babel man page

babel, obabel — a converter for chemistry and molecular modeling data files

Synopsis

babel [-H help-options]

babel [Options] [-i input-type] infile [-o output-type] outfile


obabel [-H help-options]

obabel [Options] [-i input-type | -: “SMILES-string] infile [-o output-type] -O outfile

Description

babel 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 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 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:

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>

Referenced By

chemtool(1), 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), roundtrip(1).

obabel(1) is an alias of babel(1).

July 4, 2008