Monday, March 16, 2009

Open Babel command line options

Open Babel command line options are as follows.

Open Babel converts chemical structures from one file format to another

Usage: babel <input> <output> [Options]

Each spec can be a file whose extension decides the format.
Optionally the format can be specified by preceding the file by
-i<format-type>&e.g. -icml, for input and -o<format-type> for output

See below for available format-types, which are the same as the
file extensions and are case independent.
If no input or output file is given stdin or stdout are used instead.

More than one input file can be specified and their names can contain
wildcard chars (* and ?).The molecules are aggregated in the output file.

Conversion options

-f <#> Start import at molecule # specified
-l <#> End import at molecule # specified
-e Continue with next object after error, if possible
-z Compress the output with gzip
-k Attempt to translate keywords
-H Outputs this help text
-Hxxx (xxx is file format ID e.g. -Hcml) gives format info
-Hall Outputs details of all formats
-V Outputs version number
-L <basetype> Lists plugin classes of this type
e.g. <fingerprints>, or <plugins> for a list of BaseTypes
-m Produces multiple output files, to allow:
Splitting: e.g. babel infile.mol new.smi -m
puts each molecule into new1.smi new2.smi etc
Batch conversion: e.g. babel *.mol -osmi -m
converts each input file to a .smi file

For conversions of molecules

Additional options :

-d Delete hydrogens (make implicit)
-h Add hydrogens (make explicit)
-p Add Hydrogens appropriate for pH model
-b Convert dative bonds e.g.[N+]([O-])=O to N(=O)=O
-c Center Coordinates
-C Combine mols in first file with others having same name
--filter <filterstring> Filter: convert only when tests are true:
--add <list> Add properties from descriptors:
--delete <list> Delete properties in list:
--append <list> Appends properties or descriptors in list to title:
-s"smarts" Convert only molecules matching SMARTS:
-v"smarts" Convert only molecules NOT matching SMARTS:
--join Join all input molecules into a single output molecule
--separate Output disconnected fragments separately
--property <attrib> <value> add or replace a property (SDF)
--title <title> Add or replace molecule title
--addtotitle <text> Append to title
--addformula Append formula to title
--AddPolarH Adds hydrogen to polar atoms only
--center Centers coordinates around (0,0,0)
--gen3D Generate 3D coordinates
--nodative Replace [N+]([O-])=O by N(=O)=O

Interface to OBAPI internals
API options, e.g. ---errorlevel 2
errorlevel # min warning level displayed

The following file formats are recognized:

acr -- ACR format [Read-only]
adf -- ADF cartesian input format [Write-only]
adfout -- ADF output format [Read-only]
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
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]
ccc -- CCC format [Read-only]
cdx -- ChemDraw binary format [Read-only]
cdxml -- ChemDraw CDXML format
cht -- Chemtool format [Write-only]
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
com -- Gaussian 98/03 Input [Write-only]
copy -- Copies 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 -- OpenDX cube format for APBS
cube -- OpenDX cube format for APBS
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
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 -- FastSearching
fsa -- FASTA format [Write-only]
g03 -- Gaussian98/03 Output [Read-only]
g92 -- Gaussian98/03 Output [Read-only]
g94 -- Gaussian98/03 Output [Read-only]
g98 -- Gaussian98/03 Output [Read-only]
gal -- Gaussian98/03 Output [Read-only]
gam -- GAMESS Output [Read-only]
gamin -- GAMESS Input
gamout -- GAMESS Output [Read-only]
gau -- Gaussian 98/03 Input [Write-only]
gjc -- Gaussian 98/03 Input [Write-only]
gjf -- Gaussian 98/03 Input [Write-only]
gpr -- Ghemical format
gr96 -- GROMOS96 format [Write-only]
gukin -- GAMESS-UK Input
gukout -- GAMESS-UK Output
gzmat -- Gaussian Z-Matrix Input
hin -- HyperChem HIN format
inchi -- InChI format
inp -- GAMESS Input
ins -- ShelX format [Read-only]
jin -- Jaguar input format [Write-only]
jout -- Jaguar output format [Read-only]
k -- Compare molecules using InChI [Write-only]
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Information
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Information
mmd -- MacroModel format
mmod -- MacroModel format
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
molden -- Molden input format [Read-only]
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]
msi -- Accelrys/MSI Cerius II MSI format [Read-only]
msms -- M.F. Sanner's MSMS input format [Write-only]
nw -- NWChem input format [Write-only]
nwo -- NWChem output format [Read-only]
outmol -- DMol3 coordinates format
pc -- PubChem format [Read-only]
pcm -- PCModel Format
pdb -- Protein Data Bank format
png -- PNG files with embedded data
pov -- POV-Ray input format [Write-only]
pqr -- PQR format
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]
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
smi -- SMILES format
smiles -- SMILES format
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format [Read-only]
tdd -- Thermo format
test -- Test format [Write-only]
therm -- Thermo format
tmol -- TurboMole Coordinate format
txt -- Title 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]
xtc -- XTC format [Read-only]
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format [Write-only]

cml Chemical Markup Language
XML format. This implementation uses libxml2.
Write options for CML: -x[flags] (e.g. -x1ac)
1 output CML1 (rather than CML2)
a output array format for atoms and bonds
A write aromatic bonds as such, not Kekule form
h use hydrogenCount for all hydrogens
m output metadata
x omit XML and namespace declarations
c continuous output: no formatting
p output properties
N add namespace prefix to elements

Input options, e.g. -a2

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