get.exhaustive.fragments: Generate Bemis-Murcko Fragments

In rcdk: Interface to the 'CDK' Libraries

Generate Bemis-Murcko Fragments

Description

Fragment the input molecule using the Bemis-Murcko scheme

Usage

get.exhaustive.fragments(mols, min.frag.size = 6, as.smiles = TRUE)

Arguments

mols	A list of 'jobjRef' objects of Java class 'IAtomContainer'
min.frag.size	The smallest fragment to consider (in terms of heavy atoms)
as.smiles	If 'TRUE' return the fragments as SMILES strings. If not, then fragments are returned as 'jobjRef' objects

Details

A variety of methods for fragmenting molecules are available ranging from exhaustive, rings to more specific methods such as Murcko frameworks. Fragmenting a collection of molecules can be a useful for a variety of analyses. In addition fragment based analysis can be a useful and faster alternative to traditional clustering of the whole collection, especially when it is large.

Note that exhaustive fragmentation of large molecules (with many single bonds) can become time consuming.

Value

returns a list of length equal to the number of input molecules. Each element is a character vector of SMILES strings or a list of 'jobjRef' objects.

Author(s)

Rajarshi Guha ([e-mail])

See Also

[get.murcko.fragments()]

Examples

mol <- parse.smiles('c1ccc(cc1)CN(c2cc(ccc2[N+](=O)[O-])c3c(nc(nc3CC)N)N)C')[[1]]
mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=TRUE)
mf1 <- get.murcko.fragments(mol, as.smiles=TRUE, single.framework=FALSE)

rcdk documentation built on July 9, 2023, 7:27 p.m.