get.exhaustive.fragments: Generate Bemis-Murcko Fragments

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/frags.R

Description

Fragment the input molecule using the Bemis-Murcko scheme

Usage

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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 (rajarshi.guha@gmail.com)

See Also

[get.exhuastive.fragments()]

Examples

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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)

Example output

Loading required package: rcdklibs
Loading required package: rJava

rcdk documentation built on March 13, 2020, 1:30 a.m.