alterlab-rdkit

# RDKit Cheminformatics Toolkit ## Overview RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks. ## When to Use Reach for this skill when you need fine-grained molecular control: custom sanitization, specialized fingerprints or descriptors, reaction enumeration, conformer generation, or programmatic drawing. For standard, high-level workflows with a simpler interface, prefer **datamol** (a wrapper around RDKit). ## Core Capabilities RDKit exposes twelve capability areas. Each is summarized below with the single most common call; **complete, runnable recipes for every area live in `references/code_recipes.md`.** ### 1. Molecular I/O and Creation Read and write molecules across SMILES, MOL/SDF, MOL2, PDB, and InChI. Batch-process with Supplier/Writer objects, including `ForwardSDMolSupplier` and `MultithreadedSDMolSupplier` for large or gzipped files. ```python from rdkit import Chem mol = Chem.MolFromSmiles('Cc1ccccc1') # returns Mol or None smiles = Chem.MolToSmiles(mol) # canonical SMILES ``` Every `MolFrom*` function returns `None` on failure — always check before use. Molecules are auto-san...