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 <j.david...@vernalis.com> 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 -1.2990 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 ________________________________
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