Version Compatibility

Reference examples tested with: RDKit 2024.09+ and chembl_structure_pipeline 1.2+. MolVS 0.1.1 is a legacy package; use RDKit's maintained rdMolStandardize module for custom pipelines.

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Molecular Standardization

Convert raw molecular structures into a consistent form for ML training data, deduplication, registry, and cross-database joining. Skipping standardization can create data leakage when alternate representations of one compound enter different splits, distort QSAR inputs, and cause database join misses. The ChEMBL structure pipeline (Bento et al. 2020) is built on RDKit and applies ChEMBL-specific normalization and parent-selection rules. canSARchem (Dolciami et al. 2022) adds canonical-tautomer selection before parent extraction. RDKit's maintained rdMolStandardize module provides primitives for building an explicit custom pipeline.

For format-level I/O and aromaticity perception, see chemoinformatics/molecular-io. For descriptor calculation after standardization, see chemoinformatics/molecular-descriptors.

Standardization Pipeline Stages