Hi Christos,
On Tue, Oct 16, 2012 at 5:26 AM, Christos Kannas <[email protected]> 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
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