SMILE interpreter in python #2087
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I hope you are doing well. I was wondering if you could clarify to me how the program read the SMILES. Based on the results, for example, the SMILE of the group OH ([H]O) is interpreted in Python as H2O when I post-process the data. But in the HTML file, this SMILE is drawn as OH. What interpretation are you using for the SMILE in Python? Thank you! |
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Replies: 1 comment 3 replies
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The SMILES in Python is generated by RDKit. Sadly, per rdkit/rdkit#6613, RDKit fills all atoms with implicit Hs, and there's no option to disable it. The SMILES in HTML is converted by a regex rule |
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Perhaps the conversion process should happen before Python results are outputed. |
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Thank you!! |
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Fixed in #2102 |
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The SMILES in Python is generated by RDKit. Sadly, per rdkit/rdkit#6613, RDKit fills all atoms with implicit Hs, and there's no option to disable it.
The SMILES in HTML is converted by a regex rule
https://github.com/tongzhugroup/reacnetgenerator/blob/b5a16eb90cdf1eca03738218eba5044d2f151fec/reacnetgenerator/_reachtml.py#L69-L99