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NGram and iQSPR errors in XenonPy 0.5.1 #231
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@bcanault Thank you for your information. We have observed a few conflicts after v.0.5.1 due to some updates of rdkit and scikit-learn. The first problem of ngram_tab is actually due to scikit-learn's new update. We have fixed the issue and this should be solved in the next update. Right now, you can change it to "_ = n_gram.fit(data_ss['SMILES'],train_order=5)" to temporarily solve the problem. |
@bcanault For the second problem, I have tested the tutorial myself but I did not get the error you shown. Did you use the NGram model by combing "ngram_pubchem_ikebata_reO15_O10.obj" and "ngram_pubchem_ikebata_reO15_O11to20.obj"? The error you shown seems to be related to the NGram failed to find information relevant to the molecule being modified, which often is due to the initial molecule sample having too many ring structures (under the SMILES representation) than the NGram has ever seen during its training. I recommend you to try to reproduce the problem and output the final SMILES that caused the problem. Maybe we can help you from there. |
@stewu5 Thank you very much for your reply. I am looking forward to testing your new version as soon as it becomes available :). I will give you an update when I will test it. Thank you very much for your help. |
@bcanault where you able to solve the second issue? I am running the same issue when I try to reproduce the results {unknown errors in iqspr}. I tried downgrading the version of Xenonpy, and I run into the same issue. I guess it is due to the new Rdkit package? @stewu5 Dr.Wu I am not sure what do you mean by printing the output; is it the initial samples that are being used for the iqspr runs? |
@deepakorani @bcanault |
Hi folks,
First of all, thank you very much for all your work. It's really interesting. I have tried to use XenonPy and try to rebuild your tutorial. Unfortunately, I observed 2 errors by using the following codes:
Package version: 0.5.1
NGram issue with unkown ngram_tab
I think it was replace by
ngram_table
, but I'm not sure.Unkown error in iQSPR
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