obabel - Man Page

• Convert a .mol file to XYZ coordinates: obabel path/to/file.mol -O path/to/output_file.xyz

• Convert a SMILES string to a 500x500 picture: obabel -:"SMILES -O path/to/output_file.png -xp 500

• Convert a file of SMILES string to separate 3D .mol files: obabel path/to/file.smi -O path/to/output_file.mol --gen3D -m

• Render multiple inputs into one picture: obabel path/to/file1 path/to/file2 ... -O path/to/output_file.png

tldr.sh

obabel 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/>.

If only input and output 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 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 Cartesian Input [Write-only]

• gjc -- Gaussian Cartesian Input [Write-only]

• gjf -- Gaussian Cartesian Input [Write-only]

• gpr -- Ghemical format

• gr96 -- GROMOS96 format [Write-only]

• gzmat -- Gaussian Z-Matrix Input

• 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

Standard conversion:

obabel ethanol.xyz -Oethanol.pdb

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

obabel -ismi -omol2

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

obabel infile.mol -Onew.smi -m

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/>

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 (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.

obchiral(1), obconformer(1), obenergy(1), obfit(1), obgen(1), obgrep(1), obgui(1), obminimize(1), obprobe(1), obprop(1), obrotamer(1), obrotate(1), obspectrophore(1), obtautomer(1), obthermo(1), roundtrip(1).