setIgnoreCumuleneOrRingCisTransStereo()

Hi, the JChem API says that SearchOptions.setIgnoreAlleneStereo(boolean) is deprecated in favor of setIgnoreCumuleneOrRingCisTransStereo(boolean). I'm a little concerned by the name of the new method. It seems to say that it will ignore cumulene *or* ring cis/trans stereo information. Does this mean that if I turn this flag on, cis-1,2-dimethylcyclohexane will match to trans-1,2-dimethylcyclohexane? Or does it only ignore cis/trans information in compounds such as, say, MeCH=C=C=CHMe?

Hi Bob,

The behavior of this new search option is illustrated here. The true or false value of IgnoreCumuleneOrRingCisTransStereo has no effect on dimethylcyclohexane or 2-butene matching, only cumulated systems (with odd number >= 3) are considered.

Best regards,

Krisztina

kvajda wrote:

Hi Bob, The behavior of this new search option is illustrated here. The true or false value of IgnoreCumuleneOrRingCisTransStereo has no effect on dimethylcyclohexane or 2-butene matching, only cumulated systems (with odd number >= 3) are considered.

Good enough. Curious, though, that the name of the function contains "OrRing" when it really has nothing to do with rings. I would name it, "IgnoreOddNumberedCumuleneCisTransStereo."

Please, look at the attached picture. The minimal odd number (3) considered by IgnoreCumuleneOrRingCisTransStereo can be fulfilled with 3 conjugated double bonds, 2 double bonds + 1 ring, 1 double bond + 2 rings, and 3 rings without any double bond.

Krisztina

Ah, I see. OK then. I suggest you include these examples in your documentation.