obabel

babel(1)                    User's Reference Manual                   babel(1)

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                   Open Babel 2.2