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Describe the bug
When a molecule is instantiated from an input mol block, double bonds with an adjacent wavy bond are interpreted as having an undefined/unknown stereochemical configuration (regardless the direction of the wavy bond and whether it originates from a nearby potential stereocenter or not). If wedging is re-applied and the molecule is serialized back to mol format, the wavy single bond is restored and the double bond is not assigned any explicit stereo type if the wavy bond begins from one the double bond ends, but is marked with an explicitly unknown stereo configuration if the wavy bond begins from the substituent.
Expected behavior
The behavior on input makes sense to me, and I think the double bond shouldn't be tagged with an "either" stereo type in the output molblock if an adjacent wavy bond is present, independently from the direction of the wavy bond.
Configuration (please complete the following information):
RDKit version: current tip of the master branch
OS: Fedora 39
Python version (if relevant): 3.12 (probably not relevant)
Are you using conda? no
If you are not using conda: how did you install the RDKit? from source code
The text was updated successfully, but these errors were encountered:
rvianello
changed the title
Inconsistent serialization to mol format of undefined double bond stereochemisty depending on direction of incident wavy bond
Inconsistent serialization to mol format of undefined double bond stereochemisty depending on direction of adjacent wavy bond
Apr 17, 2024
Describe the bug
When a molecule is instantiated from an input mol block, double bonds with an adjacent wavy bond are interpreted as having an undefined/unknown stereochemical configuration (regardless the direction of the wavy bond and whether it originates from a nearby potential stereocenter or not). If wedging is re-applied and the molecule is serialized back to mol format, the wavy single bond is restored and the double bond is not assigned any explicit stereo type if the wavy bond begins from one the double bond ends, but is marked with an explicitly unknown stereo configuration if the wavy bond begins from the substituent.
To Reproduce
outputs
but
outputs:
Expected behavior
The behavior on input makes sense to me, and I think the double bond shouldn't be tagged with an "either" stereo type in the output molblock if an adjacent wavy bond is present, independently from the direction of the wavy bond.
Configuration (please complete the following information):
The text was updated successfully, but these errors were encountered: