| 1 | Molecular I/O and creation | SMILES, MOL files and blocks, InChI, SDF and SMILES suppliers, multithreaded reading, writers |
| 2 | Sanitization and validation | disabling automatic sanitization, manual and partial sanitization, detecting problems first |
| 3 | Analysis and properties | atom and bond iteration, ring information and SSSR, chirality and stereochemistry, fragments |
| 4 | Descriptors | MW, LogP, TPSA, H-bond donors/acceptors, rotatable bonds, aromatic rings, bulk calculation, drug-likeness |
| 5 | Fingerprints and similarity | topological, Morgan/ECFP via rdFingerprintGenerator, MACCS, atom pair, torsion, Avalon; Tanimoto and other metrics; Butina clustering |
| 6 | Substructure searching | SMARTS queries, match retrieval, and a library of common patterns |
| 7 | Chemical reactions | reaction SMARTS, applying reactions, reaction fingerprints |
| 8 | 2D and 3D coordinates | depiction, template alignment, ETKDG embedding, force-field optimization, RMSD, constrained embedding |
| 9 | Visualization | single and grid images, substructure highlighting, custom drawer options, Jupyter integration, fingerprint bit environments |
| 10 | Molecular modification | explicit hydrogens, Kekulization, aromaticity, substructure replacement, charge neutralization |
| 11 | Hashes and standardization | Murcko scaffold and canonical hashes, regioisomer hashes, randomized SMILES for augmentation |
| 12 | Pharmacophore and 3D features | feature factories and feature extraction |
