obabel - Man Page

• Convert a .mol file to XYZ coordinates: obabel path/to/file.mol -O path/to/output_file.xyz

• Convert a Simplified Molecular Input Line Entry System string to a 500x500 picture: obabel -:"smiles_string" -O path/to/output_file.png -xp 500

• Convert a file of SMILES string to separate 3D .mol files: obabel path/to/file.smi -O path/to/output_file.mol --gen3D -m

• Render multiple inputs into one picture: obabel path/to/file1 path/to/file2 ... -O path/to/output_file.png

tldr.sh

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/>.

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

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]

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

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).

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

obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotamer(1), obrotate(1). The web pages for Open Babel can be found at: <http://openbabel.org/>

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.

obchiral(1), obconformer(1), obenergy(1), obfit(1), obgen(1), obgrep(1), obgui(1), obminimize(1), obprobe(1), obprop(1), obrotamer(1), obrotate(1), obspectrophore(1), obtautomer(1), obthermo(1), roundtrip(1).