/rcdk/man/atoms.Rd
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 20\code{get.point3d} returns the 3D coordinates of the atom 21 22\code{get.point2d} returns the 2D coordinates of the atom 23 24\code{get.atomic.number} returns the atomic number of the atom 25 26\code{get.hydrogen.count} returns the number of implicit H's on the atom. 27Depending on where the molecule was read from this may be \code{NULL} or an integer 28greater than or equal to 0 29 30\code{get.charge} returns the partial charge on the atom. If charges have not been set the 31return value is \code{NULL}, otherwise the appropriate charge. 32 33\code{get.formal.charge} is returns the formal charge on the atom. By default the formal 34charge will be 0 (i.e., \code{NULL} is never returned) 35 36\code{is.aromatic} returns \code{TRUE} if the atom is aromatic, \code{FALSE} 37otherwise 38 39\code{is.aliphatic} returns \code{TRUE} if the atom is part of an aliphatic chain, 40\code{FALSE} otherwise 41 42\code{is.in.ring} returns \code{TRUE} if the atom is in a ring, \code{FALSE} 43otherwise 44 45\code{get.atom.index} returns the index of the atom in the molecule (starting from 0) 46 47\code{get.connected.atoms} returns a list of atoms that are connected to the specified atom 48} 49\usage{ 50get.symbol(atom) 51get.point3d(atom) 52get.point2d(atom) 53get.atomic.number(atom) 54get.hydrogen.count(atom) 55get.charge(atom) 56get.formal.charge(atom) 57get.connected.atoms(atom, mol) 58get.atom.index(atom, mol) 59is.aromatic(atom) 60is.aliphatic(atom) 61is.in.ring(atom) 62} 63\arguments{ 64 \item{atom}{A \code{jobjRef} representing an IAtom object} 65 \item{mol}{A \code{jobjRef} representing an IAtomContainer object} 66} 67\value{ 68 In the case of \code{get.point3d} the return value is a 69 3-element vector containing the X, Y and Z coordinates of the 70 atom. If the atom does not have 3D coordinates, it returns a 71 vector of the form \code{c(NA,NA,NA)}. Similarly for 72 \code{get.point2d}, in which case the return vector is of 73 length 2. 74} 75\keyword{programming} 76\seealso{ 77 \code{\link{get.atoms}} 78} 79\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}