Datasets:
Update MutagenLou2023 Preprocessing.py
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MutagenLou2023 Preprocessing.py
CHANGED
@@ -49,15 +49,20 @@ for id, alert in problems:
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print(f"ID: {id}, problem: {alert[0]}")
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# Result interpretation
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# - Can't kekulize mol: The error message means that kekulization would break the molecules down, so it couldn't proceed
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# It doesn't mean that the molecules are bad, it just means that normalization failed
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# Unusual charge on atom 0 number of radical electrons set to zero:
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# - () is present: The error message is not about a salt, not about a fragment,
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# It is showing there is a molecule () (ex) Benzene is present
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#5. Select columns and rename the dataset
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print(f"ID: {id}, problem: {alert[0]}")
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# Result interpretation
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# - WARNING: not removing hydrogen atom without neighbors : There are hydrogen atoms in the molecule that are not bonded to any other atoms.
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# - Can't kekulize mol: The error message means that kekulization would break the molecules down, so it couldn't proceed
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# It doesn't mean that the molecules are bad, it just means that normalization failed
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# - Unusual charge on atom 0 number of radical electrons set to zero: It means that if nValence <0, sets it 0 and shows the warning
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# https://github.com/rdkit/rdkit/blob/d6171aaade470100605f3e99918d31cd46a09199/Code/GraphMol/MolOps.cpp#L451
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# - Aborted reionization due to unexpected situation: It means that H wouldn't move when ppos < ipos and poccur[-1] == ioccur[-1]
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# https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/charge.py#L206
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# - () is present: The error message is not about a salt, not about a fragment,
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# It is showing there is a molecule () (ex) Benzene is present
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#5. Select columns and rename the dataset
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