ScreenMd-threshold

Its given that


-L is the dissimilarity threshold.


But its not working while we are using one descriptor.Its working with more than one descriptors only.


Why it so?


threshold here means dissimilarity threshold or something other





i have one more question its about -Z(zero threshold)


is it applicable to median hypothesis only?


please help me

Quote:

But its not working while we are using one descriptor.Its working with more than one descriptors only. Why it so?

It's because the threshold with each individual descriptor component is controlled in the corresponding XML configuration file.

Quote:

threshold here means dissimilarity threshold or something other

Yes, it does mean the dissimilarity threshold.

Quote:

i have one more question its about -Z(zero threshold) is it applicable to median hypothesis only?

Yes, that's correct.





Regards,


Miklos

Thank you for your reply





"It's because the threshold with each individual descriptor component is controlled in the corresponding XML configuration file"





In the case of certain descripters like LogD,LogP etc we dont need the xml file for its command line run.so in that case how it will be controlled.


I tried to create xml file for logp,mass etc but its not working.Is there any specific values for lowerbound,upperbound etc specified in xml file for each descripter.From where i will get xml file for these descripters.





I have one more question


In the case of descripters other than PF and CF The output contains


ABSDiff..What is actually mean.


Tanimotp is not applicable to all descripters.So Abs is Euclidean itself?


Can you please tell about this Abs

Quote:

In the case of certain descripters like LogD,LogP etc we dont need the xml file for its command line run.so in that case how it will be controlled.

LogD should work, a sample config file is provided under examples/config.


In some cases (logP, mass) you need to use the API, but that's not ment for end users really.

Quote:

Is there any specific values for lowerbound,upperbound etc specified in xml file for each descripter.

These values refer to the pH range considered in the related calculations. Values depends on your needs.

Quote:

ABSDiff..What is actually mean.

This refers to the absolute value off the difference of the two descriptor values.

Quote:

So Abs is Euclidean itself

No, but it's similar. Euclidean is the root of the sum of square of the differences, see http://www.chemaxon.com/jchem/doc/user/ScreenMD.html#euclidean





AbsDiff is simpler to compute but has different analytic properties.

Dear sir,


I am using academic package of Jchem.so i cant access xml editor


For LogD xml configuration file is given.


can we make xml configarion file for scalar descriptors like logp,mass etc and for BCUT.


I edited existing xml file and tried to make for logp.its not working


can you please tell me what all changes i should make to create xml for logp and for others.

Hi there,





the CXN xml editor has been discontinued. Please use a third party product, or, the simplest alternative: just use a text editor to modify the xml configurations.





In the present implementation logp does not take an external configuration file. What parameters would you like to change in the logP calculation?





Regards


Miklos