Hi Ling,
this can be a workaround if RDKit does not have a built-in function
to extract a submolecule by atom ids. You may assign atom property
labels to these atoms and then looping over atoms in EditableMol remove
those ones which do not have this property assigned.
Kind regards,
Pavel.
On 02/04/2021 02:30, Ling Chan wrote:
Yes, Kangway, that was what I first tried, as mentioned in the first
post. I did not have any problem with obtaining the primary fragments
(applying all cuts) . Just that I have not yet figured out how to
obtain the secondary fragments, either from recombining the
primary fragments, or from fragmenting from the initial molecule (by
not applying all cuts).
Chuang, Kangway <kangway.chu...@ucsf.edu
<mailto:kangway.chu...@ucsf.edu>> 於 2021年4月1日週四 下午5:20寫道：
Hi Ling,
I think I've run into something similar before, have you tried
using FragmentOnBonds followed by Chem.GetMolFrags? GetMolFrags
lets you toggle a few things (e.g. (bool)asMols=False [,
(bool)sanitizeFrags=True) to provide some workarounds with
sanitization.
Best,
Kangway
------------------------------------------------------------------------
*From:* Ling Chan <lingtrek...@gmail.com
<mailto:lingtrek...@gmail.com>>
*Sent:* Thursday, April 1, 2021 5:08 PM
*To:* Mark Mackey <m...@cresset-group.com
<mailto:m...@cresset-group.com>>
*Cc:* RDKit <rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>>
*Subject:* Re: [Rdkit-discuss] rejoining pairs of fragments after
fragmenting a molecule
>> /I did manage to achieve what I want by going
through Chem.MolFragmentToSmiles and then convert the Smiles back
to a Mol. But is there a neater way?/
Oops, I wrote too soon. Actually I did not achieve what I want.
The conversion from the smiles from Chem.MolFragmentToSmiles
sometimes crashes, because of Sanitization problem.
Ling Chan <lingtrek...@gmail.com <mailto:lingtrek...@gmail.com>> 於
2021年4月1日週四 下午4:11寫道：
Thank you Mark for your suggestion. It sounds good and I gave
it a try. However, this leads to another question that may
sound dumb.
I have the atom indices of a fragment. For example, the
fragment comes from atoms [3,4,5,9,10,11,14] of the original
molecule. How can I extract this fragment from the molecule?
I tried
(1) using EditableMol and deleting atoms one by one using
RemoveAtom. But this does not work since the atom numbering
changes after each deletion.
(2) going through FragmentOnBonds. But the output of
FragmentOnBonds have the atom indices reshuffled so I cannot
directly use my index list to fish out my fragment.
I did manage to achieve what I want by going
through Chem.MolFragmentToSmiles and then convert the Smiles
back to a Mol. But is there a neater way? Basically, is there
a Chem.MolFragmentToMol function?
Thank you again.
Ling
Mark Mackey <m...@cresset-group.com
<mailto:m...@cresset-group.com>> 於 2021年4月1日週四
上午1:58寫道：
Hi Ling,
Having done something similar (but not in RDKit), I would
suggest a different algorithm. I think that fragmenting
the molecule first and then stitching the bits together is
always going to be very complicated. Instead, just
fragment the molecule in the ways that you want:
- Find the set B of all breakable bonds according to your
rules. I’m assuming here that B contains only acyclic bonds.
- To get all of the pairwise pieces, for each element b of
B break all bonds in B _except_ b. Keep the fragment
containing b, and clean up.
- To get all of the triplets, for each tuple (b1, b2) in
B, break all bonds in B except b1 and b2. Keep the
fragment containing b1 only if it also contains b2.
Regards,
Mark
**
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*Cresset*
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*From:*Ling Chan <lingtrek...@gmail.com
<mailto:lingtrek...@gmail.com>>
*Sent:* 31 March 2021 20:56
*To:* RDKit <rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>>
*Subject:* [Rdkit-discuss] rejoining pairs of fragments
after fragmenting a molecule
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 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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