JChem PostgreSQL Cartridge FAQ and Known Issues

    FAQ

    How to cut off data fields from structures stored in sdf format

    In case you want to remove the data fields from the structures stored in sdf format, the following UPDATE statement can be helpful:

    UPDATE <table> SET <structure_column> = substring(<structure_column>::text,'^.*M\ \ END')::molecule('molecule_subtype');

    Example:

    UPDATE mytable SET mol = substring(mol::text,'^.*M\ \ END')::molecule('sample');

    How to apply different business rules on the same chemical structure dataset

    The following business rules can be defined in the molecule type files.

    • standardizer configuration
    • assuming absolute or relative stereochemistry
    • switching tautomer search on or off
    • fingerprint configuration

    If you want more than one combination of the above listed business rule parameters be available - for example you want to run searches with and without tautomer search - you have to create separate table columns with different molecule types. Unfortunately, this means duplication, multiplication of the stored chemical structure data.

    Known Issues

    False similarity search results in the case of molecule types with tautomer=GENERIC parameter

    In the case molecule types with tautomer=GENERIC parameter, similarity search gives false results. These is no workaround at the moment, please do not execute similarity search in structure columns having molecule type with tautomer=GENERIC parameter.