Open Babel on Biowulf
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.
References:
- Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison Open Babel: An open chemical toolbox Journal of Cheminformatics (2011) 3:33
Documentation
Important Notes
- Module Name: OpenBabel (see the modules page for more information)
- Singlethreaded
- Environment variables set
- OPENBABEL_HOME
- OPENBABEL_EXAMPLES
- Example files in $OPENBABEL_EXAMPLES
The executables are version dependent:
- 2.4.1
- 3.0.0
Executables
- babel - a converter for chemistry and molecular modeling data files
- obabel - a converter for chemistry and molecular modeling data files
- obchiral - print molecular chirality information
- obconformer - generate low-energy conformers
- obenergy - calculate the energy for a molecule
- obfit - superimpose two molecules based on a SMARTS pattern
- obgen - generate 3D coordinates for a molecule
- obgrep - an advanced molecular grep program using SMARTS
- obminimize - optimize the geometry, minimize the energy for a molecule
- obprobe - create electrostatic probe grid
- obprop - print standard molecular properties
- obrotamer - generate conformer/rotamer coordinates
- obrotate - batch-rotate dihedral angles matching SMARTS patterns
- obspectrophore - calculate a Spectrophore, a one-dimensional descriptor generated from the property field surrounding the molecule
Executables
- obabel - a converter for chemistry and molecular modeling data files
- obconformer - generate low-energy conformers
- obenergy - calculate the energy for a molecule
- obfit - superimpose two molecules based on a SMARTS pattern
- obfitall - ???
- obgen - generate 3D coordinates for a molecule
- obgrep - an advanced molecular grep program using SMARTS
- obminimize - optimize the geometry, minimize the energy for a molecule
- obmm - OpenBabel molecular mechanics program
- obprobe - create electrostatic probe grid
- obprop - print standard molecular properties
- obrotamer - generate conformer/rotamer coordinates
- obrotate - batch-rotate dihedral angles matching SMARTS patterns
- obspectrophore - calculate a Spectrophore, a one-dimensional descriptor generated from the property field surrounding the molecule
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load OpenBabel [user@cn3144 ~]$ obabel -ixyz benzene.xyz -O benzene.pdb [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. OpenBabel.sh). For example:
#!/bin/bash module load OpenBabel obabel -ipdb benzene.pdb -O benzene.xyz
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] OpenBabel.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. OpenBabel.swarm). For example:
obabel mymols.sdf -f 1 -l 10 -Ooutputfile1.sdf obabel mymols.sdf -f 11 -l 20 -O outputfile2.sdf obabel mymols.sdf -f 21 -l 30 -O outputfile3.sdf obabel mymols.sdf -f 31 -l 40 -O outputfile4.sdf
Submit this job using the swarm command.
swarm -f OpenBabel.swarm --module OpenBabelwhere
| --module OpenBabel | Loads the OpenBabel module for each subjob in the swarm |