NAME

     obabel — 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:
           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:
           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>

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.