/rcdk/man/atoms.Rd

 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})}