Second Generation Search Engine Deprecated Features

Search options

Ignore tetrahedral stereo / charge / isotope in search - until version 23.17.0

By default, the specified tetrahedral stereo configuration, charge and isotope value is required to match in the hit structures.

Here we describe how the ignoretetrahedralstereo option is handled in search. The other two options ignorecharge and ignoreisotope are handled the same way, and are also recommended to apply in SUBSTRUCTURE and FULLFRAGMENT search, but not in DUPLICATE search.

In order to ignore the tetrahedral stereo configuration specified in the query structures during the search, the ignoretetrahedralstereo option can be used.

The ignoretetrahedralstereo search option is a query transformation parameter. If ignoretetrahedralstereo is set, the tetrahedral stereo bonds of the query molecule are transformed to single bonds in the background of the search, but the tetrahedral stereo bonds of the target molecules stay intact.

The usage of ignoretetrahedralstereo search option is recommended in SUBSTRUCTURE and FULLFRAGMENT search, but is not recommended in DUPLICATE search.

Duplicate search with fully ignored tetrahedral stereo properties - like in JChem Base or JChem Oracle Cartridge - cannot be executed by the products using this second generation search engine. When searching for enantiomers, diastereomers FULLFRAGMENT search with ignoretetrahedralstereo option is recommended with taking into account the other less strict features of FULLFRAGMENT search compared to DUPLICATE search (the hit structures can contain more fragments, isotopes, charged atoms, ...)

Query	Target	without ignoretetrahedralstereo [Default]	with ignoretetrahedralstereo
			in substructure and fullfragment search in duplicate search