babel -- a converter for chemistry and molecular modeling data files
babel [-H help-options]
babel [OPTIONS] [-i input-type] infile [-o output-type] outfile
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.
If only input and ouput files are given, Open Babel will guess the file type from the filename extension.
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]
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
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
obfit(1) , obgrep(1) , obprop(1) , obrotate(1) The web pages for Open Babel can be found at: <http://openbabel.sourceforge.net/>
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 (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.