[Cdk-devel] Ring Configuration in SMILES

[John M. <jo...@eb...>]

Hi All,

Would you consider the following as valid smiles?

	[H]C/12(CCCCC\2([H])(CCCC1))	- depictions

This example is from SmilesGeneratorTest.testCisTransDecalin(), it is trying to represent is the cis/trans ring configuration but is this possible in the specification? In my mind it should simply the clockwise/anti-clockwise chiral atoms?

	[H][C@@]12CCCC[C@@]1([H])CCCC2 - depicitions

From the ambit depictions the toolkits which handle chiral smiles input don't seem like the cis/trans configuration of the ring. I've checked the Daylight and OpenSMILES manuals but can't find any mention of cis/trans ring configurations.

Thoughts?

Thanks,
J