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
Babel is a cross-platform program designed to interconvert between many
file formats used in molecular modeling and computational chemistry and
related areas.
Open Babel is also a complete programmers toolkit for developing
chemistry software. For more information, se the Open Babel web pages
<http://openbabel.org/>.
OPTIONS
If only input and ouput files are given, Open Babel will guess the file
type from the filename extension.
-a options
Format-specific input options. See -H format-ID for options allowed
by a particular format
--addtotitle
Append text to the current molecule title
--addformula
Append the molecular formula after the current molecule title
-b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
-c Center atomic coordinates at (0,0,0)
-C Combine molecules in first file with others having the same name
-e Continue after errors
-d Delete Hydrogens
---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
-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
Join all input molecules into a single output molecule entry
-k Translate computational chemistry modeling keywords (e.g., GAMESS
and Gaussian)
-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)
--property
Add or replace a property (e.g., in an MDL SD file)
-s SMARTS
Convert only molecules matching the SMARTS pattern specified
--separate
Separate disconnected fragments into individual molecular records
-t All input files describe a single molecule
--title title
Add or replace molecular title
-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:
acr -- Carine ASCI Crystal
alc -- Alchemy format
arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
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]
can -- Canonical SMILES format
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
ccc -- CCC format [Read-only]
cdx -- ChemDraw binary format [Read-only]
cdxml -- ChemDraw CDXML format
cht -- Chemtool format [Write-only]
cif -- Crystallographic Information File
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
fa -- FASTA format [Write-only]
fasta -- FASTA format [Write-only]
fch -- Gaussian formatted checkpoint file format [Read-only]
fchk -- Gaussian formatted checkpoint file format [Read-only]
fck -- Gaussian formatted checkpoint file format [Read-only]
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 -- Open Babel FastSearching database
fsa -- FASTA format [Write-only]
g03 -- Gaussian 98/03 Output [Read-only]
g98 -- Gaussian 98/03 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]
gjc -- Gaussian 98/03 Cartesian Input [Write-only]
gjf -- Gaussian 98/03 Cartesian Input [Write-only]
gpr -- Ghemical format
gr96 -- GROMOS96 format [Write-only]
hin -- HyperChem HIN format
inchi -- IUPAC InChI [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
molreport -- Open Babel molecule report [Write-only]
moo -- MOPAC Output format [Read-only]
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mopout -- MOPAC Output format [Read-only]
mpc -- MOPAC Cartesian format
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
sy2 -- Sybyl Mol2 format
tdd -- Thermo format
test -- Test format [Write-only]
therm -- Thermo format
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
obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1),
obrotamer(1). The web pages for Open Babel can be found at:
<http://openbabel.org/>
AUTHORS
A cast of many, including the 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.org/wiki/THANKS>
COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2007 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.