obabel - Man Page

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.

-: "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

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

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/>

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>

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