Hi James, Thanks for the quick reply!
You're quite right, I'm simply interested in the virtual reaction to remove the boronates. Thank you for fixing my incorrect mapping. At some point, I had had the aryl carbon properly specified, but I clearly lost my way with it along my quest. Sadly, the reaction_smarts = "[c:1][B;R0](O)O>>[*:1]" still does not remove any of the boronates from my input smiles, but it sounds like everything else about the specification of the reaction is correct, so I'll get there at some point with the right reaction_smarts. Thanks again, Katrina On Mon, Aug 21, 2023 at 3:26 AM James Davidson <j.david...@vernalis.com> wrote: > 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 > > ------------------------------ > > PLEASE READ - This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or postmas...@vernalis.com. Email is not > a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > Vernalis (R&D) Limited (no. 1985479) > Granta Park, Great Abington > Cambridge, CB21 6GB, United Kingdom > Tel: +44 (0)1223 895 555 > ------------------------------ >
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