How to retrieve the enumerated structures from Marvin applet

It is really nice to have markush enumeration available thrugh Marvin applet, but how do I retrieve those enumerated sructures programatically?

Use Markush Enumeration Plugin via Java API.


Javadoc link: MarkushEnumerationPlugin API. See API usage examples in the javadoc header.





Zsolt

It seems in setInputMolecule(Molecule mol) method, mol need both Markush structure and R groups.





is it possible I can set Markush structure fisrt, but set R groups from sd files?





Hao

hzheng wrote:

It seems in setInputMolecule(Molecule mol) method, mol need both Markush structure and R groups.

The R group definitions are parts of the Markush structure, so yes, both are needed.

Quote:

is it possible I can set Markush structure fisrt, but set R groups from sd files?

You can read R group definitions from SDFiles, and construct Markush structures with different R groups.


See also: http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/RgMolecule.html





After the RgMolecule is constructed, you can set it as input molecule for MarkushEnumerationPlugin with method setInputMolecule(Molecule mol), and then run the plugin.





Apologies for the late answer.





Zsolt

We will also implement an SD file -> R-group definition loading function in MarvinSketch and in a utility class for version 5.2. It will be available Q1 2009.





Attachment points will be possible to add by transformation rules of Standardizer.


(Currently transformation rules cannot handle attachment points, but it will also be available in version 5.2.)





Best regards,


Szabolcs