sanitize_molecule#

sanitize_molecule(mol, update_charges=True, sanitize_aromaticity=False, sanitize_kekulize=False)[source]#

Sanitize TMC molecule by updating formal charges to apparent value based on connectivity and use RDKit sanitization without SANITIZE_SETAROMATICITY or SANITIZE_KEKULIZE.

Parameters:

  • mol (rdkit.Chem.rdchem.Mol) – RDKit molecule to sanitize

  • update_charges (bool, optional, default=True) – If True, the charges are updated to apparent values based on connectivity

  • sanitize_aromaticity (bool, options, default=False) – If False, removes the flag Chem.SanitizeFlags.SANITIZE_SETAROMATICITY

  • sanitize_kekulize (bool, options, default=False) – If False, removes the flag Chem.SanitizeFlags.SANITIZE_KEKULIZE

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