rcdk (version 2.9.21)

get.fragmenter: Molecule Fragmentation Methods

Description

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.

Usage

get.fragmenter()
get.murcko.fragments(mol, fragmenter, min.ring.size = 6, as.smiles = TRUE)

Arguments

mol

A molecule object. It should be a jobjRef object with class IAtomContainer

fragmenter

A jobjRef representing the CDK fragmenter class, obtained via get.fragmenter

min.ring.size

The size of the smallest rings to be considered

as.smiles

If TRUE, the return value is a vector of SMILES strings representing the fragments. Otherwise it is a list of IAtomContainer objects

Value

• get.fragmenter() returns an instance of GenerateFragments which is primarily meant to be used as input to the specific fragmentation methods.

  get.murcko.fragments returns a vector of SMILES strings if as.smiles is TRUE otherwise a list of IAtomContainer objects, representing the individual fragments. The latter form is useful if you plan to manipulate the fragments in terms of their chemical structures (such as calculating descriptors and so on).

See Also

load.molecules, parse.smiles,

Examples

mol <- parse.smiles('c1ccc(cc1)CN(c2cc(ccc2[N+](=O)[O-])c3c(nc(nc3CC)N)N)C')
f <- get.fragmenter()
frags.mols <- get.murcko.fragments(mol, f, as.smiles=FALSE)
frags <- get.murcko.fragments(mol, f, as.smiles=TRUE)