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 <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:

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: <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.