convMolFormat {Rcpi} | R Documentation

## Chemical File Formats Conversion

### Description

Chemical File Formats Conversion

### Usage

    convMolFormat(infile, outfile, from, to)

### Arguments

`infile` | A character string. Indicating the input file location.
`outfile` | A character string. Indicating the output file location.
`from` | The format of `infile`. A character string supported by OpenBabel. See the note section for the supported formats.
`to` | The desired format of `outfile`. A character string supported by OpenBabel. See the note section for the supported formats.

### Details

This function converts between various chemical file formats via OpenBabel. The complete supported file format list could be found at http://openbabel.org/docs/dev/FileFormats/Overview.html.

### Value

`NULL`

### Note

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]

### Author(s)

Nan Xiao <https://nanx.me>

### Examples

    sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')
    # SDF to SMILES

    convMolFormat(infile = sdf, outfile = 'aa.smi',
                  from = 'sdf', to = 'smiles')
    # SMILES to MOPAC Cartesian format

    convMolFormat(infile = 'aa.smi', outfile = 'aa.mop',
                  from = 'smiles', to = 'mop')

[Package Rcpi version 1.20.1 Index]