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 <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.

-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:

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: <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.