rdkit-cli v0.3.2

Added

• stereo: New command for stereochemistry analysis — CIP label assignment (R/S, E/Z), stereocenter perception, enhanced stereo group inspection, and stereo cleanup/canonicalization
• energy: New command for force field energy calculations — single-point MMFF/UFF energy and structure minimization with convergence reporting
• pharmacophore: New command for pharmacophore feature perception (Donor, Acceptor, Aromatic, etc.) and 2D pharmacophore fingerprint similarity search
• fingerprints: Added Avalon, MHFP (MinHash), and 2D pharmacophore (Gobbi) fingerprint types
• descriptors: Added 42 Molecular Quantum Numbers (MQN) and 10 3D shape descriptors (PMI, NPR, Asphericity, Eccentricity, SpherocityIndex, PBF); new --mqn, --3d, and --generate-conformers flags
• similarity: Added 8 metrics (AllBit, Asymmetric, BraunBlanquet, Kulczynski, McConnaughey, OnBit, RogotGoldberg, Tversky with alpha/beta); new shape subcommand for 3D shape similarity (Tanimoto, Protrude, Tversky)
• filter: Expanded structural alert catalogs — --catalog option supports PAINS, PAINS_A/B/C, Brenk, NIH, ZINC, and all combined; added alerts subcommand as alias
• conformers: Added constrained subcommand for template-constrained 3D embedding and torsion subcommand for dihedral angle scanning with energy profiles
• reactions: Added map subcommand for atom-atom mapping inspection (text/JSON) and fingerprint subcommand for reaction difference/structural fingerprints
• scaffold: Added network subcommand for scaffold network construction (CSV/JSON output) using rdScaffoldNetwork
• props: Added charges subcommand for Gasteiger partial charges and crippen subcommand for per-atom LogP/MR contributions
• fragment: Added brics-build subcommand for recombining BRICS fragments into new molecules
• depict: Added highlight subcommand for SMARTS-based atom/bond highlighting with custom RGB colors

Changed

• Total command count increased from 29 to 32 (stereo, energy, pharmacophore)
• Total fingerprint types increased from 6 to 9
• Total descriptor count increased from ~133 to ~185
• Similarity metrics increased from 5 to 13