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.. PubChemPy documentation master file, created by
sphinx-quickstart on Thu Jan 23 10:39:02 2014.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
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.
.. toctree::
:maxdepth: 2
guide/introduction
guide/install
guide/gettingstarted
guide/searching
guide/compound
guide/substance
guide/properties
guide/pandas
guide/download
guide/advanced
guide/contribute
API documentation
-----------------
Comprehensive API documentation with information on every function, class and method.
.. toctree::
:maxdepth: 2
api
.. _`PubChem PUG REST web service`: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST_Tutorial.html
.. _`GitHub`: https://github.com/mcs07/PubChemPy
.. _`Issue Tracker`: https://github.com/mcs07/PubChemPy/issues
.. _`tutorial`: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST_Tutorial.html
.. _`documentation`: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html
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