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/rcdk/man/getsmiles.Rd

http://github.com/rajarshi/cdkr
Unknown | 37 lines | 36 code | 1 blank | 0 comment | 0 complexity | 48ea9caab1b902fd4c121aca70567568 MD5 | raw file
  1. \name{get.smiles}
  2. \alias{get.smiles}
  3. \title{
  4. Get the SMILES for a Molecule
  5. }
  6. \description{
  7. The function will generate a SMILES representation of an
  8. IAtomContainer object. The default parameters of the CDK SMILES
  9. generator are used. This can mean that for large ring systems the
  10. method may fail. See CDK Javadocs for more information
  11. }
  12. \usage{
  13. get.smiles(molecule, type = 'generic', aromatic = FALSE, atomClasses = FALSE)
  14. }
  15. \arguments{
  16. \item{molecule}{A Java object of class \code{IAtomContainer}}
  17. \item{type}{The type of SMILES to output. Possible values are
  18. \enumerate{
  19. \item generic - non-canonical SMILES string, different atom ordering produces different SMILES. No isotope or stereochemistry encoded.
  20. \item unique - canonical SMILES string, different atom ordering produces the same* SMILES. No isotope or stereochemistry encoded.
  21. \item isomeric - non-canonical SMILES string, different atom ordering produces different SMILES. Isotope and stereochemistry is encoded.
  22. \item absolute - canonical SMILES string, different atom ordering produces the same SMILES. Isotope and stereochemistry is encoded.
  23. }}
  24. \item{aromatic}{If \code{TRUE} aromatic SMILES are generated. The default is to output Kekule form}
  25. \item{atomClasses}{If \code{TRUE} include atom classes.}
  26. }
  27. \value{
  28. An R character object containing the SMILES
  29. }
  30. \examples{
  31. sp <- get.smiles.parser()
  32. smiles <- c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1','C1CCC1CC(CN(C)(C))CC(=O)CC')
  33. mols <- parse.smiles(smiles)
  34. }
  35. \keyword{programming}
  36. \author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}