Hi Katrina,
I'm slightly unsure what "deprotection" you are trying to represent, but I
think there are a couple of problems with the rsmarts...
reaction_smarts = "[c;H1]([B;R0](O)[O;R0:1])>>[c;H1]"
This is looking for an aromatic carbon with one hydrogen AND connected to a
non-ring boron. This pattern will never be found!
Also, you have a mapped atom on the reactant side, but no mapped atoms on the
product side.
If your reaction is aiming to hydrolyse non-cyclic boronic esters (and return
the alcohols), then you should map the oxygen atom on the product side as well
- something like:
reaction_smarts = "c[B;R0](O)[O:1]>>[*:1]"
If, instead, you are interested in the virtual reaction that removes boronates
from aryl R-groups (perhaps to calculate R-group fingerprints, etc) - then you
should map the aryl carbon on both sides instead:
reaction_smarts = "[c:1][B;R0](O)O>>[*:1]"
In either case you probably want to deduplicate products (the boronic acids and
esters will match the pattern twice).
Kind regards
James
________________________________
From: Katrina Lexa <kl...@umich.edu>
Sent: 21 August 2023 06:03
To: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] rdDeprotect & DeprotectData
Hi All,
I don't know why I'm struggling so much with this, as it seems like it should
be pretty straight forward. I'm trying to add some additional deprotection
smirks to a data-cleaning python script and I'm not having success with the new
reactions actually transforming my reactants to deprotected smiles. I have
about 10 I'd like to add, so I know I could do it with simple reactions, but
I'd rather figure out where I'm going wrong here.
My definition of deprotect data:
#deborylation
deprotection_class = "boron"
reaction_smarts = "[c;H1]([B;R0](O)[O;R0:1])>>[c;H1]"
abbreviation = "BOO"
full_name = "deboron"
bdata = rdDeprotect.DeprotectData(deprotection_class, reaction_smarts,
abbreviation, full_name)
assert bdata.isValid()
I tried adding this line:
newDeprotect = rdDeprotect.DeprotectDataVect().append(bdata)
but it seems to make no difference:
try:
#result = rdDeprotect.Deprotect(dep_m,deprotections=[bdata])
result = rdDeprotect.Deprotect(dep_m,newDeprotect)
As an example, this is one of the smiles strings in the smiles file I'm reading
in I would expect to deprotect"
Cc1cc(B(O)O)ccc1OC(C)C
Maybe I'm just awful at writing SMIRKS?
Thanks for the help here,
Katrina
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