[Rdkit-discuss] rdDeprotect & DeprotectData

[Katrina L. <kl...@um...>]

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