obabel

Table of Contents

## Name

obabel -- a converter for chemistry and molecular modeling data files

## Synopsis

obabel [-H help-options]
obabel [OPTIONS] [-i input-type | -: "SMILES-string"] infile [-o output-type] -O outfile

## Description

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/>.

## Options

If only input and output 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 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]

## 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:

    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

## 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/>

More details on the formats supported by Open Babel can be found at: <http://openbabel.org/wiki/Formats>

## 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.

Table of Contents

- Name
- Synopsis
- Description
- Options
- File Formats
- Format Options
- Examples
- See Also
- Authors
- Copyright