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 ouput 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 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
	   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 98/03 Cartesian Input [Write-only]
	   gjc -- Gaussian 98/03 Cartesian Input [Write-only]
	   gjf -- Gaussian 98/03 Cartesian Input [Write-only]
	   gpr -- Ghemical format
	   gr96 -- GROMOS96 format [Write-only]
	   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 MERCHANTABIL-
     ITY 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