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<!-- manual page source format generated by PolyglotMan v3.2, -->
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<title>man page(1) manual page</title>
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<a href='#toc'>Table of Contents</a><p>
<h2><a name='sect0' href='#toc0'>Name</a></h2>
<p>
<b>babel</b> -- a converter for chemistry and molecular modeling data files
<p>
<h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2>
<p>
<b>babel</b> [<b>-H</b> <i>help-options</i>]<br>
<b>babel</b> [<i>OPTIONS</i>] [<b>-i</b> <i>input-type</i>] <i>infile</i> [<b>-o</b> <i>output-type</i>] <i>outfile</i>
<p>
<h2><a name='sect2' href='#toc2'><b>Description</b></a></h2>
<p>
Open Babel is a cross-platform program designed to interconvert between
many file formats used in molecular modeling and computational chemistry
and related areas.
<p><p>
Note that Open Babel can also be used as a library to interconvert many
file formats and to provide standard chemistry software routines. See the
Open Babel web pages <<b>http://openbabel.sourceforge.net/</b>> for more information.
<p>
<h2><a name='sect3' href='#toc3'><b>Options</b></a></h2>
<p>
If only input and ouput files are given, Open Babel will guess the file
type from the filename extension.
<p>
<dl>
<dt><b>---errorlevel</b> <i>2</i></dt></dt>
<dd>
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
<p></dd>
<dt><b>-a</b> <i>options</i></dt></dt>
<dd>
Format-specific input options. See <b>-H</b> <i>format-ID</i> for options allowed
by a particular format
<p></dd>
<dt><b>-b</b> </dt></dt>
<dd> Convert dative bonds (e.g., [N+]([O-])=) to N(=O)=O)
<p></dd>
<dt><b>-c</b> </dt></dt>
<dd> Center atomic coordinates at (0,0,0)
<p></dd>
<dt><b>-d</b> </dt></dt>
<dd> Delete Hydrogens
<p></dd>
<dt><b>-f</b> <i>#</i> </dt></dt>
<dd>For multiple entry input, start import with molecule # as the first
entry
<p></dd>
<dt><b>-F</b> </dt></dt>
<dd> Output the available fingerprint types
<p></dd>
<dt><b>-h</b> </dt></dt>
<dd> Add hydrogens
<p></dd>
<dt><b>-H</b> </dt></dt>
<dd> Output usage information
<p></dd>
<dt><b>-H</b> <i>format-ID</i></dt></dt>
<dd>
Output formatting information and options for format specified
<p></dd>
<dt><b>-Hall</b></dt></dt>
<dd>
Output formatting information and options for all formats
<p></dd>
<dt><b>-i<format-ID></b></dt></dt>
<dd>
Specifies input format, see below for the available formats
<p></dd>
<dt><b>-j</b> </dt></dt>
<dd> Join all input molecules into a single output molecule entry
<p></dd>
<dt><b>-m</b> </dt></dt>
<dd> Produce multiple output files, to allow:
</dd>
<dt><b>-</b> </dt></dt>
<dd>Splitting one input file - put each molecule into consecutively
numbered output files
</dd>
<dt><b>-</b> </dt></dt>
<dd>Batch conversion - convert each of multiple input files
into a specified output format
<p></dd>
<dt><b>-l</b> <i>#</i> </dt></dt>
<dd>For multiple entry input, stop import with molecule # as the last
entry
<p></dd>
<dt><b>-o</b> <i>format-ID</i></dt></dt>
<dd>
Specifies output format, see below for the available formats
<p></dd>
<dt><b>-p</b> </dt></dt>
<dd> Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
<p></dd>
<dt><b>-s</b> <i>SMARTS</i></dt></dt>
<dd>
Convert only molecules matching the SMARTS pattern specified
<p></dd>
<dt><b>-t</b> </dt></dt>
<dd> All input files describe a single molecule
<p></dd>
<dt><b>-x</b> <i>options</i></dt></dt>
<dd>
Format-specific output options. See <b>-H</b> <i>format-ID</i> for options
allowed by a particular format
<p></dd>
<dt><b>-v</b> <i>SMARTS</i></dt></dt>
<dd>
Convert only molecules <b>NOT</b> matching SMARTS pattern specified
<p></dd>
<dt><b>-V</b> </dt></dt>
<dd> Output version number and exit
<p></dd>
<dt><b>-z</b> </dt></dt>
<dd> Compress the output with gzip
<p></dd>
</dl>
<h2><a name='sect4' href='#toc4'><b>File</b> <b>Formats</b></a></h2>
<p>
The following formats are currently supported by Open Babel:
alc -- Alchemy format<br>
bgf -- MSI BGF format<br>
box -- Dock 3.5 Box format<br>
bs -- Ball and Stick format<br>
c3d1 -- Chem3D Cartesian 1 format<br>
c3d2 -- Chem3D Cartesian 2 format<br>
