/rcdk/man/atoms.Rd

http://github.com/rajarshi/cdkr · Unknown · 79 lines · 68 code · 11 blank · 0 comment · 0 complexity · 8218be44092a9b80dea3484563f92c8c MD5 · raw file

  1. \name{Atoms}
  2. \alias{get.symbol}
  3. \alias{get.point3d}
  4. \alias{get.point2d}
  5. \alias{get.atomic.number}
  6. \alias{get.hydrogen.count}
  7. \alias{get.charge}
  8. \alias{get.formal.charge}
  9. \alias{get.connected.atoms}
  10. \alias{get.atom.index}
  11. \alias{is.aromatic}
  12. \alias{is.aliphatic}
  13. \alias{is.in.ring}
  14. \title{
  15. Operations on atoms
  16. }
  17. \description{
  18. \code{get.symbol} returns the chemical symbol for an atom.
  19. \code{get.point3d} returns the 3D coordinates of the atom
  20. \code{get.point2d} returns the 2D coordinates of the atom
  21. \code{get.atomic.number} returns the atomic number of the atom
  22. \code{get.hydrogen.count} returns the number of implicit H's on the atom.
  23. Depending on where the molecule was read from this may be \code{NULL} or an integer
  24. greater than or equal to 0
  25. \code{get.charge} returns the partial charge on the atom. If charges have not been set the
  26. return value is \code{NULL}, otherwise the appropriate charge.
  27. \code{get.formal.charge} is returns the formal charge on the atom. By default the formal
  28. charge will be 0 (i.e., \code{NULL} is never returned)
  29. \code{is.aromatic} returns \code{TRUE} if the atom is aromatic, \code{FALSE}
  30. otherwise
  31. \code{is.aliphatic} returns \code{TRUE} if the atom is part of an aliphatic chain,
  32. \code{FALSE} otherwise
  33. \code{is.in.ring} returns \code{TRUE} if the atom is in a ring, \code{FALSE}
  34. otherwise
  35. \code{get.atom.index} returns the index of the atom in the molecule (starting from 0)
  36. \code{get.connected.atoms} returns a list of atoms that are connected to the specified atom
  37. }
  38. \usage{
  39. get.symbol(atom)
  40. get.point3d(atom)
  41. get.point2d(atom)
  42. get.atomic.number(atom)
  43. get.hydrogen.count(atom)
  44. get.charge(atom)
  45. get.formal.charge(atom)
  46. get.connected.atoms(atom, mol)
  47. get.atom.index(atom, mol)
  48. is.aromatic(atom)
  49. is.aliphatic(atom)
  50. is.in.ring(atom)
  51. }
  52. \arguments{
  53. \item{atom}{A \code{jobjRef} representing an IAtom object}
  54. \item{mol}{A \code{jobjRef} representing an IAtomContainer object}
  55. }
  56. \value{
  57. In the case of \code{get.point3d} the return value is a
  58. 3-element vector containing the X, Y and Z coordinates of the
  59. atom. If the atom does not have 3D coordinates, it returns a
  60. vector of the form \code{c(NA,NA,NA)}. Similarly for
  61. \code{get.point2d}, in which case the return vector is of
  62. length 2.
  63. }
  64. \keyword{programming}
  65. \seealso{
  66. \code{\link{get.atoms}}
  67. }
  68. \author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}