Open Babel

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This site replaces the former Compute Canada documentation site, and is now being managed by the Digital Research Alliance of Canada.

Ce site remplace l'ancien site de documentation de Calcul Canada et est maintenant géré par l'Alliance de recherche numérique du Canada.

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General[edit]

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

On our systems we have two kinds of modules for Open Babel installed:

openbabel[edit]

This is the serial version of Open Babel which can safely be used even on login-nodes to convert chemical structure files between different formats. This is the right module for most users.

Example[edit]

[user@login1]$ module load openbabel
[user@login1]$ wget "https://www.chemspider.com/FilesHandler.ashx?type=str&3d=yes&id=171" -O acetic_acid.mol
[user@login1]$ obabel  -i mol  acetic_acid.mol  -o pdb  -O acetic_acid.pdb

Notes:

  • The wget command downloads acetic_acid.mol as an example file.
  • The obabel command converts this molecule from the .mol format to the .pdb format.

For further information on how to use Open Babel, please refer to the Open Babel User Guide

openbabel-omp[edit]

This is the parallel version of Open Babel which has OpenMP parallelization enabled.

This module should not be used on login-nodes,
because even for simple tasks it will create as many threads as it detects CPUs on the machine, in turn causing load-spikes which will be disruptive for other users.

The parallel version of Open Babel is useful when converting very large numbers of molecule structures or calculating large numbers of cheminformatics descriptors for multiple molecules.

Make sure to set the environment variable OMP_NUM_THREADS in order to tell Open Babel how many CPUs it is allowed to use.

Example[edit]

The following job would take the Structural Data File many_molecules.sdf which in this case should contain a database with many molecules and generate Canonical SMILES representations for each of them, using two CPU-cores.

File : parallel_openbabel_job.sh

#!/bin/bash
#SBATCH --time=00:15:00
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=1000M
module load openbabel-omp
export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"

obabel  -i sdf  many_molecules.sdf  -o can  -O many_canonical_smiles.txt


Python[edit]

Open Babel's functionality can be used from other languages such as Python. The Python interface for Open Babel has been added to the both openbabel and openbabel-omp modules as extensions. Therefore both the openbabel and pybel packages can be used after loading both openbabel and a compatible Python module.

Example[edit]

$ module load python/3.11 openbabel/3.1.1
$ python
Python 3.11.5 (main, Sep 19 2023, 19:49:15) [GCC 11.3.0] on linux
>>> import openbabel
>>> print(openbabel.__version__)
3.1.1.1
>>> from openbabel import pybel
>>>