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 default 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¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load openbabel
obabel -i sdf mymols.sdf \
-o smi \
-O outputfile.smi