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cheminformatics-definitions

Pins down the RDKit definitions that differ between conventions before computing molecular descriptors, including Lipinski donor and acceptor counts (Lipinski.NumHDonors and NumHAcceptors versus rdMolDescriptors.CalcNumLipinskiHBD and HBA), TPSA with or without sulfur and phosphorus, QED weighting, standard versus non-standard InChI and InChIKey, standardization order (cleanup, salt stripping, uncharging, tautomer canonicalization), canonical versus isomeric SMILES and aromaticity models, and states which definition produced each number. Use whenever a task computes, filters or compares small-molecule properties or identifiers; use the rdkit skill for general API usage and medchem or admet skills for interpretation.

backend/cli/skills/chemistry/cheminformatics-definitions/SKILL.md

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# Cheminformatics definitions

The same molecule has several hydrogen-bond acceptor counts, several polar surface areas
and several canonical SMILES, all correct under some definition. RDKit implements more than
one of each. Compute with the definition the question uses, and print the definition next
to the number; a bare "HBA = 7" is not reproducible.

## Rules

1. **Lipinski counts.** The original rule of five counts donors as the number of N-H and
   O-H bonds and acceptors as the number of N and O atoms. In RDKit these are
   `rdMolDescriptors.CalcNumLipinskiHBD` and `CalcNumLipinskiHBA` (also exposed as
   `Lipinski.NHOHCount` and `Lipinski.NOCount`). `Lipinski.NumHDonors` and
   `Lipinski.NumHAcceptors` (same as `rdMolDescriptors.CalcNumHBD` and `CalcNumHBA`) use