Babel

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Name

babel -- a converter for chemistry and molecular modeling data files

Synopsis

babel [-H help-options]

babel [OPTIONS] [-i input-type] infile [-o output-type] outfile

Description

Open Babel is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas.

Note that Open Babel can also be used as a library to interconvert many file formats and to provide standard chemistry software routines. See the Open Babel web pages <http://openbabel.sourceforge.net/> for more information.

Options

If only input and ouput files are given, Open Babel will guess the file type from the filename extension.

---errorlevel 2
Filter the level of errors and warnings displayed:
  • 1 = critical errors only
  • 2 = include warnings too (default)
  • 3 = include informational messages too
  • 4 = include "audit log" messages of changes to data
  • 5 = include debugging messages too
-a options
Format-specific input options. See -H format-ID for options allowed by a particular format
-b
Convert dative bonds (e.g., [N+]([O-])=O to N(=O)=O
-c
Center atomic coordinates at (0,0,0)
-d
Delete Hydrogens
-f #
For multiple entry input, start import with molecule # as the first entry
-F
Output the available fingerprint types
-h
Add hydrogens
-H
Output usage information
-H format-ID
Output formatting information and options for format specified
-Hall
Output formatting information and options for all formats
-i<format-ID>
Specifies input format, see below for the available formats
-j
Join all input molecules into a single output molecule entry
-m
Produce multiple output files, to allow:
  • Splitting one input file - put each molecule into consecutively numbered output files
  • Batch conversion - convert each of multiple input files into a specified output format
-l #
For multiple entry input, stop import with molecule # as the last entry
-o format-ID
Specifies output format, see below for the available formats
-p
Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
-s SMARTS
Convert only molecules matching the SMARTS pattern specified
-t
All input files describe a single molecule
-x options
Format-specific output options. See -H format-ID for options allowed by a particular format
-v SMARTS
Convert only molecules NOT matching SMARTS pattern specified
-V
Output version number and exit
-z
Compress the output with gzip

File Formats

The following formats are currently supported by Open Babel:

  • alc -- Alchemy format
  • bgf -- MSI BGF format
  • box -- Dock 3.5 Box format
  • bs -- Ball and Stick format
  • c3d1 -- Chem3D Cartesian 1 format
  • c3d2 -- Chem3D Cartesian 2 format
  • caccrt -- Cacao Cartesian format
  • cache -- CAChe MolStruct format [Write-only]
  • cacint -- Cacao Internal format [Write-only]
  • car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
  • ccc -- CCC format [Read-only]
  • cht -- Chemtool format [Write-only]
  • cml -- Chemical Markup Language
  • cmlr -- CML Reaction format
  • com -- Gaussian 98/03 Cartesian Input [Write-only]
  • copy -- Copies raw text [Write-only]
  • crk2d -- Chemical Resource Kit 2D diagram format
  • crk3d -- Chemical Resource Kit 3D format
  • csr -- Accelrys/MSI Quanta CSR format [Write-only]
  • cssr -- CSD CSSR format [Write-only]
  • ct -- ChemDraw Connection Table format
  • dmol -- DMol3 coordinates format
  • ent -- Protein Data Bank format
  • feat -- Feature format
  • fh -- Fenske-Hall Z-Matrix format [Write-only]
  • fix -- SMILES FIX format [Write-only]
  • fpt -- Fingerprint format [Write-only]
  • fract -- Free Form Fractional format
  • fs -- FastSearching Index
  • g03 -- Gaussian98/03 Output [Read-only]
  • g98 -- Gaussian98/03 Output [Read-only]
  • gam -- GAMESS Output [Read-only]
  • gamin -- GAMESS Input [Write-only]
  • gamout -- GAMESS Output [Read-only]
  • gau -- Gaussian 98/03 Cartesian Input [Write-only]
  • gpr -- Ghemical format
  • gr96 -- GROMOS96 format [Write-only]
  • hin -- HyperChem HIN format
  • inchi -- IUPAC InChI descriptor [Write-only]
  • inp -- GAMESS Input [Write-only]
  • ins -- ShelX format [Read-only]
  • jin -- Jaguar input format [Write-only]
  • jout -- Jaguar output format [Read-only]
  • mdl -- MDL MOL format
  • mmd -- MacroModel format
  • mmod -- MacroModel format
  • mol -- MDL MOL format
  • mol2 -- Sybyl Mol2 format
  • mopcrt -- MOPAC Cartesian format
  • mopout -- MOPAC Output format [Read-only]
  • mpd -- Sybyl descriptor format [Write-only]
  • mpqc -- MPQC output format [Read-only]
  • mpqcin -- MPQC simplified input format [Write-only]
  • nw -- NWChem input format [Write-only]
  • nwo -- NWChem output format [Read-only]
  • pc -- PubChem format [Read-only]
  • pcm -- PCModel format
  • pdb -- Protein Data Bank format
  • pov -- POV-Ray input format [Write-only]
  • pqs -- Parallel Quantum Solutions format
  • prep -- Amber Prep format [Read-only]
  • qcin -- Q-Chem input format [Write-only]
  • qcout -- Q-Chem output format [Read-only]
  • report -- Open Babel report format [Write-only]
  • res -- ShelX format [Read-only]
  • rxn -- MDL RXN format
  • sd -- MDL MOL format
  • sdf -- MDL MOL format
  • smi -- SMILES format
  • test -- Test format [Write-only]
  • tmol -- TurboMole Coordinate format
  • txyz -- Tinker MM2 format [Write-only]
  • unixyz -- UniChem XYZ format
  • vmol -- ViewMol format
  • xed -- XED format [Write-only]
  • xml -- General XML format [Read-only]
  • xyz -- XYZ cartesian coordinates format
  • yob -- YASARA.org YOB format
  • zin -- ZINDO input format [Write-only]

Format Options

Individual file formats may have additional formatting options.

Input format options are preceded by ‘a’, e.g. -as

Output format options are preceded by ‘x’, e.g. -xn

For further specific information and options, use -H<format-type>
e.g., -Hcml

Examples

Standard conversion:

babel -ixyz ethanol.xyz -opdb ethanol.pdb

Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:

babel -ismi -omol2

Split a multi-molecule file into new1.smi, new2.smi, etc.:

babel infile.mol new.smi -m

See Also

obfit , obgrep , obprop , obrotate.

The web pages for Open Babel can be found at: <http://openbabel.sourceforge.net/>

Authors

A cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see the Contributor List

Copyright

Copyright © 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright © 2001-2005 by Geoffrey R. Hutchison and other contributors.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.