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

v0.3.1

Changed

• Migrated to MorganGenerator API: replaced deprecated GetMorganFingerprintAsBitVect / GetHashedMorganFingerprint with rdFingerprintGenerator.GetMorganGenerator across fingerprints, similarity, diversity, and sascorer modules. Also migrated AtomPair and TopologicalTorsion fingerprints.

• Smart parallelism defaults: global default changed from all cores (-1) to single-threaded (1), avoiding IPC overhead on fast commands. Heavy workloads (descriptors --all, descriptors --category) auto-scale to all cores. Users can always override with -n -1.

• Optimized README: replaced verbose per-command docs with compact help-style reference and benchmark table. Full command docs moved to docs/commands.md.

Removed

• Dead _fgs reference in fragment module (unused GetMorganFingerprint assignment)

v0.3.0

[0.3.0] - 2026-01-10

Added

• info: Quick molecule information from SMILES (formula, MW, LogP, TPSA, stereocenters, Lipinski violations, InChI/InChIKey)
• merge: Combine multiple molecule files with optional deduplication and source tracking
• sascorer: Calculate Synthetic Accessibility (SA) Score, Natural Product-likeness (NPC), and QED scores
• rgroup: R-group decomposition around a core SMARTS pattern with labeled attachment points
• rings: Ring system analysis - extract ring systems (fused, spiro, bridged) and analyze frequencies
• align: 3D molecular alignment to a reference structure (MCS-based or Open3DAlign)
• rmsd: RMSD calculations between 3D structures (compare to reference, pairwise matrix, conformer analysis)
• mmp: Matched Molecular Pairs analysis - fragment molecules, find pairs, apply transformations
• protonate: Protonation state enumeration at specified pH with neutralization option
• props: Property column operations - add, rename, drop, keep columns in molecule files

Changed

• Total command count increased from 19 to 29

v0.2.0

[0.2.0] - 2026-01-06

Added

• stats: Calculate dataset statistics (MolWt, LogP, TPSA, etc. with min/max/mean/median/stdev)
• split: Split files into smaller chunks (by number of chunks or chunk size)
• sample: Randomly sample molecules (by count or fraction, with reservoir sampling for large files)
• deduplicate: Remove duplicate molecules (by SMILES, InChI, InChIKey, or scaffold)
• validate: Validate molecular structures (valence, kekulization, stereo, element constraints)

Changed

• Commands are now displayed in alphabetical order in help output
• Total command count increased from 14 to 19

v0.1.0

[0.1.0] - 2026-01-06

Added

• Initial release with 14 command categories
• descriptors: Compute molecular descriptors (200+ available)
• fingerprints: Generate molecular fingerprints (morgan, maccs, rdkit, atompair, torsion, pattern)
• filter: Filter molecules by substructure, properties, drug-likeness (Lipinski/Veber/Ghose), PAINS
• convert: Convert between molecular file formats (CSV, TSV, SMI, SDF, Parquet)
• standardize: Standardize and canonicalize molecules
• similarity: Similarity search, matrix computation, and clustering
• conformers: Generate and optimize 3D conformers
• reactions: SMIRKS transformations and reaction enumeration
• scaffold: Murcko scaffold extraction and decomposition
• enumerate: Stereoisomer and tautomer enumeration
• fragment: BRICS/RECAP fragmentation and functional group analysis
• diversity: MaxMin diversity picking and diversity analysis
• mcs: Maximum Common Substructure finding
• depict: SVG/PNG molecular depictions (single, batch, grid)

Features

• Multi-core parallel processing via ProcessPoolExecutor
• Ninja-style progress display with speed and ETA
• Support for multiple I/O formats (CSV, TSV, SMI, SDF, Parquet)
• Automatic format detection from file extensions
• Lazy imports for fast CLI startup (~0.08s)
• Comprehensive test suite (182 tests)