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Install RDKit with Conda or pip, confirm that Python can import it, then parse a SMILES string or molecular file into an RDKit molecule. From there you can inspect atoms and bonds, draw structures, process molecule collections, search with SMARTS, and create fingerprint-based similarity maps. The examples below follow the RDKit 2026.03.6 documentation.
Choose an installation route
RDKit documents Conda, pip, operating-system package repositories, and source builds. Conda creates a separate environment for RDKit; pip installs it into the Python environment associated with the pip command. Use the Python interpreter from the environment where you installed the package.
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| Route | Use it when | Documented setup |
|---|---|---|
| Conda with conda-forge | You want a named environment dedicated to RDKit. | conda create -c conda-forge -n my-rdkit-env rdkit, then conda activate my-rdkit-env. |
| pip | You want to add RDKit to an existing Python environment. The guide lists platform wheels for Linux, Windows, and macOS. | pip install rdkit. |
| Operating-system package or source build | You prefer your platform’s package repository, or need to control build options. | Instructions vary by platform and build configuration; follow the matching sections of the RDKit installation guide. |
For the Conda commands, activate my-rdkit-env before starting Python. For pip, make sure pip belongs to the interpreter you plan to use.
Verify the install and parse a molecule
RDKit’s Python guide starts with from rdkit import Chem and creates molecules from SMILES. A successful parse returns a Mol object; an invalid input returns None. Check the result before calling methods on it.
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from rdkit import Chem
mol = Chem.MolFromSmiles("Cc1ccccc1")
if mol is None:
raise ValueError("Could not parse the molecular structure")
print(mol.GetNumAtoms())The example parses the SMILES representation of toluene and prints its atom count. If importing fails, first check that Python is running in the environment where RDKit was installed. If parsing returns None, check the input string or file rather than continuing with molecule analysis.
Read molecular files and collections
For file input, the guide demonstrates Chem.MolFromMolFile(...) and Chem.MolFromMolBlock(...); like the SMILES parser, these return a molecule on success or None when parsing fails. Apply the same check before analysis.
For collections, supplier classes such as Chem.SDMolSupplier and Chem.SmilesMolSupplier let you iterate over structures. Check each supplied molecule individually, because one failed record should not be treated as a valid molecule.
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from rdkit import Chem
supplier = Chem.SDMolSupplier("molecules.sdf")
for index, mol in enumerate(supplier):
if mol is None:
print(f"Skipping unreadable molecule at record {index}")
continue
print(index, mol.GetNumAtoms())The example assumes an SDF file named molecules.sdf in the current working directory; replace it with your file path.
Inspect atoms and bonds
Once you have a valid Mol, iterate through its atoms and bonds to inspect basic structural information such as element symbols, atomic numbers, and bond types.
for atom in mol.GetAtoms():
print(atom.GetIdx(), atom.GetSymbol(), atom.GetAtomicNum())
for bond in mol.GetBonds():
print(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondType())Atom and bond indices identify positions in the parsed molecule; they are useful when relating printed details to other RDKit operations.
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Draw a structure
RDKit’s drawing utilities can produce an image from a molecule with rdkit.Chem.Draw.MolToImage(). A basic example is:
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from rdkit.Chem import Draw
image = Draw.MolToImage(mol)
imageIn a notebook, evaluating the image displays it. RDKit’s guide also covers generating 2D coordinates for depictions. If compiling RDKit from source and high-quality PNG depiction is important, its installation guide identifies Cairo and enabling Cairo support as build considerations; they are not prerequisites for every installation.
Search for a substructure with SMARTS
SMARTS describes a query pattern. Build a query molecule with Chem.MolFromSmarts(), then test whether it appears in a target or retrieve matching atom-index tuples with GetSubstructMatches().
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query = Chem.MolFromSmarts("c1ccccc1")
if query is None:
raise ValueError("Could not parse the SMARTS query")
if mol.HasSubstructMatch(query):
matches = mol.GetSubstructMatches(query)
print(matches)The example searches for a six-membered aromatic carbon ring. The match is a pattern occurrence in the parsed target molecule, not a general conclusion about chemical activity or properties.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Explore fingerprint-based similarity maps
The RDKit Python guide includes a SimilarityMaps workflow using fingerprints such as atom-pair, topological-torsion, and Morgan fingerprints. These maps provide a visual way to examine fingerprint-based similarity between molecules; they are one documented comparison approach, not the only way to compare structures. See the RDKit Python guide for its similarity-map examples and related details.
When a source build needs optional features
Most users installing a packaged build do not need to configure these source-build options. They matter when compiling RDKit and requiring the associated functionality:
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- Cairo: install Cairo and enable Cairo support for high-quality PNG structure depictions.
- Eigen3: the installation guide identifies Eigen3 as needed for 3D descriptors.
- InChI: support can also be enabled in a source build.
Consult the platform-specific source-build instructions before compiling, since setup details depend on the operating system and features you want.
Documentation scope
The RDKit guide titled “Getting Started with the RDKit in Python” describes itself as an overview of using RDKit functionality from Python. It is a practical entry point for these parsing and starter workflows, while the full documentation is the place to look for details beyond these examples.
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