Screenmd custom descriptors

Hi,





I'm trying to use screenmd with a custom descriptors (estate) which are stored in the sdfiles. I assume I am using the wrong synthax but I also do not know how to implement it using the configuration xml file. Can anybody show me an example?





Thanks,





Peter

Hi Peter,





I am afraid you need to implement a few simple Java classes in order to plug your descriptor in the system. The JChem developer's guide will be a good starting point: http://www.chemaxon.com/jchem/doc/guide/screen/index.html#custom.





Hopt his helps, get back if you need further assistance.





Regards,


Miklos

Hi Miklos,





Well that explaines it I guess. I'm going to give it I try.





Thanks,





Peter

Hi Peter,





great! We are here and happy to help!





Bests,


Miklos

Hi Miklos,





I looked at the examples and was able to get them working. Obviously I do not have to write my own descriptor since it is coming from a third party application and I'm planning to use a sdfile tag. So I guess I only have to create something to make it know within the chemaxon environment.





Anyway, would I still be able to use the screenmd application or do I have to write a new application like in the example: ComparePairwise.java





I tried with the maccs example but I do not see how I should implement the new class within the environment. (I know that there is a plug-in file for marvin, is there something similar for this as well).





Cheers,





Peter

Hi Peter,





Indeed, you dont need to implement the generator class for your descriptor. You still need the generate() method, but it simply takes the descriptor from the SDF tag. SDF tags are stored in the Molecule as Properties, and they are read automatically along with the structure, so you don't need to write extra code for that.





As soon as your descriptors can be 'generated', that is, taken from the Property object, you can use screenmd without any further effort.





Does this help at all?





Miklos

Hi Miklos,





Well I gave it a try using the Maccs example. I know the descriptor it self is not well defined there but I presume it should work.





I'm getting the error below. Can you give me a last hint?





Thanks,





Peter





screenmd targets.sdf queries.sdf -k Maccs -c Maccs.xml


null


java.lang.NullPointerException


at chemaxon.descriptors.CDParameters.readValues(CDParameters.java:236)


at chemaxon.descriptors.MDParameters.readFromXmlString(MDParameters.java:897)


at chemaxon.descriptors.MDParameters.fromString(MDParameters.java:229)


at chemaxon.descriptors.CDParameters.fromString(CDParameters.java:101)


at chemaxon.descriptors.MDSet.newInstance(MDSet.java:92)


at chemaxon.descriptors.ScreenMD.initSources(ScreenMD.java:821)


at chemaxon.descriptors.ScreenMD.main(ScreenMD.java:227)

Hi Peter,





Did you implement a getDefaultDocumentFrame() method? It is mandatory.





HTH


Miklos

Yes I did, it's in the example.


I really just copied the example and compiled it without errors.


By the way, I also tried with and without a configuration file (which I actually took from the MaccsParameters.java) with the same result

I need to check this more thoroughly. I get back to you...


Miklos