Jeffry Setiadi jeff231li
matteoferla
/ set_to_neutral_pH
Last active
March 15, 2024 19:13
A small function to fix the pH protonation/deprotonation of RDKit Chem objects —fixes the charge of simple, i.e. biological cases. So amino acid is fine, but complex artificial drug won't be.
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| from rdkit import mol | |
| def set_to_neutral_pH(mol: Chem): | |
| """ | |
| Not great, but does the job. | |
| * Protonates amines, but not aromatic bound amines. | |
| * Deprotonates carboxylic acid, phosphoric acid and sulfuric acid, without ruining esters. | |
| """ | |
| protons_added = 0 |