Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

[Francois B. <ml...@li...>]

On 01/04/2021 04:55, Ling Chan wrote:
> Dear Colleagues,
> 
> I am trying to do something that I think is quite simple, but I have
> not figured out a simple way. Don't know if I am missing something. I
> am sure that ultimately I can figure it out, but I wonder if there is
> a good way.
> 
> I fragmented a molecule with some rules, using FragmentOnBonds. I did
> get a list of primary fragments.

I have an ad hoc fragmenting scheme and fragment assembly
implemented in there:

https://github.com/UnixJunkie/molenc/blob/master/bin/molenc_smisur.py

Sorry, but this is non trivial code.

Look for the function bind_molecules to connect two fragments.

The rdkit python doc might have some simpler examples, using 
well-known/published fragmenting schemes
(BRICS or Recap):
http://www.rdkit.org/docs/GettingStartedInPython.html

Regards,
F.

> I wish to recombine pairs (and triplets, but no bigger) of these
> primary fragments, but only if the resulting fragment is part of the
> original molecule. I.e. I want to undo some of the cuttings.
> (FragmentOnSomeBonds does not help, since you cannot ensure that the
> resulting fragments consist only of pairs of primary fragments.)
> 
> What is the best way to do this? The following is what I am trying.
> 
> I see that you can mark the original cut points using the dummyLabels
> argument in FragmentOnBonds. So I converted the primary fragments to
> smiles. I looked for the two sides of the original cut point and
> substituted the two dummyLables to [2H] and [3H]. I then tried to
> rejoin the fragments using a reaction string
> "[*:1][2H].[*:2][3H]>>[*:1][*:2]". Unfortunately the
> ReactionFromSmarts function does not accept this string. So I'll have
> to use Smarts search to look for [2H] and [3H], then create an
> editable molecule from the two primary fragments, look for neighbours
> of [2H] and [3H], add a bond, then delete the atoms [2H] and [3H],
> then sanitize.
> 
> Thank you for your ideas.
> 
> Ling
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