/rcdk/man/atomcontainer.Rd
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1\name{Molecule}
2\alias{get.exact.mass}
3\alias{get.natural.mass}
4\alias{is.neutral}
5\alias{convert.implicit.to.explicit}
6\title{
7 Operations on molecules
8}
9\description{
10 Various functions to perform operations on molecules.
11
12 \code{get.exact.mass} returns the exact mass of a molecule
13
14 \code{get.natural.mass} returns the natural exact mass of a molecule
15
16 \code{convert.implicit.explicit} converts implicit hydrogens
17 to explicit hydrogens. This function does not return any value
18 but rather modifies the molecule object passed to it
19
20 \code{is.neutral} returns \code{TRUE} if all atoms in the molecule
21 have a formal charge of 0, otherwise \code{FALSE}
22}
23\usage{
24get.exact.mass(molecule)
25get.natural.mass(molecule)
26convert.implicit.to.explicit(molecule)
27is.neutral(molecule)
28}
29\arguments{
30 \item{molecule}{A \code{jObjRef} representing an IAtomContainer or IMolecule object}
31}
32\value{
33 \code{exact.mass} returns a numeric
34
35 \code{get.natural.mass} returns a numeric
36
37 \code{convert.implicit.to.explicit} has no return value
38
39 \code{is.neutral} returns a boolean.
40}
41\details{
42In some cases, a molecule may not have any hydrogens (such as when read
43in from an MDL MOL file that did not have hydrogens). In such cases,
44\code{\link{convert.implicit.to.explicit}}
45will add implicit hydrogens and then convert them to explicit ones. In addition, for
46such cases, make sure that the molecule has been typed beforehand.
47}
48\keyword{programming}
49\seealso{
50 \code{\link{get.atoms}}, \code{\link{do.typing}}
51}
52\examples{
53 m <- parse.smiles('c1ccccc1')[[1]]
54
55 ## Need to configure the molecule
56 do.aromaticity(m)
57 do.typing(m)
58 do.isotopes(m)
59
60 get.exact.mass(m)
61 get.natural.mass(m)
62
63 convert.implicit.to.explicit(m)
64 get.natural.mass(m)
65 do.isotopes(m) # Configure isotopes of newly added hydrogens
66 get.exact.mass(m)
67
68 is.neutral(m)
69}
70\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}