PubChemPy documentation¶
PubChemPy provides a way to interact with PubChem in Python. It allows chemical searches by name, substructure and similarity, chemical standardization, conversion between chemical file formats, depiction and retrieval of chemical properties.
Here’s a quick example showing how to search for a compound by name:
for compound in get_compounds('glucose', 'name'):
print compound.cid
print compound.isomeric_smiles
Here’s how you get calculated properties for a specific compound:
vioxx = Compound.from_cid(5090)
print vioxx.molecular_formula
print vioxx.molecular_weight
print vioxx.xlogp
All the heavy lifting is done by PubChem’s servers, using their database and chemical toolkits.
Features¶
- Search PubChem Substance and Compound databases by name, SMILES, InChI and SDF.
- Retrieve the standardised Compound record for a given input structure.
- Convert between SDF, SMILES, InChI, PubChem CID and more.
- Retrieve calculated properties, fingerprints and descriptors.
- Generate 2D and 3D coordinates.
- Get IUPAC systematic names, trade names and all known synonyms for a given Compound.
- Download compound records as XML, ASNT/B, JSON, SDF and depiction as a PNG image.
- Construct property tables using pandas DataFrames.
- A complete Python wrapper around the PubChem PUG REST web service.
- Supports Python versions 2.7 – 3.4.
Useful links¶
- Source code is available on GitHub.
- Ask a question or report a bug on the Issue Tracker.
- PUG REST API tutorial and documentation.
User guide¶
A step-by-step guide to getting started with PubChemPy.
API documentation¶
Comprehensive API documentation with information on every function, class and method.