Removing salt from a molecule

 

Dear Chemaxon Team, 

We want to remove the salt from a molecule, if the molecule
contains the salt.  

For example, if the molecule has the structure with salt(s) in
it, we want to separate the salt(s) from the molecule. 

Finally we need the output as 1.) Structure without salt, 2.) Salt(s). 

So we will maintain 2 Jchem Structure tables, one to store ‘the
Structure without salt’, and the second table to store ‘the Salts’. 

Is there any option to implement this functionality using the
Jchem.

 

And we will be doing the development using the Jchem .Net
API.  This should be taking care of processing a large .sdf file with
nearly 1 lakh molecules(performance vice).

Jchem version:JChem .NET API 5.10.3.437 

 

We had seen the removal of a component using the Jchem
standardizer( e.g: keep large-for structure without salt, keep small-for salt). 

But we need the proper details from the Chemaxon Team regarding
the removal of salt from a molecule structure. 

Please let us know the solution for this ASAP. 

 

Thanks & Regards,

D. Senthil Kumar vijai.

As you mentioned Standardizer can keep the largest fragment and remove the others, or remove the largest fragment and keep the others, so using Standardizer's "remove fragment" action it is possible to implement the functions you described. If the other fragments are not always salts (they can be e.g. solvents)  then this will not work and you should use the API to implement salt removal.

In a future version we plan to implement a more advanced salt removal which will use a slat dictionary and will store the removed salt information in SDF propert fields. This can be expected in JChem 6.1.

Regards,
Zsolt

Dear Zsolt,

Thanks for your reply.

For your kind information, We had analysed and had arrived to a conclusion that the removal of small component using the standardizer will not solve our purpose(removal of salt from the structure).  

In Real time, There can be so many scenarios,  consider some of them as follows:

1.) if the salt contains more than one salt, how to extract them

2.) the small component always will not be a salt. In this case removal of small component using the standardizer will not be a solution.

So we need to look into all the options, and need to achieve the solution.

Thats why we asked you how to remove only the salt from the structure.  We ask you once again that whether the Jchem has the intelligence to detect the salt from the structure. 

Also you mentioned to use the API "If the other fragments are not always salts (they can be e.g. solvents)  then this will not work and you should use the API to implement salt removal".  Can you just provide the information which API has this option and some samples or links?  

This would be very much helpful for us to explore and to find the solution for this using Jchem APIs.

As you mentioned, regarding the addition of the salt details in the SDF property fields which can be expected in JChem 6.1.;

At present we are looking for the removal of salt from the structure using Jchem API, as we cannot wait for that release.

Please reply us ASAP.

Thanks & Regards,

D. Senthil kumar vijai.

Dear Chemaxon Team,

Will the Jchem Base (java/.net api) supports the following functionalities? 

-->Identification, split and registration of salt and solvent structures

If the Jchem Base support these features, let us know the details of the supporting APIs to do those features ASAP.

 

Thanks & Regards,

D. Senthil kumar vijai.

Dear D. Senthil Kumar vijai,

JChem API cannot recognize salts. It can recognize molecule fragments, and can compare them against other molecules (e.g. to a salt dictionary).

Could you provide us some sample molecules which contain salts? We can implement a code example in Java or .NET (let us know your preference) that demonstrates how to separate salts.

Sorry for not replaying sooner.

Regards,
Zsolt

Dear Zsolt,

 

Thanks for your reply...

Can you please take your own sample molecule with salt in it. 

You can implement a code example in .NET that demonstrates how to separate salts.

Please reply us regarding the same ASAP.

 

Thanks & Regards,

D. Senthil kumar vijai.

 

Dear D. Senthil Kumar vijai,

We will contact you in email.

Zsolt

Dear Zsolt,

Thanks, we will wait for your mail.

 

Thanks & Regards,

D. Senthil kumar vijai.