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SiMolecule / centres

Perception and labelling of stereogenic centres in chemical structures
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Atropisomer configuration dependent on atom and bond ordering when one aryl ring has only 1 ortho substituent #15

Closed iclkevin closed 6 months ago

iclkevin commented 7 months ago

The two attached MOL files (ext changed to .txt so I can attach it) are the same exact structure. However, CENTRES marks the aryl-aryl connecting bond as "M" in one and "P" in the other. Both structures should be "P". I tested this both within our system using the CENTRES API and using the command line JAR provided in the releases downloads.

We noticed this issue only occurs when one ortho position is hydrogen, and the other ortho position is carbon or lighter, but we didn't text extensively beyond this. Please let me know if I can help.

atrop2_P.txt atrop2_M.txt

johnmay commented 6 months ago

Should be fixed but I think there is more work to be done with unifying how the cis/trans and atropisomers handle the nuance of having two diagraphs/roots.

Fixes #14 and Fixes #15

iclkevin commented 6 months ago

With the updates, all of our tests pass. Thank you. Just to clarify, your statement about more work to be done, do you mean code can be made clearer and more efficient, or is it that you see further configuration assignment problems occurring?