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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 nor-
     mal 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	re-
     striction 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 chem-
     istry 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 consec-
		     utively 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	al-
	   lowed 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 Li-
     cense for more details.

Open Babel 2.2			 July 4, 2008			Open Babel 2.2

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | FILE FORMATS | FORMAT OPTIONS | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT

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