Hi James,
Interesting problem!
You are right that the bond you are interested in has STEREONONE, but I am not
sure that STEREONONE necessarily translates to having a bond stereo value of 0.
(philosophical question?)
https://gist.github.com/adelenelai/0e2c4c90f33bac9197d7a11495b4f164
Like the example of FC=CF I showed (undefined stereochemistry), it could be
that having symmetry on the double bond is treated as a case of undefined
stereochemistry, and hence double bond stereo value = 3.
Warm regards,
Adelene
Doctoral Researcher
Environmental Cheminformatics
UNIVERSITÉ DU LUXEMBOURG
Campus Belval | Luxembourg Centre for Systems Biomedicine
6, avenue du Swing, L-4367 Belvaux
T +356 46 66 44 67 18
[github.png] adelenelai
From: James Davidson
Sent: Tuesday, December 22, 2020 11:46:32 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Simple question about double bond stereo in molblock
output
Dear All,
I wonder if I can quickly sanity-check something(?).
I have noticed that symmetrical double bonds output with a bond stereo setting
of “3” (cis or trans (either) double bond) in the standard molblock output.
Is this expected/intentional? I would have expected a setting of “0” (use
coords to determine cis or trans) for a non-stereo double bond.
(I am using 2020.09.1)
Here’s a simple example:
m = Chem.MolFromSmiles('FC(F)=CC1=CC=CC=C1')
print(Chem.MolToMolBlock(m))
RDKit 2D
10 10 0 0 0 0 0 0 0 0999 V2000
5.2500 -1.29900. F 0 0 0 0 0 0 0 0 0 0 0 0
3.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
3. -2.59810. F 0 0 0 0 0 0 0 0 0 0 0 0
3.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
0.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 2 3
4 5 1 0
5 6 2 0
6 7 1 0
7 8 2 0
8 9 1 0
9 10 2 0
10 5 1 0
M END
This behaviour is maybe what I would expect if the bond was explicitly set
using bond.SetStereo(Chem.BondStereo.STEREOANY), but in the absence of this I
would expect the bond to default to STEREONONE, and I guess I would expect this
to be bond stereo “0” in the output molblock. What am I missing?
Kind regards
James
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