NAME¶
babel, obabel —
a converter for
chemistry and molecular modeling data files
SYNOPSIS¶
babel, obabel |
[-H
help-options] |
babel, obabel |
[OPTIONS]
[-i
input-type] infile
[-o
output-type]
outfile |
obabel |
[OPTIONS]
[-i input-type |
-:
“SMILES-string”]
infile [-o
output-type] -O
outfile |
DESCRIPTION¶
babel, obabel is a cross-platform program designed to
interconvert between many file formats used in molecular modeling and
computational chemistry and related areas.
obabel and
babel, obabel are slightly
different. The first is closer to the normal Unix convention for commandline
programs and more flexible when the user needs to specify parameter values on
options. With
babel this only works when the option is the
last on the line; with
obabel no such restriction applies.
It further has a shortcut for entering SMILES strings, which can be used in
place of an input file.
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.
- -:
“SMILES-string”
- Enter SMILES string and use it in place of an input file.
The SMILES string should be enclosed in quotation marks. More than one can
be used, and a molecule title can be included if enclosed in quotes.
- -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
- -O
outfile
- Specify the output file. This option applies to
obabel only.
- -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
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]
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.