obabel (1) - Linux Manuals

obabel: a converter for chemistry and molecular modeling data files

Command to display obabel manual in Linux: $ man 1 obabel

NAME

babel , obabel - a converter for chemistry and molecular modeling data files

SYNOPSIS

[-H help-options ]
[OPTIONS ] [-i input-type ] infile [-o output-type ] outfile

obabel [-H help-options ]
obabel [OPTIONS ] [-i input-type | -: Qo SMILES-string Qc infile ] [-o output-type ] -O outfile

DESCRIPTION

is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas.

obabel and are slightly different. The first is closer to the normal Unix convention for commandline programs and more flexible when the user needs to specify parameter values on options. With babel this only works when the option is the last on the line; with obabel no such restriction applies. It further has a shortcut for entering SMILES strings, which can be used in place of an input file.

Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se 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.

-: Qo SMILES-string Qc Enter SMILES string and use it in place of an input file. The SMILES string

should be enclosed in quotation marks. 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 2

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 file ...

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 file ...

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. This option applies to obabel only.

-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:

acr -- Carine ASCI Crystal
alc -- Alchemy format
arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
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]
ccc -- CCC format [Read-only]
cdx -- ChemDraw binary format [Read-only]
cdxml -- ChemDraw CDXML format
cht -- Chemtool format [Write-only]
cif -- Crystallographic Information File
cml -- Chemical Markup Language
cmlr -- CML Reaction format
com -- Gaussian 98/03 Cartesian Input [Write-only]
copy -- Copies raw text [Write-only]
crk2d -- Chemical Resource Kit 2D diagram format
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
dmol -- DMol3 coordinates format
ent -- Protein Data Bank format
fa -- FASTA format [Write-only]
fasta -- FASTA format [Write-only]
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]
fix -- SMILES FIX format [Write-only]
fpt -- Fingerprint format [Write-only]
fract -- Free Form Fractional format
fs -- Open Babel FastSearching database
fsa -- FASTA format [Write-only]
g03 -- Gaussian 98/03 Output [Read-only]
g98 -- Gaussian 98/03 Output [Read-only]
gam -- GAMESS Output [Read-only]
gamin -- GAMESS Input [Write-only]
gamout -- GAMESS Output [Read-only]
gau -- Gaussian 98/03 Cartesian Input [Write-only]
gjc -- Gaussian 98/03 Cartesian Input [Write-only]
gjf -- Gaussian 98/03 Cartesian Input [Write-only]
gpr -- Ghemical format
gr96 -- GROMOS96 format [Write-only]
hin -- HyperChem HIN format
inchi -- IUPAC InChI [Write-only]
inp -- GAMESS Input [Write-only]
ins -- ShelX format [Read-only]
jin -- Jaguar input format [Write-only]
jout -- Jaguar output format [Read-only]
mdl -- MDL MOL format
mmd -- MacroModel format
mmod -- MacroModel format
mol -- MDL MOL format
mol2 -- Sybyl Mol2 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]
mpc -- MOPAC Cartesian format
mpd -- Sybyl descriptor format [Write-only]
mpqc -- MPQC output format [Read-only]
mpqcin -- MPQC simplified input format [Write-only]
nw -- NWChem input format [Write-only]
nwo -- NWChem output format [Read-only]
pc -- PubChem format [Read-only]
pcm -- PCModel format
pdb -- Protein Data Bank format
pov -- POV-Ray input format [Write-only]
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep 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]
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
smi -- SMILES format
sy2 -- Sybyl Mol2 format
tdd -- Thermo format
test -- Test format [Write-only]
therm -- Thermo format
tmol -- TurboMole Coordinate format
txyz -- Tinker MM2 format [Write-only]
unixyz -- UniChem XYZ format
vmol -- ViewMol format
xed -- XED format [Write-only]
xml -- General XML 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:

"babel -ixyz ethanol.xyz -opdb ethanol.pdb"

Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:

"babel -ismi -omol2"

Split a multi-molecule file into new1.smi, new2.smi, etc.:

"babel infile.mol new.smi -m"

AUTHORS

An -nosplit A cast of many, including the currrent maintainers An Geoff Hutchison , An Chris Morley , An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

COPYRIGHT

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.