obabel - Man Page

a converter for chemistry and molecular modeling data files


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


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


Append text to the current molecule title


Append the molecular formula after the current molecule title


Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O


Center atomic coordinates at (0,0,0)


Combine molecules in first file with others having the same name


Continue after errors


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


Output the available fingerprint types


Add hydrogens


Output usage information

-H format-ID

Output formatting information and options for format specified


Output formatting information and options for all formats


Specifies input format, see below for the available formats


Join all input molecules into a single output molecule entry


Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian)


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.


Add Hydrogens appropriate for pH (use transforms in phmodel.txt)


Add or replace a property (e.g., in an MDL SD file)


Convert only molecules matching the SMARTS pattern specified


Separate disconnected fragments into individual molecular records


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


Convert only molecules NOT matching SMARTS pattern specified


Output version number and exit


Compress the output with gzip

File Formats

The following formats are currently supported by Open Babel:

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


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/>


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>

Referenced By

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).

October 10, 2019