Do these 3 things before closing this tab:
1Fix the driver behind crashes, sound loss and screen glitches2Repair Windows errors before they cause bigger problems3Scan for outdated or missing drivers - takes under a minuteInstall RDKit with Conda for an isolated environment or with pip in an existing Python setup, then use its Python API to load and inspect molecular structures. The examples below take you from installation to parsing SMILES and molecular files, inspecting atoms and bonds, drawing molecules, reading collections, and searching for substructures.
Choose an installation method
RDKit’s official installation guide covers Conda, pip, operating-system package repositories, and building from source. These two commands are documented routes; use the one that fits your Python environment. See the RDKit installation guide for platform-specific details and other methods.
| Route | Use it when | Command |
|---|---|---|
| Conda | You want RDKit in a dedicated environment managed through conda-forge. | conda create -c conda-forge -n my-rdkit-env rdkitconda activate my-rdkit-env |
| pip | You want to install it into an existing Python environment. The guide reports platform wheels for Linux, Windows, and macOS. | pip install rdkit |
| Operating-system package or source build | You prefer a platform package repository or need to compile RDKit and configure optional features. | Follow the matching operating-system or source-build instructions in the official guide. |
After installation, run Python from the same environment where RDKit was installed. For Conda, activate my-rdkit-env before starting Python or running a script.
Parse a molecule and check the result
The RDKit Python guide starts with from rdkit import Chem and demonstrates creating a molecule from SMILES, a text notation for chemical structures. A successful parse returns an RDKit Mol object. An invalid input can instead return None, so check before calling methods on the result.
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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())This example parses a SMILES string and prints the number of atoms in the resulting molecule. RDKit’s Getting Started with the RDKit in Python guide also demonstrates loading a molecule from a file or a MOL block:
from rdkit import Chem
mol_from_file = Chem.MolFromMolFile("structure.mol")
mol_from_block = Chem.MolFromMolBlock(mol_block_text)
for mol in (mol_from_file, mol_from_block):
if mol is None:
print("Could not parse this input")
else:
print(mol.GetNumAtoms())Replace structure.mol with your file path and mol_block_text with the MOL block content. Both file-oriented functions can fail to parse input and return None; do not assume that a file being present means its structure was read successfully.
Inspect atoms and bonds
Once parsing succeeds, iterate through the molecule’s atoms and bonds to inspect basic structural information such as element symbols, atomic numbers, and bond types.
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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 indices let you identify the endpoints of a bond in the same molecule. These properties are a useful first inspection; they do not by themselves establish that the supplied structure represents the compound you intended.
Draw a molecule
RDKit’s drawing module can create a depiction from a parsed molecule. The guide demonstrates rdkit.Chem.Draw.MolToImage(); its drawing examples also discuss generating 2D coordinates for depictions.
from rdkit.Chem import Draw
image = Draw.MolToImage(mol)
image.save("molecule.png")For a source build intended to produce high-quality PNG depictions, the installation guide says to install Cairo and enable Cairo support during the build. This is an optional build consideration, not a prerequisite stated for every RDKit installation.
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Read a collection of structures
Supplier classes let you process collections instead of loading one structure at a time. For example, Chem.SDMolSupplier reads an SDF file, and Chem.SmilesMolSupplier reads a collection of SMILES. Check each result because a supplier can yield None for a structure it cannot read.
from rdkit import Chem
supplier = Chem.SDMolSupplier("structures.sdf")
for index, mol in enumerate(supplier):
if mol is None:
print(f"Could not read structure {index}")
continue
print(index, mol.GetNumAtoms())Use the corresponding supplier for your input format, and keep the failure check inside the loop so one unreadable entry does not lead to method calls on None.
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Search for a substructure with SMARTS
SMARTS describes a structural query. Parse it with Chem.MolFromSmarts(), then test a molecule with HasSubstructMatch() or retrieve matching atom-index tuples with GetSubstructMatches().
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query = Chem.MolFromSmarts("[OH]")
if query is None:
raise ValueError("Could not parse the SMARTS query")
if mol.HasSubstructMatch(query):
matches = mol.GetSubstructMatches(query)
print(matches)The example checks for a query matching an oxygen attached to hydrogen. Choose a SMARTS pattern that expresses the structural feature you actually want to find; a successful match indicates that the pattern occurs in the parsed molecule.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Explore fingerprint similarity maps
The Python guide includes a SimilarityMaps workflow using fingerprints, including atom-pair, topological-torsion, and Morgan fingerprints. Such a map visualizes fingerprint-based similarity information for a molecule; it is one documented way to compare structures visually, not the only way to compare molecules.
Refer to the guide’s fingerprint and similarity-map examples for the required setup and API details: Getting Started with the RDKit in Python.
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When a source build needs optional features
A standard Conda or pip installation is the simpler starting point for the Python workflows above. If you compile RDKit yourself, choose build options according to the features you need; the installation guide distinguishes these optional dependencies from basic installation.
- Cairo: the guide recommends Cairo support for high-quality PNG structure depiction.
- Eigen3: the guide identifies Eigen3 as needed for 3D descriptors.
- InChI: the guide also documents enabling InChI support in a source build.
Follow the installation guide’s section for your operating system and desired build features rather than assuming these components are required for every user.
Quick Recap
Troubleshoot the first run
ModuleNotFoundError: No module named 'rdkit': confirm that the Python interpreter running your script is the one associated with the environment where you installed RDKit. If using the Conda example, activatemy-rdkit-envfirst.- A parse function returns
None: verify the input string or file content and handle the failure before using molecule methods. RDKit may also emit diagnostics for invalid input. - A PNG or optional descriptor feature is unavailable: check whether your installation method and, for source builds, selected optional dependencies and build options support that feature.
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