This document describes the main features, configuration possibilities and functional features of the second generation search engine implemented in the following products.
The hits of substructure search are given back ordered by the relevance (similarity) between the hit structure and the query structure.
The most relevant hit structures are given back almost simultaneously with the modification of the query structure.
The Xmx size, cache sizes, and further parameters need to be set before running the servers. Here is a helping page provided for the calculation of the approximate configuration parameters.
The business rules relating the interpretation mode of the chemical structures are defined in molecule types. These rules cover the followings:
The molecule types must be set before initializing the new servers.
|Where to define molecule type(s)|
|JChem Choral||<choral_home>/data/tapes/<type_name.type> files|
|JChem PostgreSQl Cartridge||/etc/chemaxon/types/<type_name.type> files|
|JChem Microservices DB||jws-config/common-config/application.properties file or
|Application mode of molecule type(s)|
|JChem Choral||as index type and as search type|
|JChem PostgreSQl Cartridge||as column type|
|JChem Microservices DB||as table property|
The standardizer actions can be defined in two forms as
There are three tautomer search modes provided
OFF Tautomers are not taken into account during the search
GENERIC The generic tautomer - representing all theoretically possible tautomers - of the target is matched with the query structure itself. This method is applied in substructure search, full fragment search, duplicate, and superstructure search.
It is a hybrid tautomer search mode. The query structure is compared to the generic tautomer of target at substructure and similarity search , while normal canonical tautomers are compared at duplicate search. In full fragment search from version 20.12 to 20.14 the generic tautomer of the target is used, while from version 20.15 normal canonical tautomers are compared.
By default, all stereo molecules - independently of the presence or absence of the chiral flag - are regarded as molecules with absolute stereo configuration.
If you want exclusively molecules with chiral to be handled as absolute (and molecules without chiral flag to be handled as relative) you must set stereoAssumption = RELATIVE in the molecule type definition.
By default, the specified tetrahedral stereo configuration is required to match in the hit structures. In order to ignore the tetrahedral stereo configuration specified in the query structures during the search, the ignoretetrahedralstereo option can be used.
| in substructure search
in duplicate search
|JChem PostgreSQl Cartridge||ignoretetrahedralstereo|
|JChem Microservices DB||stereoSearchIgnoreTetrahedralStereo|
By default, the double bond stereo configuration of all the double bonds of the hit structures must be the same as that of the query structures. See first examples below.
The dbsmarkedonly search option makes possible to check the E/Z configuration of only those double bonds that are marked.
|JChem PostgreSQl Cartridge||dbsmarkedonly|
|JChem Microservices DB||stereoSearchOnMarkedDoubleBondOnly|
In the products based on the second generation search engine, the axial stereo information is taken into account in duplicate search, while in the products JChem Base and JChem Oracle Cartridge - using the first generation search engine - the axial stereo information is not taken into account, by default.
Duplicate search results
|Query||Target||Second generation search engine||First generation search engine [Default]||First generation search engine with ignoreAxialStereo=false|
The highlight function compares a query structure with a target structure and highlights the bonds and atoms of the target structure matching with the query structure. The alignment mode and the color applied for highlighting can be set. Three alignment modes are available:
The hit structure's position on the screen is the same as that of the target structure.
The hit structure is rotated till its part corresponding to the query gets the same position as the query structure has.
The hit structure's position on the screen is partially aligned to the query structure.
|JChem Choral||function highlight
|JChem PostgreSQl Cartridge||function highlight|
|JChem Microservices DB||/rest-v1/db/highlight|