convMolFormat: Chemical File Formats Conversion

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

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)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

Examples

sdf = system.file('sysdata/OptAA3d.sdf', package = 'BioMedR')
# 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')

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.