Chemical Formats
Tools to convert chemical formats
Overview
Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation.
Labii is developing a list of widgets that can convert one chemical format to other chemical formats. Here is a list of widgets:
Widget | Type | Description |
Section | Convert chemical formats with Open Babel | |
Section | Resolve a structure identifier to a file |
Obabel
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. This widget uses the Obabel function from the Open Babel to convert nearly all the chemical formats and it very practical to quickly move from one program to another.
To convert format:
Copy and paste the data into the Input field.
You can also load the data from one of the Chemical Drawing widget by selecting a section.
Make sure the Input format is correct
Select the Output format
Click the Submit
Copy or click Download to download the transformed data.
Supported formats:
mol -- MDL MOL format
pdb -- Protein Data Bank format
smi -- SMILES format
xyz -- XYZ cartesian coordinates format
CONFIG -- DL-POLY CONFIG
CONTCAR -- VASP format
HISTORY -- DL-POLY HISTORY
POSCAR -- VASP format
VASP -- VASP format
abinit -- ABINIT Output Format
acesin -- ACES input format
acesout -- ACES output format
acr -- ACR format
adf -- ADF cartesian input format
adfout -- ADF output format
alc -- Alchemy format
arc -- Accelrys/MSI Biosym/Insight II CAR format
ascii -- ASCII format
axsf -- XCrySDen Structure Format
bgf -- MSI BGF format
box -- Dock 3.5 Box format
bs -- Ball and Stick format
c09out -- Crystal 09 output format
c3d1 -- Chem3D Cartesian 1 format
c3d2 -- Chem3D Cartesian 2 format
cac -- CAChe MolStruct format
caccrt -- Cacao Cartesian format
cache -- CAChe MolStruct format
cacint -- Cacao Internal format
can -- Canonical SMILES format
car -- Accelrys/MSI Biosym/Insight II CAR format
castep -- CASTEP format
ccc -- CCC format
cdx -- ChemDraw binary format
cdxml -- ChemDraw CDXML format
cht -- Chemtool format
cif -- Crystallographic Information File
ck -- ChemKin format
cml -- Chemical Markup Language
cmlr -- CML Reaction format
com -- Gaussian 98/03 Input
copy -- Copy raw text
crk2d -- Chemical Resource Kit diagram(2D)
crk3d -- Chemical Resource Kit 3D format
csr -- Accelrys/MSI Quanta CSR format
cssr -- CSD CSSR format
ct -- ChemDraw Connection Table format
cub -- Gaussian cube format
cube -- Gaussian cube format
dat -- Generic Output file format
dmol -- DMol3 coordinates format
dx -- OpenDX cube format for APBS
ent -- Protein Data Bank format
fa -- FASTA format
fasta -- FASTA format
fch -- Gaussian formatted checkpoint file format
fchk -- Gaussian formatted checkpoint file format
fck -- Gaussian formatted checkpoint file format
feat -- Feature format
fh -- Fenske-Hall Z-Matrix format
fhiaims -- FHIaims XYZ format
fix -- SMILES FIX format
fps -- FPS text fingerprint format (Dalke)
fpt -- Fingerprint format
fract -- Free Form Fractional format
fs -- Fastsearch format
fsa -- FASTA format
g03 -- Gaussian Output
g09 -- Gaussian Output
g92 -- Gaussian Output
g94 -- Gaussian Output
g98 -- Gaussian Output
gal -- Gaussian Output
gam -- GAMESS Output
gamess -- GAMESS Output
gamin -- GAMESS Input
gamout -- GAMESS Output
gau -- Gaussian 98/03 Input
gjc -- Gaussian 98/03 Input
gjf -- Gaussian 98/03 Input
got -- GULP format
gpr -- Ghemical format
gr96 -- GROMOS96 format
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
inp -- GAMESS Input
ins -- ShelX format
jin -- Jaguar input format
jout -- Jaguar output format
k -- Compare molecules using InChI
lmpdat -- The LAMMPS data format
log -- Generic Output file format
mcdl -- MCDL format
mcif -- Macromolecular Crystallographic Info
mdl -- MDL MOL format
ml2 -- Sybyl Mol2 format
mmcif -- Macromolecular Crystallographic Info
mmd -- MacroModel format
mmod -- MacroModel format
mna -- Multilevel Neighborhoods of Atoms (MNA)
mol2 -- Sybyl Mol2 format
mold -- Molden format
molden -- Molden format
molf -- Molden format
molreport -- Open Babel molecule report
moo -- MOPAC Output format
mop -- MOPAC Cartesian format
mopcrt -- MOPAC Cartesian format
mopin -- MOPAC Internal
mopout -- MOPAC Output format
mp -- Molpro input format
mpc -- MOPAC Cartesian format
mpd -- MolPrint2D format
mpo -- Molpro output format
mpqc -- MPQC output format
mpqcin -- MPQC simplified input format
mrv -- Chemical Markup Language
msi -- Accelrys/MSI Cerius II MSI format
msms -- M.F. Sanner's MSMS input format
nul -- Outputs nothing
nw -- NWChem input format
nwo -- NWChem output format
out -- Generic Output file format
outmol -- DMol3 coordinates format
output -- Generic Output file format
pc -- PubChem format
pcm -- PCModel Format
pdbqt -- AutoDock PDQBT format
png -- PNG 2D depiction
pos -- POS cartesian coordinates format
pov -- POV-Ray input format
pqr -- PQR format
pqs -- Parallel Quantum Solutions format
prep -- Amber Prep format
pwscf -- PWscf format
qcin -- Q-Chem input format
qcout -- Q-Chem output format
report -- Open Babel report format
res -- ShelX format
rsmi -- Reaction SMILES format
rxn -- MDL RXN format
sd -- MDL MOL format
sdf -- MDL MOL format
smiles -- SMILES format
svg -- SVG 2D depiction
sy2 -- Sybyl Mol2 format
t41 -- ADF TAPE41 format
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
vmol -- ViewMol format
xed -- XED format
xml -- General XML format
xsf -- XCrySDen Structure Format
xtc -- XTC format
yob -- YASARA.org YOB format
zin -- ZINDO input format
CACTVS Formats
CACTVS is known as CADD Group Chemoinformatics Tools and User Services (https://cactus.nci.nih.gov/). The NCI/CADD group is a research unit within the Chemical Biology Laboratory at the National Cancer Institute.
The chemoinformatic toolkit CACTVS can resolve a structure identifier into a chemical format.
Click the Submit to convert the file format. The file can be downloaded by clicking the Download button.
Supported formats:
alc -- Alchemy format
cdxml -- ChemDraw CDXML format
cerius -- MSI Cerius II format
charmm -- Chemistry at HARvard Macromolecular Mechanics file format
cif -- Crystallographic Information File
cml -- Chemical Markup Language
ctx -- Gaussian input data file
gjf -- Gaussian 98/03 Input
gromacs -- GROMACS file format
hyperchem -- HyperChem file format
jme -- Java Molecule Editor format
maestro -- Schroedinger MacroModel structure file format
mol -- MDL MOL format
mol2 -- Sybyl Mol2 format
mrv -- Chemical Markup Language
pdb -- Protein Data Bank format
sdf -- MDL MOL format
sdf3000 -- Symyx Structure Data Format 3000
sln -- SYBYL Line Notation
smiles -- SMILES format
xyz -- XYZ cartesian coordinates format
Last updated
