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

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 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 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 WITH-
     OUT 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			Open Babel 3.1

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

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