Hi,
I was working on detection of the stereochemistry in sugar rings in chair conformation, while I came across two things:
- The configuration for C1 and C3 is detected not correct in my opinion, if the substituent is drawn on the same y level as the ring atom.
- The detected stereochemisrtry is different if the chair is tilted by for example 30°.
horizontal chair conf
SMILES with stereo detected with CyclicCarbohydrateRecognition:
S[C@H]1O[C@@H]([C@H]([C@H]([C@@H]1O)O)O)CO
Depiction of SMILES:
horizontal.mol.txt
tilted chair conf
SMILES with stereo detected with CyclicCarbohydrateRecognition:
S[C@H]1O[C@@H]([C@@H]([C@@H]([C@@H]1O)O)O)CO
Depiction of SMILES:
tilted.mol.txt
Have I got it wrong somehow? Have I missed something?
If not, please let me know if you have any ideas on how to fix this.
Regarding point 1, I am already working on a solution that does not use strict deltaY criteria for lower ring atoms and their substituents, but instead introduces a soft criterion.
Hi,
I was working on detection of the stereochemistry in sugar rings in chair conformation, while I came across two things:
horizontal chair conf
SMILES with stereo detected with
CyclicCarbohydrateRecognition:S[C@H]1O[C@@H]([C@H]([C@H]([C@@H]1O)O)O)CODepiction of SMILES:
horizontal.mol.txt
tilted chair conf
SMILES with stereo detected with
CyclicCarbohydrateRecognition:S[C@H]1O[C@@H]([C@@H]([C@@H]([C@@H]1O)O)O)CODepiction of SMILES:
tilted.mol.txt
Have I got it wrong somehow? Have I missed something?
If not, please let me know if you have any ideas on how to fix this.
Regarding point 1, I am already working on a solution that does not use strict deltaY criteria for lower ring atoms and their substituents, but instead introduces a soft criterion.