Re: [Rdkit-discuss] [RDKit Discuss]:Compound Fragmentation

[Greg L. <gre...@gm...>]

Hi Christos,

On Tue, Oct 16, 2012 at 5:26 AM, Christos Kannas <chr...@gm...> wrote:
>
> I'm in the process of putting down the requirements for writing a module
> which will provide access to the various compound fragmentation modules of
> RDKit.
> From my search through the documentation I've found support for BRICS, RECAP
> and via FragmentCatalog, which generates fragments from a set of Functional
> Groups (...\RDKit_2012_06_1_py27\Data\FunctionalGroups.txt).

Interesting idea!

> Are there any other modules that can be used to decompose compounds?

There are a few functions that can be used to identify paths/subgraphs
of molecules that can be combined with Chem.PathToSubmol to decompose
compounds: Chem.FindAllSubgraphsOfLengthMToN,
Chem.FindAllPathsOfLengthN (unfortunately not currently available in
the MToN form), Chem.FindAtomEnvironmentOfRadius.

Here's a short example:
In [2]: m = Chem.MolFromSmiles('c1ccccc1OC')

In [3]: ps = Chem.FindAllSubgraphsOfLengthMToN(m,2,4)

In [4]: ps[0]
Out[4]: [(0, 1), (0, 7), (1, 2), (2, 3), (3, 4), (4, 7), (4, 5), (5, 6), (5, 7)]

In [5]: ps[1]
Out[5]:
[(0, 1, 2),
 (0, 1, 7),
 (0, 7, 5),
 (0, 7, 4),
 (1, 2, 3),
 (2, 3, 4),
 (3, 4, 7),
 (3, 4, 5),
 (4, 7, 5),
 (4, 5, 6),
 (5, 6, 7)]

In [6]: smol = Chem.PathToSubmol(m,ps[1][1])

In [7]: Chem.MolToSmiles(smol)
Out[7]: 'cccc'

-greg