/rcdk/man/atoms.Rd
http://github.com/rajarshi/cdkr · Unknown · 79 lines · 68 code · 11 blank · 0 comment · 0 complexity · 8218be44092a9b80dea3484563f92c8c MD5 · raw file
- \name{Atoms}
- \alias{get.symbol}
- \alias{get.point3d}
- \alias{get.point2d}
- \alias{get.atomic.number}
- \alias{get.hydrogen.count}
- \alias{get.charge}
- \alias{get.formal.charge}
- \alias{get.connected.atoms}
- \alias{get.atom.index}
- \alias{is.aromatic}
- \alias{is.aliphatic}
- \alias{is.in.ring}
- \title{
- Operations on atoms
- }
- \description{
- \code{get.symbol} returns the chemical symbol for an atom.
- \code{get.point3d} returns the 3D coordinates of the atom
- \code{get.point2d} returns the 2D coordinates of the atom
- \code{get.atomic.number} returns the atomic number of the atom
- \code{get.hydrogen.count} returns the number of implicit H's on the atom.
- Depending on where the molecule was read from this may be \code{NULL} or an integer
- greater than or equal to 0
- \code{get.charge} returns the partial charge on the atom. If charges have not been set the
- return value is \code{NULL}, otherwise the appropriate charge.
- \code{get.formal.charge} is returns the formal charge on the atom. By default the formal
- charge will be 0 (i.e., \code{NULL} is never returned)
- \code{is.aromatic} returns \code{TRUE} if the atom is aromatic, \code{FALSE}
- otherwise
- \code{is.aliphatic} returns \code{TRUE} if the atom is part of an aliphatic chain,
- \code{FALSE} otherwise
- \code{is.in.ring} returns \code{TRUE} if the atom is in a ring, \code{FALSE}
- otherwise
- \code{get.atom.index} returns the index of the atom in the molecule (starting from 0)
- \code{get.connected.atoms} returns a list of atoms that are connected to the specified atom
- }
- \usage{
- get.symbol(atom)
- get.point3d(atom)
- get.point2d(atom)
- get.atomic.number(atom)
- get.hydrogen.count(atom)
- get.charge(atom)
- get.formal.charge(atom)
- get.connected.atoms(atom, mol)
- get.atom.index(atom, mol)
- is.aromatic(atom)
- is.aliphatic(atom)
- is.in.ring(atom)
- }
- \arguments{
- \item{atom}{A \code{jobjRef} representing an IAtom object}
- \item{mol}{A \code{jobjRef} representing an IAtomContainer object}
- }
- \value{
- In the case of \code{get.point3d} the return value is a
- 3-element vector containing the X, Y and Z coordinates of the
- atom. If the atom does not have 3D coordinates, it returns a
- vector of the form \code{c(NA,NA,NA)}. Similarly for
- \code{get.point2d}, in which case the return vector is of
- length 2.
- }
- \keyword{programming}
- \seealso{
- \code{\link{get.atoms}}
- }
- \author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}