Rdkit molecule standardization

Purpose

Turn a single SMILES string into a deterministic standardization summary using RDKit MolStandardize.

When to use

• You need a local starter for the taxonomy leaf molecule-standardization.
• You want to strip salts or counterions before downstream featurization.
• You want a compact JSON summary with fragment-parent, uncharged, and canonical-tautomer SMILES.

When not to use

• You need conformers, docking, or quantum chemistry.
• You need bulk normalization across large compound libraries.

Inputs

• One SMILES string passed by --smiles or a single-line file passed by --smiles-file
• Optional molecule name
• Optional JSON output path

Outputs

• JSON summary with cleaned, fragment-parent, uncharged, and canonical-tautomer SMILES
• Charge before and after standardization
• Formula and heavy-atom count for the standardized molecule

Requirements

• slurm/envs/chem-tools with RDKit and MolStandardize

Procedure

1. Run slurm/envs/chem-tools/bin/python skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization/scripts/standardize_rdkit_molecule.py --smiles-file skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization/examples/sodium_acetate.smiles --name sodium-acetate.
2. Inspect fragment_parent_smiles to confirm salt stripping.
3. Inspect uncharged_smiles and canonical_tautomer_smiles before reusing the molecule downstream.

Validation

• The script exits successfully with the chem-tools prefix.
• The sodium acetate example standardizes to CC(=O)O.
• The runtime output matches assets/sodium_acetate_standardized.json.

Failure modes and fixes

• Invalid SMILES: verify the input string or the first non-empty line in the SMILES file.
• Missing RDKit environment: run the script with slurm/envs/chem-tools/bin/python.

Safety and limits

• This is a molecule-cleanup helper only.
• It does not imply medicinal-chemistry, ADMET, or synthesis interpretation.

Provenance

• RDKit documentation: https://www.rdkit.org/docs/
• RDKit MolStandardize API: https://www.rdkit.org/docs/source/rdkit.Chem.MolStandardize.rdMolStandardize.html

Related skills

• rdkit-molecular-descriptors
• chembl-molecule-search