NAME

       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:
             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:
             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>

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.

Open Babel 2.2                                    July 4, 2008                                          babel(1)