[Rdkit-discuss] A couple of questions regarding ReactionFromSmarts

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

Hi,
 
First of all, I'd like to start by saying how much I've been enjoying
exploring the functionality of RDKit - great job, Greg!
I have a couple of questions regarding
'rdkit.Chem.AllChem.ReactionFromSmarts':
 
(1)  I see that the reaction objects can be created from MDL Reaction
Files/Blocks - is there a way to do the reverse, and save a reaction
object in MDL .rxn format?  I tried using investigating the
rxn.ToBinary() attribute, but didn't get very far...  The reason I
wanted to do this, is that I was trying to figure-out how to generate a
form of the reaction object (generated from reaction SMARTS) that was
suitable for converting into a 2D depiction of the transformation.
 
(2) I know that reaction SMARTS isn't SMIRKS, but I have noticed some
behaviour that I would not expect - however, this could be down to my
SMARTS-naivety; my SMIRKS-naivety; or both!  I initially tried the
following:
 
from rdkit import Chem
from rdkit.Chem import AllChem
rxn_smarts =
'[!#1:1]-[NH:2]-[C:3](=[O:4])-[C,c:5]>>[!#1:1]-[C:3](=[O:4])-[NH:2]-[C,c
:5]'
sm = Chem.MolFromSmiles('CC(=O)NC')
rxn = AllChem.ReactionFromSmarts(rxn_smarts)
prods = rxn.RunReactants((sm,))
prod = Chem.MolToSmiles(prod[0][0])
 
 
This gives me prod = '[H]C(=O)NC'
 
If I replace with <<rxn_smarts =
'[!H:1]-[NH:2]-[C:3](=[O:4])-[C,c:5]>>[!H:1]-[C:3](=[O:4])-[NH:2]-[C,c:5
]'>>, I get the behaviour I want - with prod = 'CNC(=O)C'.  So I think I
can get the behaviour I want, but was curious if I am using the SMARTS !
operator incorrectly in conjunction with atomic numbers, or whether this
may be a bug?
 
Kind regards
 
James

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