NAME

obabel — a converter for chemistry and molecular modeling data files

SYNOPSIS

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, see 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 might need to be enclosed in quotation marks to avoid shell interpretation. More than one can be used, and a molecule title can be included if enclosed in quotes.

-aoptions

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 n

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

-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

-xoptions

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:

• abinit -- ABINIT Output Format [Read-only]
• acesin -- ACES input format [Write-only]
• acesout -- ACES output format [Read-only]
• acr -- ACR format [Read-only]
• adf -- ADF cartesian input format [Write-only]
• adfband -- ADF Band output format [Read-only]
• adfdftb -- ADF DFTB output format [Read-only]
• adfout -- ADF output format [Read-only]
• alc -- Alchemy format
• aoforce -- Turbomole AOFORCE output format [Read-only]
• arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
• ascii -- ASCII format [Write-only]
• axsf -- XCrySDen Structure Format [Read-only]
• bgf -- MSI BGF format
• box -- Dock 3.5 Box format
• bs -- Ball and Stick format
• c09out -- Crystal 09 output format [Read-only]
• c3d1 -- Chem3D Cartesian 1 format
• c3d2 -- Chem3D Cartesian 2 format
• cac -- CAChe MolStruct format [Write-only]
• 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]
• castep -- CASTEP format [Read-only]
• ccc -- CCC format [Read-only]
• cdjson -- ChemDoodle JSON
• cdx -- ChemDraw binary format [Read-only]
• cdxml -- ChemDraw CDXML format
• cht -- Chemtool format [Write-only]
• cif -- Crystallographic Information File
• cjson -- Chemical JSON
• ck -- ChemKin format
• cml -- Chemical Markup Language
• cmlr -- CML Reaction format
• cof -- Culgi object file format
• com -- Gaussian Input [Write-only]
• confabreport -- Confab report format [Write-only]
• CONFIG -- DL-POLY CONFIG
• CONTCAR -- VASP format
• CONTFF -- MDFF format
• copy -- Copy raw text [Write-only]
• crk2d -- Chemical Resource Kit diagram(2D)
• 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
• cub -- Gaussian cube format
• cube -- Gaussian cube format
• dallog -- DALTON output format [Read-only]
• dalmol -- DALTON input format
• dat -- Generic Output file format [Read-only]
• dmol -- DMol3 coordinates format
• dx -- OpenDX cube format for APBS
• ent -- Protein Data Bank format
• exyz -- Extended XYZ cartesian coordinates format
• fa -- FASTA format
• fasta -- FASTA format
• 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]
• fhiaims -- FHIaims XYZ format
• fix -- SMILES FIX format [Write-only]
• fps -- FPS text fingerprint format (Dalke) [Write-only]
• fpt -- Fingerprint format [Write-only]
• fract -- Free Form Fractional format
• fs -- Fastsearch format
• fsa -- FASTA format
• g03 -- Gaussian Output [Read-only]
• g09 -- Gaussian Output [Read-only]
• g16 -- Gaussian Output [Read-only]
• g92 -- Gaussian Output [Read-only]
• g94 -- Gaussian Output [Read-only]
• g98 -- Gaussian Output [Read-only]
• gal -- Gaussian Output [Read-only]
• gam -- GAMESS Output [Read-only]
• gamess -- GAMESS Output [Read-only]
• gamin -- GAMESS Input
• gamout -- GAMESS Output [Read-only]
• gau -- Gaussian Input [Write-only]
• gjc -- Gaussian Input [Write-only]
• gjf -- Gaussian Input [Write-only]
• got -- GULP format [Read-only]
• gpr -- Ghemical format
• gr96 -- GROMOS96 format [Write-only]
• gro -- GRO format
• gukin -- GAMESS-UK Input
• gukout -- GAMESS-UK Output
• gzmat -- Gaussian Z-Matrix Input
• hin -- HyperChem HIN format
• HISTORY -- DL-POLY HISTORY [Read-only]
• inchi -- InChI format
• inchikey -- InChIKey [Write-only]
• inp -- GAMESS Input
• ins -- ShelX format [Read-only]
• jin -- Jaguar input format
• jout -- Jaguar output format [Read-only]
• k -- Compare molecules using InChI [Write-only]
• lmpdat -- The LAMMPS data format [Write-only]
• log -- Generic Output file format [Read-only]
• lpmd -- LPMD format
• mae -- Maestro format
• maegz -- Maestro format
• mcdl -- MCDL format
• mcif -- Macromolecular Crystallographic Info
• MDFF -- MDFF format
• mdl -- MDL MOL format
• ml2 -- Sybyl Mol2 format
• mmcif -- Macromolecular Crystallographic Info
• mmd -- MacroModel format
• mmod -- MacroModel format
• mna -- Multilevel Neighborhoods of Atoms (MNA) [Write-only]
• mol -- MDL MOL format
• mol2 -- Sybyl Mol2 format
• mold -- Molden format
• molden -- Molden format
• molf -- Molden 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]
• mp -- Molpro input format [Write-only]
• mpc -- MOPAC Cartesian format
• mpd -- MolPrint2D format [Write-only]
• mpo -- Molpro output format [Read-only]
• mpqc -- MPQC output format [Read-only]
• mpqcin -- MPQC simplified input format [Write-only]
• mrv -- Chemical Markup Language
• msi -- Accelrys/MSI Cerius II MSI format [Read-only]
• msms -- M.F. Sanner's MSMS input format [Write-only]
• nul -- Outputs nothing [Write-only]
• nw -- NWChem input format [Write-only]
• nwo -- NWChem output format [Read-only]
• orca -- ORCA output format [Read-only]
• orcainp -- ORCA input format [Write-only]
• out -- Generic Output file format [Read-only]
• outmol -- DMol3 coordinates format
• output -- Generic Output file format [Read-only]
• paint -- Painter format [Write-only]
• pc -- PubChem format [Read-only]
• pcjson -- PubChem JSON
• pcm -- PCModel Format
• pdb -- Protein Data Bank format
• pdbqt -- AutoDock PDBQT format
• png -- PNG 2D depiction
• pointcloud -- Point cloud on VDW surface [Write-only]
• pos -- POS cartesian coordinates format [Read-only]
• POSCAR -- VASP format
• POSFF -- MDFF format
• pov -- POV-Ray input format [Write-only]
• pqr -- PQR format
• pqs -- Parallel Quantum Solutions format
• prep -- Amber Prep format [Read-only]
• pwscf -- PWscf 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]
• rinchi -- RInChI [Write-only]
• rsmi -- Reaction SMILES format
• rxn -- MDL RXN format
• sd -- MDL MOL format
• sdf -- MDL MOL format
• siesta -- SIESTA format [Read-only]
• smi -- SMILES format
• smiles -- SMILES format
• smy -- SMILES format using Smiley parser [Read-only]
• stl -- STL 3D-printing format [Write-only]
• svg -- SVG 2D depiction [Write-only]
• sy2 -- Sybyl Mol2 format
• t41 -- ADF TAPE41 format [Read-only]
• tdd -- Thermo format
• text -- Read and write raw text
• therm -- Thermo format
• tmol -- TurboMole Coordinate format
• txt -- Title format
• txyz -- Tinker XYZ format
• unixyz -- UniChem XYZ format
• VASP -- VASP format
• vmol -- ViewMol format
• wln -- Wiswesser Line Notation [Read-only]
• xed -- XED format [Write-only]
• xml -- General XML format [Read-only]
• xsf -- XCrySDen Structure 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:

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 current 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.