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 -1.2990 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
3.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0000 -2.5981 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 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
________________________________
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
________________________________
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
