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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