caccrt -- Cacao Cartesian format<br>
cache -- CAChe MolStruct format [Write-only]
cacint -- Cacao Internal format [Write-only]
car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
ccc -- CCC format [Read-only]<br>
cht -- Chemtool format [Write-only]
cml -- Chemical Markup Language<br>
cmlr -- CML Reaction format<br>
com -- Gaussian 98/03 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<br>
ent -- Protein Data Bank format<br>
feat -- Feature format<br>
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 -- FastSearching<br>
g03 -- Gaussian98/03 Output [Read-only]
g98 -- Gaussian98/03 Output [Read-only]
gam -- GAMESS Output [Read-only]<br>
gamin -- GAMESS Input [Write-only]<br>
gamout -- GAMESS Output [Read-only]
gau -- Gaussian 98/03 Cartesian Input [Write-only]
gpr -- Ghemical format<br>
gr96 -- GROMOS96 format [Write-only]
hin -- HyperChem HIN format<br>
inchi -- IUPAC InChI descriptor [Write-only]
inp -- GAMESS Input [Write-only]<br>
ins -- ShelX format [Read-only]<br>
jin -- Jaguar input format [Write-only]
jout -- Jaguar output format [Read-only]
mdl -- MDL MOL format<br>
mmd -- MacroModel format<br>
mmod -- MacroModel format<br>
mol -- MDL MOL format<br>
mol2 -- Sybyl Mol2 format<br>
mopcrt -- MOPAC Cartesian format<br>
mopout -- MOPAC Output format [Read-only]
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]<br>
pcm -- PCModel format<br>
pdb -- Protein Data Bank format<br>
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]<br>
rxn -- MDL RXN format<br>
sd -- MDL MOL format<br>
sdf -- MDL MOL format<br>
smi -- SMILES format<br>
test -- Test format [Write-only]<br>
tmol -- TurboMole Coordinate format
txyz -- Tinker MM2 format [Write-only]
unixyz -- UniChem XYZ format<br>
vmol -- ViewMol format<br>
xed -- XED format [Write-only]<br>
xml -- General XML format [Read-only]
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format<br>
zin -- ZINDO input format [Write-only]
<p>
<h2><a name='sect5' href='#toc5'><b>Format</b> <b>Options</b></a></h2>
<p>
Individual file formats may have additional formatting options.
<p><p>
Input format options are preceded by ‘a’, e.g. -as
<p><p>
Output format options are preceded by ‘x’, e.g. -xn
<p><p>
For further specific information and options, use -H<format-type>
e.g., -Hcml
<p>
<h2><a name='sect6' href='#toc6'><b>Examples</b></a></h2>
<p>
Standard conversion:<br>
babel -ixyz ethanol.xyz -opdb ethanol.pdb
Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
babel -ismi -omol2<br>
Split a multi-molecule file into new1.smi, new2.smi, etc.:
babel infile.mol new.smi -m
<p>
<h2><a name='sect7' href='#toc7'><b>See</b> <b>Also</b></a></h2>
<p>
<a href='obfit.1'>obfit(1)</a>
, <a href='obgrep.1'>obgrep(1)</a>
, <a href='obprop.1'>obprop(1)</a>
, <a href='obrotate.1'>obrotate(1)</a>
The web pages for Open Babel
can be found at: <<b>http://openbabel.sourceforge.net/</b>>
<p>
<h2><a name='sect8' href='#toc8'><b>Authors</b></a></h2>
<p>
A cast of many, including currrent maintainers Geoff Hutchison, Chris
Morley, Michael Banck, and innumerable others who have contributed fixes
and additions. For more contributors to Open Babel, see <<b>http://openbabel.sourceforge.net/THANKS.shtml</b>>
<p>
<h2><a name='sect9' href='#toc9'><b>Copyright</b></a></h2>
<p>
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. Some portions
Copyright (C) 2001-2005 by Geoffrey R. Hutchison
<p><p>
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.
<p><p>
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.
<p>
<hr><p>
<a name='toc'><b>Table of Contents</b></a><p>
<ul>
<li><a name='toc0' href='#sect0'>Name</a></li>
<li><a name='toc1' href='#sect1'>Synopsis</a></li>
<li><a name='toc2' href='#sect2'>Description</a></li>
<li><a name='toc3' href='#sect3'>Options</a></li>
<li><a name='toc4' href='#sect4'>File Formats</a></li>
<li><a name='toc5' href='#sect5'>Format Options</a></li>
<li><a name='toc6' href='#sect6'>Examples</a></li>
<li><a name='toc7' href='#sect7'>See Also</a></li>
<li><a name='toc8' href='#sect8'>Authors</a></li>
<li><a name='toc9' href='#sect9'>Copyright</a></li>
</ul>
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