Hi,
I am using rdChemReactions to perform substructure transformations as
defined by configurable reaction smarts. When I create the reaction and run
a mol through it that I expect to be transformed by the indicated reaction
smarts, I see that the bonds have been changed according to the smarts, but
the charges are not changed.
I am using the following smarts to define the transformation:
[#8-:2]-[#7+:1]=[O:3]>>[O:2]=[N:1]=[O:3]
The input molecule is as follows:
Mrv16c5 10061718252D
9 9 0 0 0 0 999 V2000
-0.5916 -0.0678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3060 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3060 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5916 -1.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1229 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1229 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5916 0.7572 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
-1.3061 1.1697 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
0.1229 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 7 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
M END
$$$$
and the output ends up being:
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-1.3061 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.5916 0.7572 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.1229 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.5916 -0.0678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3060 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1229 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3060 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1229 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5916 -1.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 2 0
4 2 1 0
4 5 2 0
6 4 1 0
5 7 1 0
8 6 2 0
7 9 2 0
9 8 1 0
M CHG 2 1 -1 2 1
M END
It seems the that NO bond is successfully converted to a double bond, but
the charges have not been changed, even though the reaction smarts
indicates that they N and O should be changed to neutral. Are there any
glaring issues with using reactions to do transformations like this?
Thanks!
-Chris
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