could action / rule of standardizer be reported somehow?

Hi,

is it possible, that standradizer reports somehow (e.g. stard_comment field in SDFIle output) the action / rule, which is used on the specific molecule (e.g. Aromatize, Removal (of which fragment?), Clean). And next question, it is possible to "name" the templates, which are used in Clean and report the specific name somehow (e.g. Crown18-skeleton, prophyrin-skeleton, etc.)?

Best, Hinnerk

PS: I use standardizer within IJC.

Hi,

Standardizer can report the list of actions performend on the molecule, but currently this is available only via API; a code example can be found here: http://www.chemaxon.com/jchem/doc/dev/standardizer/index.html . In the future we will add more advanced reporting capabilities to the Standardizer application (GUI and command line too).

How urgent is this feature for you?

Zsolt

Additionally, Structure Checker can report many issues already even in an sdfile field. A batch execution GUI of Structure Checker is installed by JChem installer.

Hi,
many thax for the quick answers!

In general it is no problem for me to call an API, as long as it has a C interface :-) </ironic>

This feature would be quite helpful in developing rules for standardizer. Espacially in a Clean-action rule, since this should not affect any fingerprint and therefore unwanted clean action is hard to find in a large sample.
As a workaround I could use substructure match with highliting, but this is not easy with severall templates.

Since I have only a license to use standaradizer within IJC environment, I think, there is no way to access standardizer via command-line / api, or is it possible to call com-im-ijc-standardizer.jar somehow?

http://www.chemaxon.com/jchem/doc/dev/standardizer/index.htm is empty (at least under FF and ie8)

Hi Hinnerk,

If you are wanting to do this in IJC then it should be possible to write a script that read though the structures in a table, called standardizer (using API) with each structure and then wrote the results back to a different field(s).

This might be useful for developing new standardizer configurations.

The same probably applies to structure checker.

If this would be useful to you then we could help you write such a  script. It wouldn't need C :-)

Tim

Hi Tim,

it would be great, if you could provide such a script (the workflow as you described, is sufficient). At least a small sample will be very usefull. Expanding / adapting it to my needs should be possible. Java is not that complex, as far as I know. :-)

Best, Hinnerk

Hinnerk Rey wrote:

http://www.chemaxon.com/jchem/doc/dev/standardizer/index.htm is empty (at least under FF and ie8)

It's http://www.chemaxon.com/jchem/doc/dev/standardizer/index.html (the "l" at the end was missing, sorry). I fixed it in my previous post.

Zsolt