% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/505-convMolFormat.R
\name{convMolFormat}
\alias{convMolFormat}
\title{Chemical File Formats Conversion}
\usage{
convMolFormat(infile, outfile, from, to)
}
\arguments{
\item{infile}{A character string. Indicating the input file location.}

\item{outfile}{A character string. Indicating the output file location.}

\item{from}{The format of \code{infile}.
A character string supported by OpenBabel.
See the note section for the supported formats.}

\item{to}{The desired format of \code{outfile}.
A character string supported by OpenBabel.
See the note section for the supported formats.}
}
\value{
\code{NULL}
}
\description{
Chemical File Formats Conversion
}
\details{
This function converts between various chemical file formats via OpenBabel.
The complete supported file format list could be found at
\url{http://openbabel.org/docs/dev/FileFormats/Overview.html}.
}
\note{
The supported formats include:
            \itemize{
            \item abinit -- ABINIT Output Format [Read-only]
            \item acr -- ACR format [Read-only]
            \item adf -- ADF cartesian input format [Write-only]
            \item adfout -- ADF output format [Read-only]
            \item alc -- Alchemy format
            \item arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
            \item axsf -- XCrySDen Structure Format [Read-only]
            \item bgf -- MSI BGF format
            \item box -- Dock 3.5 Box format
            \item bs -- Ball and Stick format
            \item c3d1 -- Chem3D Cartesian 1 format
            \item c3d2 -- Chem3D Cartesian 2 format
            \item cac -- CAChe MolStruct format [Write-only]
            \item caccrt -- Cacao Cartesian format
            \item cache -- CAChe MolStruct format [Write-only]
            \item cacint -- Cacao Internal format [Write-only]
            \item can -- Canonical SMILES format
            \item car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
            \item castep -- CASTEP format [Read-only]
            \item ccc -- CCC format [Read-only]
            \item cdx -- ChemDraw binary format [Read-only]
            \item cdxml -- ChemDraw CDXML format
            \item cht -- Chemtool format [Write-only]
            \item cif -- Crystallographic Information File
            \item ck -- ChemKin format
            \item cml -- Chemical Markup Language
            \item cmlr -- CML Reaction format
            \item com -- Gaussian 98/03 Input [Write-only]
            \item CONFIG -- DL-POLY CONFIG
            \item CONTCAR -- VASP format [Read-only]
            \item copy -- Copy raw text [Write-only]
            \item crk2d -- Chemical Resource Kit diagram(2D)
            \item crk3d -- Chemical Resource Kit 3D format
            \item csr -- Accelrys/MSI Quanta CSR format [Write-only]
            \item cssr -- CSD CSSR format [Write-only]
            \item ct -- ChemDraw Connection Table format
            \item cub -- Gaussian cube format
            \item cube -- Gaussian cube format
            \item dat -- Generic Output file format [Read-only]
            \item dmol -- DMol3 coordinates format
            \item dx -- OpenDX cube format for APBS
            \item ent -- Protein Data Bank format
            \item fa -- FASTA format
            \item fasta -- FASTA format
            \item fch -- Gaussian formatted checkpoint file format [Read-only]
            \item fchk -- Gaussian formatted checkpoint file format [Read-only]
            \item fck -- Gaussian formatted checkpoint file format [Read-only]
            \item feat -- Feature format
            \item fh -- Fenske-Hall Z-Matrix format [Write-only]
            \item fhiaims -- FHIaims XYZ format
            \item fix -- SMILES FIX format [Write-only]
            \item fpt -- Fingerprint format [Write-only]
            \item fract -- Free Form Fractional format
            \item fs -- Fastsearch format
            \item fsa -- FASTA format
            \item g03 -- Gaussian Output [Read-only]
            \item g09 -- Gaussian Output [Read-only]
            \item g92 -- Gaussian Output [Read-only]
            \item g94 -- Gaussian Output [Read-only]
            \item g98 -- Gaussian Output [Read-only]
            \item gal -- Gaussian Output [Read-only]
            \item gam -- GAMESS Output [Read-only]
            \item gamess -- GAMESS Output [Read-only]
            \item gamin -- GAMESS Input
            \item gamout -- GAMESS Output [Read-only]
            \item gau -- Gaussian 98/03 Input [Write-only]
            \item gjc -- Gaussian 98/03 Input [Write-only]
            \item gjf -- Gaussian 98/03 Input [Write-only]
            \item got -- GULP format [Read-only]
            \item gpr -- Ghemical format
            \item gr96 -- GROMOS96 format [Write-only]
            \item gro -- GRO format
