Cheminformatics

RDKit

Molecule properties, standardization and substructure search, and explicit bond edits from atom-mapped reactions.

RDKit is the open-source cheminformatics toolkit. Given SMILES or an SD file, a run reports canonical structures with descriptors, Lipinski counts, standardized parent forms, InChI, molecule hashes, Murcko scaffolds, ring and stereochemistry analysis, SMARTS substructure matches, fingerprints and the maximum common substructure of the set. Given atom-mapped reaction SMILES, it reports the reaction's participants, its element and formal-charge balance, the quality of its atom mapping, and the bonds formed, broken or changed in order -- the reaction centre a precedent search or an enzyme design starts from.

Documentation ↗ Input parameters ↗ Examples ↗ Home page ↗ Source code ↗ License ↗

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Input

Official documentation ↗

Job name Names the table this run leaves: <job name>.csv.

Molecules One molecule per line, in the format RDKit's SmilesMolSupplier reads: a SMILES string, then optionally whitespace and a name. Lines beginning with # are ignored. Up to 5000 molecules and 200,000 characters per run. In this form: A molecule RDKit cannot parse is reported as a row with an error rather than failing the run, so one bad line in a list does not lose the rest.

Reactions One reaction per line as reactants>>products, or reactants>agents>products, then optionally whitespace and a name. Atom maps are required for reliable bond-edit extraction: every atom should be mapped exactly once per side. Up to 1000 reactions per run.

Molecule or reaction file Upload a SMILES list (.smi, .txt, .csv) or an SD file (.sdf, .mol); an SD file is recognised by its own connection table and read with RDKit's SDMolSupplier, keeping the _Name field as each molecule's name. For the reaction task, upload one reaction SMILES per line.

Molecule properties

Official documentation ↗

Descriptors The common set is formula, molecular weight and exact mass, cLogP, TPSA, hydrogen-bond donors and acceptors, rotatable bonds, rings, aromatic rings, heavy atoms, fraction of sp3 carbons, formal charge and the number of Lipinski rule-of-five violations. Every descriptor is RDKit's own Descriptors.CalcMolDescriptors, which is upwards of two hundred columns.

Standardized parent forms Adds the four rdMolStandardize parents as columns: cleanup, fragment parent (the largest fragment), charge parent (neutralized) and tautomer parent. Useful as search keys; keep the original charged, stereospecific molecule for anything that has to account for mass or charge.

InChI and InChIKey Adds InChI and InChIKey columns, when the RDKit build includes InChI support. The InChIKey is the usual key for matching a molecule across databases.

Molecule hash strings Adds the rdMolHash strings from the Cookbook's molecule-hash recipe: canonical SMILES, the tautomer-insensitive HetAtomTautomer hash, the Murcko scaffold hash, the anonymous graph and the net charge. Two molecules that agree on a hash are the same under that hash's notion of sameness.

Structure and substructure

Official documentation ↗

Murcko scaffold Adds the Bemis-Murcko scaffold (the ring systems and the linkers between them, with side chains removed) and its generic form, where every atom becomes carbon and every bond single.

Rings and aromaticity Adds the number of rings in the symmetrized smallest set of smallest rings, the number of ring systems (fused rings counted once), the number of aromatic rings and the number of aromatic atoms.

Stereochemistry Adds the stereocentres and stereo bonds RDKit's FindPotentialStereo finds, and how many of them are unspecified in the input -- which is what says whether a SMILES string names one stereoisomer or a family of them.

Substructure query (SMARTS) A SMARTS pattern matched against every molecule, as in the Cookbook's functional-group recipes: for example [NX1]#[CX2] for a nitrile or [CX3](=O)[OX2H1] for a carboxylic acid. Adds the number of matches and the atom indices of the first one. Leave empty to skip.

Maximum common substructure Runs rdFMCS.FindMCS across every molecule that parsed and reports the largest substructure they all share, as SMARTS, with its atom and bond counts. This is one answer for the whole set rather than a column, so it is reported in the run's JSON rather than the table. Needs at least two molecules.

MCS timeout (seconds) rdFMCS.FindMCS's own timeout. A search that runs out of time still returns the largest substructure it had found, flagged as having timed out.

Fingerprint Adds a fingerprint column as a bit string, through rdFingerprintGenerator. Morgan with radius 2 is the usual ECFP4 analogue. MACCS keys are a fixed 166-bit set and ignore the size and radius below.

Fingerprint size (bits) The folded length of the fingerprint. Ignored for MACCS keys.

Morgan radius How far from each atom the Morgan environment reaches. Radius 2 corresponds to ECFP4. Used only by the Morgan fingerprint.

Reaction analysis

Official documentation ↗

Per-participant summaries Reports each reactant, agent and product on its own: canonical SMILES, formula, formal charge, and how many of its atoms carry a map number.

Element and charge balance Counts every element, implicit hydrogens included, and the formal charge on each side, and reports the difference. Agents are excluded from the count, as they are from the bond edits.

Bonds formed, broken and changed Compares the mapped bonds on each side and reports the bonds formed, the bonds broken, the bonds whose order changed, and the atom maps making up the reaction centre. Only reliable when the atom mapping is complete, which is reported alongside it.

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