"obabel -L formats" - List of File Formats Supported

This section provides a list of molecule file formats supported by Open Babel obtained by the 'obabel -L formats' command.

The main advantage of using Open Babel instead of other tools is that it supports a large number molecule file formats, total of 184.

You can use "obabel -L formats" command to get a list of File Formats Supported by Open Babel:

herong$ obabel -L formats

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]
cht -- Chemtool format [Write-only]
cif -- Crystallographic Information File
ck -- ChemKin format
cof -- Culgi object file format
com -- Gaussian Input [Write-only]
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
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]
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]
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]
xsf -- XCrySDen Structure Format [Read-only]
xyz -- XYZ cartesian coordinates format
yob -- YASARA.org YOB format
zin -- ZINDO input format [Write-only]

Table of Contents

 About This Book

 SMILES (Simplified Molecular-Input Line-Entry System)

 Open Babel: The Open Source Chemistry Toolbox

Using Open Babel Command: "obabel"

 What Is "obabel" Command

 "obabel -i ..." - Input Data Format and Source

 "obabel -o ... -O" - Output Data Format and Destination

 "obabel -... --..." - Generic Conversion Options

 "obabel" Command Option Argument Syntax

 "obabel ... --gen2D" - Calculated 2D Coordinates

 "obabel ... -f # -l #" - Split Large Molecule File

 "obabel -h/-d" - Add/Remove Hydrogens in Molecule Data

 "obabel --append ..." - Calculate Molecule Properties

"obabel -L formats" - List of File Formats Supported

 "obabel -a..." - Extra Options for Input Reading

 "obabel -x..." - Extra Options for Output Writing

 "obabel" vs. "babel" Open Babel Commands

 Generating SVG Pictures with Open Babel

 Substructure Search with Open Babel

 Similarity Search with Open Babel

 Fingerprint Index for Fastsearch with Open Babel

 Stereochemistry with Open Babel

 Command Line Tools Provided by Open Babel

 RDKit: Open-Source Cheminformatics Software

 rdkit.Chem.rdchem - The Core Module

 rdkit.Chem.rdmolfiles - Molecular File Module

 rdkit.Chem.rdDepictor - Compute 2D Coordinates

 rdkit.Chem.Draw - Handle Molecule Images

 Molecule Substructure Search with RDKit

 rdkit.Chem.rdmolops - Molecule Operations

 Daylight Fingerprint Generator in RDKit

 Morgan Fingerprint Generator in RDKit

 RDKit Performance on Substructure Search

 Introduction to Molecular Fingerprints

 OCSR (Optical Chemical Structure Recognition)

 AlphaFold - Protein Structure Prediction

 Resources and Tools

 Cheminformatics Related Terminologies


 Full Version in PDF/EPUB