Each of molecules uploaded will be standardized through all the following types. Usually, it is suitable for most cases. But not every kind of molecule can pass through this Standardization.

| Standardization types:

Sanitization

• Nitro N=O: CN(=O)=O >> C[N+](=O)[O-] and C1=CC=CN(=O)=C1 >> C1=CC=C[N+]([O-])=C1
• Nitro N#O: C-N=N#N >> C-N=[N+]=[N-]
• Perchlorate: Cl(=O)(=O)(=O)[O-] >> [Cl+3]([O-])([O-])([O-])[O-]
• Calculate explicit and implicit valence of all atoms. Fails when atoms have illegal valence.
• Calculate symmetrized SSSR. Slowest step, fails in rare cases.
• Kekulize. Fails if a Kekule form cannot be found or non-ring bonds are marked as aromatic.
• Assign radicals if hydrogens set and bonds+hydrogens+charge < valence.
• Set aromaticity, if none set in input. Go round rings, Huckel rule to set atoms+bonds as aromatic.
• Set conjugated property on bonds where applicable.
• Set hybridisation property on atoms.
• Remove chirality markers from sp and sp2 hybridised centers.
• Remove explicit H count from atoms.

Disconnect metals

• Break covalent bonds between metals and organic atoms under certain conditions.
• First, disconnect N, O, F from any metal. Then disconnect other non-metals from transition metals.
• For every bond broken, adjust the charges of the begin and end atoms accordingly.

Apply normalization rules

• Uncharge-separate sulfones
• Charge-separate nitro groups
• Charge-separate pyridine oxide
• Charge-separate azide
• Charge-separate diazo and azo groups
• Charge-separate sulfoxides
• Hydrazine-diazonium system

Reionize acids

• Reionize acid groups, and keep the strongest acids ionize first.

Recalculate stereochemistry

• Use built-in RDKit functionality to force a clean recalculation of stereochemistry.