PubChemPy

Overview

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.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is released under the MIT License and all use must adhere to that license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/python/pubchempy/1.0.4        # Uses Anaconda python 5.2.0 (python 3.6)

The Anaconda Python modulefile will be loaded automatically.

Running the application

Please do not run PubChemPy on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

# We recommend loading modulefiles in jobscripts. Use your requried version.
module load apps/python/pubchempy/1.0.4

python mypubchem.py

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

Given an example parallel jobscript, including suitable PE

Further info

• PubChemPy docs website

Updates

None.