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/rcdk/man/frags.Rd

http://github.com/rajarshi/cdkr
Unknown | 49 lines | 48 code | 1 blank | 0 comment | 0 complexity | 5b36bcce3056e386bbe063d5b3edd853 MD5 | raw file
 1\name{get.murcko.fragments}
 2\alias{fragment}
 3\alias{get.exhaustive.fragments}
 4\alias{get.murcko.fragments}
 5\title{
 6  Molecule Fragmentation Methods
 7}
 8\description{
 9A variety of methods for fragmenting molecules are available ranging from
10exhaustive, rings to more specific methods such as Murcko frameworks. Fragmenting a
11collection of molecules can be a useful for a variety of analyses. In addition
12fragment based analysis can be a useful and faster alternative to traditional 
13clustering of the whole collection, especially when it is large.
14
15Note that exhaustive fragmentation of large molecules (with many single bonds) can become
16time consuming.
17}
18\usage{
19get.murcko.fragments(mols, min.frag.size = 6, as.smiles = TRUE, single.framework = FALSE)
20get.exhaustive.fragments(mols, min.frag.size = 6, as.smiles = TRUE)
21}
22\arguments{
23\item{mols}{A molecule object or list of molecule objects. Each object should have a \code{jclass} of
24\code{IAtomContainer}}
25\item{min.frag.size}{The size of the smallest fragments to be considered}
26\item{as.smiles}{If \code{TRUE}, the fragments are returned as SMILES strings, otherwise as
27 \code{IAtomContainer} objects}
28\item{single.framework}{If \code{TRUE}, then a single framework (i.e., the framework consisting of the
29union of all ring systems and linkers) is returned for each molecule. Otherwise, all combinations
30of ring systems and linkers are returned}
31}
32\examples{
33mol <- parse.smiles('c1ccc(cc1)CN(c2cc(ccc2[N+](=O)[O-])c3c(nc(nc3CC)N)N)C')[[1]]
34mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=TRUE)
35mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=FALSE)
36}
37\value{
38\code{get.murcko.fragments} returns a list with each element being a list with two elements: \code{rings} and
39\code{frameworks}. Each of these elements is either a character vector of SMILES strings or a list of
40\code{IAtomContainer} objects.
41\code{get.exhaustive.fragments} returns a list of length equal to the number of input molecules. Each
42element is a character vector of SMILES strings or a list of \code{IAtomContainer} objects.
43}
44\keyword{programming}
45\seealso{
46  \code{\link{load.molecules}},
47  \code{\link{parse.smiles}},
48}
49\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}