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Babel

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Description Content
module load chem/babel
Availability bwUniCluster | BwForCluster_Chemistry
License GPL
Citing Open Babel Citation
Links Homepage | Documentation
Graphical Interface No

1 Description

Babel converts between different formats of 3D-position data for molecules (e.g. proteins or DNA). Current versions can also do partial charge calculations and molecular mechanics calculations. A list of openbabel capabilities can be found at https://openbabel.org/wiki/Capabilities

2 Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

On the command line of the the bwUni or bwFor clusters, you can get a list of the available i versions using

module avail chem/babel

3 Usage

3.1 Loading the module

You can load the default version of babel with the command

module load chem/babel

If you wish to load a specific (older) version, you can do so using e.g.

module load chem/babel/0.0.0

to load the version 0.0.0

3.2 Program Binaries

babel (also: obabel) - main program. Converter for chemistry and molecular modeling data files.

All of these programs come with a man-page that you can access after loading the module by typing e.g.

man babel
  • obchiral - print molecular chirality information
  • obconformer - generate conformer coordinates using a Monte Carlo search
  • obenergy - calculate the energy for a molecule
  • obfit - superimpose two molecules based on a pattern
  • obgen - generate 3D coordinates for a molecule e.g. from SMILES
  • obgrep - molecular search program using SMARTS
  • obminimize - optimize the geometry, minimize the energy for a molecule
  • obprobe - create electrostatic probe grid
  • obprop - print standard molecular properties
  • obrms - compute heavy-atom RMSD of identical compound structures
  • obrotamer - generate conformer/rotamer coordinates
  • obrotate - batch-rotate dihedral angles matching SMARTS patterns
  • obspectrophore - SPECTROPHORE calculator
  • roundtrip - comparison program for testing roundtrip conversion


4 Examples

You can copy a simple interactive example to your home directory and run it, using:

mkdir ~/babel-examples/
cp -r $BABEL_EXA_DIR/ ~/babel-examples/
cd ~/babel-examples/
cat README    # readme-file contains instructions on how to run examples

As babel is in general meant to be used to do quick conversions between different formats, no submit-script for the queuing system is provided.