Standardiser

How can one be sure that jc_insert is standardising to the same exact


same specifications as the automatic jcman.import standardisation?





If I processed a SMILES that was already standardised during a jcman


import through a JC_INSERT statement, is it possible that this SMILES


would be re-standardised in a different way by JC_INSERT?





Please explain where jcman / jc_insert obtain there configuration


information from with respect to standardisation and if I need to


synchronise these two process to standardise in the same way, how I


might go about doing so? (jcman refs an xml file I think but how does


JC_INSERT work in this respect?)

Both JChemManager and jc_insert obtain the standardizer configuration from the "current" JChem properties table. The "current" JChem properties table is defined as follows: (1) for JChemManager it is specified as a connection property; (2) for jc_insert it is specified as an argument (the third argument) to the function. For both JChemManager and jc_insert, the default JChem properties table is: JChemProperties.





The standardization configuration can be defined for a given JChem table during the creation of that table by JChemManager. Whether repeated standardization (using the same configuration) results in a different structure or not depends on the configuration of the standardizer. The default standardization (aromatize + dehydrogenize) will not further change a structure which has already been transformed using the same configuration. An atypical configuration (such as: add a specific functional group to a structure) may change a structure each time the structure undergoes standardization.





Keeping the standardization of imported/inserted structures in sync with JChemManager and jc_insert is normally automatic. Just make sure you use the same JChem properties table for both and that you do not change (e. g. manually) the standardizer configuration after the JChem table has been created.