Break Molecule into its fragments / Merge Fragments together

Good afternoon





Using the Molecule API in java, I can


count the framgents for a Molecule - molecule.getFragCount();


split the Molecule into fragments - molecule.convertToFrags();


fuse Fragments together - combinedMolecules.fuse(molecule, false);





Is there a jc operator or jcf function which would allow me to do the same thing from PL/SQL?





Thanks


Catherine

Hi Catherine,





In JChem 5.1 there will be a fragmentCount Chemical Terms function (you can use it with jc_evaluate) which will count the fragments of a Molecule.





Adding the other two functions to Chemical Terms is also in our feature request list, now we have increased its priority.





Zsolt

Thanks


Catherine

Hello,

Are the jc-functions now available for PL/SQL?

Thanks,

Mike

Hi, Mike!

The jc_evaluate and jc_evaluate_x operator can be used with JChem Cartridge indices and we have functions that can be used without creating an index in the jcf package. For example, now he fragment count and fragments can be selected like this:

With the operators:

select ,jc_evaluate(<indexed_coluumn>,'fragmentCount()') from <table_name> where ...;


select jc_evaluate_x(<indexed_coluumn>,'chemTerms:fragments()') from <table_name> where ...;

With the jcf package functions:

select jcf.evaluate('C.C','fragmentCount()') from dual;

select jcf.evaluate_x('C.C','chemTerms:fragments()') from dual;

 

You can see more examples in the documentation here:

https://www.chemaxon.com/jchem/doc/dev/cartridge/cartapi.html#jc_evaluate

 

Regards,

Tamas

Hi Tamas,

 

Thank you for the functions for getting the fragments. Are there functions available to combine 2 molecules to a single one like the fuse-method in the Java API?

 

Regards,

 

Mike

Hi,

We realized that the
"fuse" function does not really fit into Chemical Terms because
CT functions are executed on a single molecule and the fuse
function would require at least two molecules.

Let us know if you really need
the fuse function, and please describe your use case.

Thank you,

Tamas

Hi Tamas,

I'd need this function to add a salt structure to the main molecule.

Currently we get the information which salt we have to add in database API (pl/sql job). It would be great to change the molecule using the cartridge without the need of an external program (e. g. Java).

 

Best regards,

 

Mike

Hi,

I'm not exactly sure that I understand it perfectly, but I think that in your case fuse in the Molecule API adds a new fragment to the existing Molecule with the fused molecule. You can achieve it is by converting your molecule to a smiles or smarts type format with the jc_molconvert function, and after that you only have to concatenate the two strings separated by a dot (.) character which means new fragment in those formats.

Regards,

Tamas

Hi Tamas,

That's correct. I have to combine 2 molecules into 1. The convertion using the smiles format might work, but I'll loose the position information of the atoms and maybe I'll break some of our drawing rules.

 

Best regards,

 

Mike

Hi,

We agree that it is not the perfect solution, so we can add a new overloaded version of the jc_molconvert function, which can accept two input parameters, and the parameters can be fused together without conversion and manual string concatenation.

We can provide this feature in version 6.1, which is planned to be released at the end of this summer. Is itacceptable for you, or do you require a more urgent solution?

Regards,

Tamas

Hi Tamas,

Thank you very much for your support.

It would be great to have the functionality available in 6.1.

 

Best regards,

 

Mike

Hi,

We actually decided not to overload the jc_molcovert function, but we will create a seperate jc_fuse function with two input molecules. It will work the same way as I described earlier and will be ready for the 6.1 version.

Regards,

Tamas

Hi,

We have the 6.1 version released with the new jc_fuse function.

Regards,

Tamas

Hi Tamas,

Thank you very much. I will try it, as soon as we we upgraded our cartridge.

Mike