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Open Babel

Open Babel is a chemical toolbox designed to search, convert, analyse or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas.

Open Babel is available as a module on Apocrita.

Usage

To run the latest installed version of Open Babel, simply load the openbabel module:

$ module load openbabel
$ obabel  -h

Usage:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]

For usage documentation, run obabel -H.

Example job

Here is an example job to convert Structure Data Format files to SMILES format, running on 1 core and 2GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load openbabel
obabel -i sdf mymols.sdf \
       -o smi \
       -O outputfile.smi

References