/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})}