exact match, setStereoSearch(false)

After setting





setSearchType(SearchConstants.EXACT)





is there a difference between:





setStereoSearch(false)





and





setExactStereoMatching(false)





and is either one necessary? The API documentation is not clear.





-- Bob

Yes, there is difference.





setStereoSearch() switches on/off stereo searching. By default it is true for all search types.





setExactStereoSearch() setting only has effect when stereoSearch is true. If exactStereoSearch is true, it means that all stereo information should be the same in the query and target ("all stereo info is exactly the same"). It mainly has an effect when the query has no stereo information: it only matches non-stereo target. Similarly, a query with a wiggly tetrahedral center will only match wiggly tetrahedral center, and not specific R and S configurations. By default, this setting is false for all search types except for PERFECT search, where it is true.





From the above, after setSearchType(EXACT), setStereoSearch(false) is necessary, but after this setExactSearchType(false) has no effect.





We will enhance the documentation regarding these methods.

Szabolcs wrote:

setStereoSearch() switches on/off stereo searching. By default it is true for all search types.

So when it is false, if there is a bold wedge in the query, it will match to a hashed wedge in the target?





And when the query has a cis double bond, it will match to a trans double bond in the target?

Yes, in that case the search would ignore all stereo information.