convMolFormat | R Documentation |
Chemical File Formats Conversion
convMolFormat(infile, outfile, from, to)
infile |
A character string. Indicating the input file location. |
outfile |
A character string. Indicating the output file location. |
from |
The format of |
to |
The desired format of |
This function converts between various chemical file formats via OpenBabel. The complete supported file format list could be found at https://openbabel.org/docs/FileFormats/Overview.html.
NULL
The supported formats include:
abinit – ABINIT Output Format [Read-only]
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]
axsf – XCrySDen Structure 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]
castep – CASTEP 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]
CONFIG – DL-POLY CONFIG
CONTCAR – VASP format [Read-only]
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
dat – Generic Output file format [Read-only]
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 [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]
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]
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 98/03 Input [Write-only]
gjc – Gaussian 98/03 Input [Write-only]
gjf – Gaussian 98/03 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 [Write-only]
jout – Jaguar output format [Read-only]
k – Compare molecules using InChI [Write-only]
log – Generic Output file format [Read-only]
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) [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]
out – Generic Output file format [Read-only]
outmol – DMol3 coordinates format
output – Generic Output file format [Read-only]
pc – PubChem format [Read-only]
pcm – PCModel Format
pdb – Protein Data Bank format
pdbqt – AutoDock PDQBT format
png – PNG 2D depiction
POSCAR – VASP format [Read-only]
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]
rsmi – Reaction SMILES format
rxn – MDL RXN format
sd – MDL MOL format
sdf – MDL MOL format
smi – SMILES format
smiles – SMILES format
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
vmol – ViewMol format
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]
sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')
# SDF to SMILES
## Not run:
convMolFormat(infile = sdf, outfile = 'aa.smi',
from = 'sdf', to = 'smiles')
## End(Not run)
# SMILES to MOPAC Cartesian format
## Not run:
convMolFormat(infile = 'aa.smi', outfile = 'aa.mop',
from = 'smiles', to = 'mop')
## End(Not run)
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