OBABEL(1)

📦
version 3.2.1 · 3 versions
, in arch rolling, opensuse-leap 16.0

🌸 obabel(1) — User's Reference Manual, but make it group chat ✨

🎀 NAME 🎀

obabel — a converter for chemistry and molecular modeling data files. Like, it takes your molecular data and gives it a whole new file-format outfit, bestie. 💅

✨ SYNOPSIS ✨

Okay so here's the exact vibe:

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. No cap, it's the format-swapping main character. 🔥

Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, see the Open Babel web pages at https://openbabel.org/. 🫶

💖 OPTIONS 💖

If only input and output files are given, Open Babel will guess the file type from the filename extension. Lowkey detective work, honestly. 🔍

  • -:SMILES-string — enter a 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. Chemistry glow-up, fr fr. ⚗️
  • -c — center atomic coordinates at (0,0,0). Put it in the middle, periodt. 🎯
  • -C — combine molecules in first file with others having the same name. Reunion episode energy. 👯
  • -e — continue after errors. We keep it moving, bestie. 🚶‍♀️
  • -d — delete Hydrogens. Bye-bye, lil H's. 👋
  • ---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. Start at the part you actually care about. ⏩
  • -F — output the available fingerprint types. Fingerprints but make it chemistry. 🔎
  • -h — add hydrogens. Hydrating your molecule, iconic. 💧
  • -H — output usage information. The classic "how do I work this thing" button. 🆘
  • -Hformat-ID — output formatting information and options for format specified. Peep the format's whole lore. 📖
  • -Hall — output formatting information and options for all formats. The full encyclopedia, no skips. 📚
  • -iformat-ID — specifies input format, see below for the available formats. Tell it what you're feeding it. 🍽️
  • -j, --join — join all input molecules into a single output molecule entry. Friendship bracelet mode. 🫶
  • -k — translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian). Translator era. 🗣️
  • -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. Exit stage left. 🚪
  • -oformat-ID — specifies output format, see below for the available formats. Tell it what outfit to leave in. 👗
  • -Ooutfile — specify the output file. Name the destination, bestie. 📁
  • -p — add Hydrogens appropriate for pH (use transforms in phmodel.txt). pH-pilled hydrogen behavior. 🧪
  • --property — add or replace a property (e.g., in an MDL SD file). Property makeover moment. 💅
  • -s SMARTS — convert only molecules matching the SMARTS pattern specified. If it matches, it slays. 🎯
  • --separate — separate disconnected fragments into individual molecular records. Break it up, break it up. ✂️
  • -t — all input files describe a single molecule. Teamwork, but for files. 🤝
  • --title title — add or replace molecular title. Give it a name worth remembering. 🏷️
  • -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. The "not invited to the group chat" filter. 🙅‍♀️
  • -V — output version number and exit. Quick little version check, then dip. 👋
  • -z — compress the output with gzip. Tiny file, big serve. 🗜️

🌈 FILE FORMATS 🌈

okay so Open Babel currently supports literally all of these formats, bestie — full roster, no skips, no cap:

  • 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]

That's the whole roster 💅 the bracket labels are exactly as Open Babel lists them.

🎀 FORMAT OPTIONS 🎀

okay so 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 — that's where the format-specific tea lives ✨

🌸 ENVIRONMENT 🌸

  • OB_RANDOM_SEED — Seed for the pseudo random number generator; a random seed is used if this is unset or null. This feature is effective if Open Babel is built with the -DOB_USE_OBRANDOMMT cpreprocessor flag (it 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 🫶

you'll also want to hang out with obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotamer(1), and obrotate(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 <https://openbabel.org/docs/Introduction/thanks.html> 💖

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.

xoxo, your Unix bestie 💖 — this page's footer says Open Babel 3.2, dated May 26, 2026, and the manpage tag is OBABEL(1). 🎀

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