R-Group enumeration

hi,





We are trying to achieve R-Group Enumeration functionality through the ChemAxon API given a scaffold with defined R-group locations and a list of fragments. Is there a defined method / process for doing this?





Regards,





Madhu K Donepudi

Hi Madhu,





In the next major Marvin version (4.2) we will have a new Markush enumeration plugin that will do R-group enumeration also. You can try it out online: http://www.chemaxon.com/shared/alpha/marvin/examples/applets/example-sketch1.1.html





(Just load or draw your R-group structure into the sketcher and go for Tools > Markush enumeration)





It is also accessible in the released version of JChem (from 3.1) as API only. Let us know if you need this option.





Best regards,


Szabolcs

hi Szabolcs,





We are trying to access the functionality through jchem API. Can you please point me to the relevant java calls/documentation to achieve the functionality.





thank you





Madhu

Please find some information below about how to use the Markush enumeration API in the current, JChem 3.2. version:





1. Markush enumeration is available through class MolEnumerator in package chemaxon.enumeration. It can enumerate R-groups, link nodes, atom lists and bond lists.





2. A license key is required to use it. We will send that separately for evaluation. (Without a key, only a limited number of molecules are generated.)





3. The following code part highlights how to use the class:

Code:

Molecule mol; // Markush molecule to enumerate       MolEnumerator me = MolEnumerator.createMarkushEnumerator(mol);       while (e.hasMoreElements()) {           Molecule eMol = (Molecule) e.nextElement();           // use next enumerated molecule       }

4. In the JChem distribution, there are two wrapper command-line batch files called "enumerate.bat" and "count.bat" for enumeration and to report the number of enumerable structures. Without argument they give a help.





Best regards,


Szabolcs

Szabolcs wrote:

In the next major Marvin version (4.2) we will have a new Markush enumeration plugin that will do R-group enumeration also. You can try it out online: http://www.chemaxon.com/shared/alpha/marvin/examples/applets/example-sketch1.1.html

The Markush enumeration plugin is also accessible from API. The documentation of the API can be found here: http://www.chemaxon.com/shared/alpha/marvin/doc/api/chemaxon/marvin/calculations/EnumerationPlugin.html





Let us know if you choose this option and need further help.





Note: this is an alpha version, use only for development.





Best regards,


Zsolt

Is there a License Key available for the Markush Enumeration Tool in Marvin 4.2.0.alpha that is available to the academic package users? Without the license it throws an exception after ten calls in an enumeration.

Yes, the plugin will use a different license key. We will send you that by email.

Dear mdconnolly,





If you send me your email address related to your academic license I will be very happy to send you the license key for Markush Enumeration.





Cheers,


Nora Lapusnyik


nlapusnyik _at_ chemaxon.com