Open Babel

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Description Content
module load chem/openbabel
Availability BwForCluster_JUSTUS_2
License GPL
Citing References
Links Homepage | Documentation
Graphical Interface No

1 Description

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

2 Availability

Open Babel is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the Cluster Information System (CIS).

In order to check which versions of Open Babel are installed on the compute cluster, run the following command:

$ module avail chem/openbabel

3 Usage

3.1 Loading the module

You can load the default version of Open Babel with the following command:

$ module load chem/openbabel

The command will also load all modules Open Babel requires to function properly (e.g., the numerical library Eigen).

If you wish to load another (older) version of Open Babel, you can do so using

$ module load chem/openbabel/<version>

with <version> specifying the desired version.

3.2 Program Binaries

The main program of Open Babel is the conversion tool:

  • obabel -- a converter for chemistry and molecular modeling data files

To get help using the Open Babel conversion tool execute the following command:

$ obabel -H

Furthermore, a man page is available and can be accessed by typing:

$ man obabel

The Open Babel package includes a variety of additional tools:

  • obconformer -- generate conformer coordinates
  • obenergy -- calculate the energy for a molecule
  • obgen -- generate 3D coordinates for a molecule
  • obgui -- Open Babel graphical user interface
  • obprobe -- create electrostatic probe grid
  • obrms -- Calculate the heavy-atom RMSD between two chemically identical structures
  • obrotate -- batch-rotate dihedral angles matching SMARTS patterns
  • obsym -- detect 3D point group symmetry
  • obthermo -- extract the thermochemistry for a molecule
  • obchiral -- print molecular chirality information
  • obdistgen -- generate rough 3D coordinates for SMILES (or other 0D files
  • obfit -- superimpose two molecules based on a pattern
  • obgrep -- an advanced molecular search program using SMARTS
  • obminimize -- optimize the geometry, minimize the energy for a molecule
  • obprop -- print standard molecular properties
  • obrotamer -- generate conformer/rotamer coordinates
  • obspectrophore -- SPECTROPHORE calculator
  • obtautomer -- enumerate tautomer SMILES and canonical tautomer SMILES
  • roundtrip -- a comparison program for testing roundtrip conversion