LIMIT][--filter FILTER_NAME] rd_filters --wrconfig CONFIG_FILE rd_filters --show...

Good idea, I'll make this change

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