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');
UPDATE mytable SET mol = substring(mol::text,'^.*M\ \ END')::molecule('sample');
The following business rules can be defined in the molecule type files.
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.
By default, the extensions chemaxon_type and chemaxon_framework are installed into the PUBLIC schema of the PostgreSQL database. However, there can be cases when these extensions must be installed into a different schema. For example, if there is an object - like a table - named to molecule already present in the PUBLIC schema.
The following steps should be executed:
CREATE SCHEMA chemaxon; CREATE EXTENSION chemaxon_type WITH SCHEMA chemaxon; CREATE EXTENSION chemaxon_framework WITH SCHEMA chemaxon; CREATE EXTENSION hstore; -- this extension does not need to be installed into the chemaxon schema
In order to make searches able to use these extensions, search_path must be modified.
Session level modification:
SET search_path TO chemaxon,public;
Database level modification:
ALTER DATABASE <db_name> SET search_path TO chemaxon,public;
See further possibilities in PostgreSQL documentation about schema search path.
JPC can only be successfully installed if the
CREATE EXTENSION HSTORE;
step of the installation process can be executed.
HSTORE extension is part of the contrib package of PostgreSQL database (for example postgresql-contrib-12), so it is necassary to have the contrib package installed.
Use the is_valid_molecule method. Note, there are some structures which are qualified as valid, but cannot be indexed by the cartridge.
Check the logs on the server in /var/log/jchem-psql/. The log level can be set in /etc/chemaxon/jpc-log4j.xml, see documentation.
In the client log when running insert scripts, the insert is successful, but warnings appear:
INSERT INTO <table_name>
Warnings: <...> Invalid molecule source: <error> See PostgreSQL documentation .
By this query (preferably on an indexed table):
select * from test except select * from test where '*'|<|mol;
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. From version 21.9.0 similarity search works correctly even in the case of molecule types with tautomer=GENERIC parameter.