Re: [Rdkit-discuss] rdDeprotect & DeprotectData

[James D. <J.D...@ve...>]

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...@um...>
Sent: 21 August 2023 06:03
To: RDKit Discuss <rdk...@li...>
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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