            \item gukin -- GAMESS-UK Input
            \item gukout -- GAMESS-UK Output
            \item gzmat -- Gaussian Z-Matrix Input
            \item hin -- HyperChem HIN format
            \item HISTORY -- DL-POLY HISTORY [Read-only]
            \item inchi -- InChI format
            \item inchikey -- InChIKey [Write-only]
            \item inp -- GAMESS Input
            \item ins -- ShelX format [Read-only]
            \item jin -- Jaguar input format [Write-only]
            \item jout -- Jaguar output format [Read-only]
            \item k -- Compare molecules using InChI [Write-only]
            \item log -- Generic Output file format [Read-only]
            \item mcdl -- MCDL format
            \item mcif -- Macromolecular Crystallographic Info
            \item mdl -- MDL MOL format
            \item ml2 -- Sybyl Mol2 format
            \item mmcif -- Macromolecular Crystallographic Info
            \item mmd -- MacroModel format
            \item mmod -- MacroModel format
            \item mna -- Multilevel Neighborhoods of Atoms (MNA) [Write-only]
            \item mol -- MDL MOL format
            \item mol2 -- Sybyl Mol2 format
            \item mold -- Molden format
            \item molden -- Molden format
            \item molf -- Molden format
            \item molreport -- Open Babel molecule report [Write-only]
            \item moo -- MOPAC Output format [Read-only]
            \item mop -- MOPAC Cartesian format
            \item mopcrt -- MOPAC Cartesian format
            \item mopin -- MOPAC Internal
            \item mopout -- MOPAC Output format [Read-only]
            \item mp -- Molpro input format [Write-only]
            \item mpc -- MOPAC Cartesian format
            \item mpd -- MolPrint2D format [Write-only]
            \item mpo -- Molpro output format [Read-only]
            \item mpqc -- MPQC output format [Read-only]
            \item mpqcin -- MPQC simplified input format [Write-only]
            \item mrv -- Chemical Markup Language
            \item msi -- Accelrys/MSI Cerius II MSI format [Read-only]
            \item msms -- M.F. Sanner's MSMS input format [Write-only]
            \item nul -- Outputs nothing [Write-only]
            \item nw -- NWChem input format [Write-only]
            \item nwo -- NWChem output format [Read-only]
            \item out -- Generic Output file format [Read-only]
            \item outmol -- DMol3 coordinates format
            \item output -- Generic Output file format [Read-only]
            \item pc -- PubChem format [Read-only]
            \item pcm -- PCModel Format
            \item pdb -- Protein Data Bank format
            \item pdbqt -- AutoDock PDQBT format
            \item png -- PNG 2D depiction
            \item POSCAR -- VASP format [Read-only]
            \item pov -- POV-Ray input format [Write-only]
            \item pqr -- PQR format
            \item pqs -- Parallel Quantum Solutions format
            \item prep -- Amber Prep format [Read-only]
            \item pwscf -- PWscf format [Read-only]
            \item qcin -- Q-Chem input format [Write-only]
            \item qcout -- Q-Chem output format [Read-only]
            \item report -- Open Babel report format [Write-only]
            \item res -- ShelX format [Read-only]
            \item rsmi -- Reaction SMILES format
            \item rxn -- MDL RXN format
            \item sd -- MDL MOL format
            \item sdf -- MDL MOL format
            \item smi -- SMILES format
            \item smiles -- SMILES format
            \item svg -- SVG 2D depiction [Write-only]
            \item sy2 -- Sybyl Mol2 format
            \item t41 -- ADF TAPE41 format [Read-only]
            \item tdd -- Thermo format
            \item text -- Read and write raw text
            \item therm -- Thermo format
            \item tmol -- TurboMole Coordinate format
            \item txt -- Title format
            \item txyz -- Tinker XYZ format
            \item unixyz -- UniChem XYZ format
            \item vmol -- ViewMol format
            \item xed -- XED format [Write-only]
            \item xml -- General XML format [Read-only]
            \item xsf -- XCrySDen Structure Format [Read-only]
            \item xyz -- XYZ cartesian coordinates format
            \item yob -- YASARA.org YOB format
            \item zin -- ZINDO input format [Write-only]
            }
}
\examples{
sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')
# SDF to SMILES
\donttest{
convMolFormat(infile = sdf, outfile = 'aa.smi',
              from = 'sdf', to = 'smiles')}
# SMILES to MOPAC Cartesian format
\donttest{
convMolFormat(infile = 'aa.smi', outfile = 'aa.mop',
              from = 'smiles', to = 'mop')}
}
\author{
Nan Xiao <\url{https://nanx.me}>
}
\keyword{OpenBabel}
\keyword{convMolFormat}
\keyword{convert}
\keyword{format}
