Use of SaltStrip standardizing (in cartridge)

Hi All,

With our current cartridge we're using a saltstrip function and are checking now the function <StripSalts ID="stripsalts"/> as part of the ChemAxon indexing statement.

3 questions raised:
A)
In the documentation (https://www.chemaxon.com/jchem/doc/user/standardizer_actions.html)
it is said that you can use a custom salt dictionary and that the salt fragment is stored in a separate field
How can we do this using the saltstrip standardize command as part of the indexing statement in the cartridge?

B)
We would like to define some exclusions like onium compounds as ammonium, sulfonium. How can we do this if we use the saltstrip in the database/cartridge.

C)
We would like to have protons added or removed to balance the charge.

Thanks for your help - Edith

Hi Edith,

A)
In the documentation (https://www.chemaxon.com/jchem/doc/user/standardizer_actions.html style="color: #0000ff; font-size: 12.800000190734863px; line-height: 17px;">)
it is said that you can use a custom salt dictionary and that the salt fragment is stored in a separate field
How can we do this using the saltstrip standardize command as part of the indexing statement in the cartridge?

You can specify the standardizer configuration for JChem indexes using the std_config index parameter (or the std_conf:sql index parameter in case of a long standardizer configuration). This will affect most JChem Cartridge functions operating on the given JChem index (most eminently structure search): the structures will be handled as if the salt component didn't exist.

We will answer your other questions shortly.

Peter

Hi Edith,

B) Defining an exclusion: 
When you set up a custom salt dictionary, simply omit the compounds you want to exclude.
You can set up the dictionary it in Standardizer Editor (GUI) for example. 

In version 6.1, we are going to introduce a new feature in Standardizer GUI: "copy as action string", and also a new editor to the strip salt action, where you can define your salt compounds more easily. 

Combining these two new features: you can use the GUI to set up the dictionary and then copy the configuration as action string, or save this configuration as XML. 
You can use either action string or XML configuration in cartridge.

C)
I recommend using a neutralize action after strip salt action to solve this issue.

Best regards, 

Viktoria

A)
In the documentation (https://www.chemaxon.com/jchem/doc/user/standardizer_actions.html style="color: #0000ff; font-size: 12.800000190734863px; line-height: 17px;">)
it is said that you can use a custom salt dictionary and that the salt fragment is stored in a separate field
How can we do this using the saltstrip standardize command as part of the indexing statement in the cartridge?

Hi Peter, Thanks for this hint. We already use this functionality (with std_conf:sql index parameter)  and like it very much. Edith

Hi Victoria - Thanks for the answer. It is good to know about the plans - but perhaps we've to talk via a livemeeting.
We want to use the standardizing action as part of the create index in the database - and by now I can't see an example how to define the exclusion list and include this in the standardizing action.
Furthermore  I can't see a way how we could standardize with "neutralize" only those substances that are undergoing the saltstripping standardizing. We can't neutralize all substances - we want to neutralize just the "saltstripped".  It seems this is not possible at the moment? Best regards ,Edith

Hi Edith,

I am sending my answer via e-mail.

Best Regards, 
Viktoria