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molecular-io

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

When to use

• loading chemical libraries
• debugging parse failures
• preparing molecules for downstream standardization
• descriptor calculation
• docking
• converting molecular file formats
• handling aromaticity perception
• handling stereochemistry

When not to use

• full standardization
• canonicalization
• salt stripping
• tautomer enumeration
• generating 3D conformers from parsed 2D molecules

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