OBABEL(1) General Commands Manual (urm) OBABEL(1) NAME obabel - a converter for chemistry and molecular modeling data files SYNOPSIS obabel -Hhelp-options obabel [OPTIONS] [-iinput-type | -:SMILES-string] infile [-ooutput-type] -Ooutfile 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 . 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 -Hformat-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 -Hformat-ID Output formatting information and options for format specified -Hall Output formatting information and options for all formats -iformat-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 -oformat-ID Specifies output format, see below for the available formats -Ooutfile 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 -Hformat-type, e.g., -Hcml ENVIRONMENT OB_RANDOM_SEED Seed for pseudo random number generator; random seed is used if unset or null. This feature is effective if Open Babel is built with -DOB_USE_OBRANDOMMT cpreprocessor flag (will be automatically enabled when version 4 is released). 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), obrotamer(1), obrotate(1). The web pages for Open Babel can be found at: 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 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 3.2 May 26, 2026 Open Babel 3.2