Generate Bemis-Murcko Fragments

Fragment the input molecule using the Bemis-Murcko scheme

Usage

get.murcko.fragments(
  mols,
  min.frag.size = 6,
  as.smiles = TRUE,
  single.framework = FALSE
)

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

single.framework

If `TRUE`, then a single framework (i.e., the framework consisting of the union of all ring systems and linkers) is returned for each molecule. Otherwise, all combinations of ring systems and linkers are returned

Value

Returns a list with each element being a list with two elements: `rings` and `frameworks`. Each of these elements is either a character vector of SMILES strings or a list of `IAtomContainer` 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.

See also

[get.exhuastive.fragments()]

Author

Rajarshi Guha (rajarshi.guha@gmail.com)

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)