--- name: "obabel" section: "1" platform: "linux" package: "openbabel" version: "3.2.1-1" release: "Arch Linux 2026-11-01" platforms: ["linux"] url: "https://new.carta.tech/obabel" --- # obabel(1) a converter for chemistry and molecular modeling data files ## 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 chemistry software. For more information, see the Open Babel web pages \<**https://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. - **-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** *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 - **-x***options* 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** ## 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)](/obenergy/1.md), [obfit(1)](/obfit/1.md), [obgrep(1)](/obgrep/1.md), [obminimize(1)](/obminimize/1.md), [obprop(1)](/obprop/1.md), [obrotamer(1)](/obrotamer/1.md), [obrotate(1)](/obrotate/1.md). 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 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.