Perfect!
I was struggling with the tuple in the reaction syntax. Adding the comma did
the trick for the reaction, previously i was using rxn.RunReactants((m)) and
receiving errors.
very much appreciate the steps for the deprotection. The reaction is much more
straightforward for my use case.
Brian
________________________________
From: Kangway Chuang <chuang.kang...@gene.com>
Sent: Wednesday, March 2, 2022 7:31 PM
To: Bennion, Brian <benni...@llnl.gov>
Cc: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] deprotection of dimthyl acetal?
Hi Brian,
The Deprotect function will apply any number of deprotections that are stored
as the DeprotectData (see rdkit.Chem.rdDeprotect.GetDeprotections() to get the
list). In your case, you can set up a custom DeprotectData deprotection:
from rdkit.Chem.rdDeprotect import DeprotectData
# Set up the deprotection
reaction_class = "hydrolysis"
reaction_smarts = "[CX4;H3][O][C:1][O][CX4;H3]>>[C:1]=[O]"
abbreviation = "(OMe)2"
full_name = "dimethylacetal"
data = DeprotectData(reaction_class, reaction_smarts, abbreviation, full_name)
assert data.isValid()
data is now an instance of DeprotectData, which you can pass into the Deprotect
function along with your example molecule:
# get an example ketal
mol = Chem.MolFromSmiles('COC1(CCCCC1)OC')
# make the call to get the transformed molecule, in this case, cyclohexanone
result = rdkit.Chem.rdDeprotect.Deprotect(mol, deprotections=[data]) # pass in
your newly created deprotection wrapped in a list
If you're only trying to apply a single chemical reaction, you could just
create a ChemicalReaction to achieve the same result:
from rdkit.Chem import rdChemReactions
# Set up your chemical reaction
reaction_smarts = "[CX4;H3][O][C:1][O][CX4;H3]>>[C:1]=[O]"
rxn = rdChemReactions.ReactionFromSmarts(reaction_smarts)
# Run your chemical reaction on your molecule
mol = Chem.MolFromSmiles('COC1(CCCCC1)OC')
products = rxn.RunReactants((mol,)) # make sure you're passing a tuple
Hope this points you in the right direction.
Best,
Kangway Chuang, Ph. D. (he/him/his)
Senior AI Scientist and Group Lead
AI | ML Department in Research Biology
Genentech Research and Early Development
+1 (805) 754-0058
chuang.kang...@gene.com<mailto:chuang.kang...@gene.com>
On Wed, Mar 2, 2022 at 3:58 PM Bennion, Brian via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>>
wrote:
Hello All,
I have poking about the docs and some emails trying to find a way to deprotect
a group compounds.
The docs describe the DeprotectData module but I am not making the connection
to how that will operate on my molecules.
my tentative smarts is here
[CX4;H3][O][C:1][O][CX4;H3]>>[C:1]=[O]
I was able to access the function and assert the "dataIsValid" for the example
case. So I am just missing that next and maybe last step where I can deprotect
a list of compounds with this module.
Thank you
brian
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