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.

Open Babel 3.1                                    Oct 10, 2019                                         obabel(1)