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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-])=) 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
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(1) , obgrep(1) , obprop(1) , obrotate(1) 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 <http://openbabel.sourceforge.net/THANKS.shtml>

Copyright

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison

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

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.

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