obabel(1)

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 <http://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 -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

-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 -H format-type, e.g., -Hcml

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

AUTHORS
-nosplit 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 <http://openbabel.org/wiki/THANKS>

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.