Setting the Dissimilarity Threshold in ScreenMD

Hello

I wanted to check and make sure I am using the right syntax when running screenmd, specifically with respect to threshold.

In the following command I am hoping to run a screen with Pharmacophore Fingerprints, using the Tanimoto Metric with a Dissimilarity Threshold of 0.3:

screenmd targets.sdf queries.sdf -g -k PF -c pharma-frag.xml -o mytable.table -M Tanimoto -m 0.3

Does this look correct?  My understanding is that by default this threshold is 0.2?  When I run the command above with a threshold of 0.99 I do not see any more 'matches' than the default which seems incorrect.

Thank you

Dennis 

In case it helps, here is the test set I am using...

Hi Dennis, 

thank you for the report, we could reproduce it. We are working on to solve it asap. 

 

Best regards,

Monika

dmoccia wrote:

Hello I wanted to check and make sure I am using the right syntax when running screenmd, specifically with respect to threshold. In the following command I am hoping to run a screen with Pharmacophore Fingerprints, using the Tanimoto Metric with a Dissimilarity Threshold of 0.3: screenmd targets.sdf queries.sdf -g -k PF -c pharma-frag.xml -o mytable.table -M Tanimoto -m 0.3 Does this look correct?  My understanding is that by default this threshold is 0.2?  When I run the command above with a threshold of 0.99 I do not see any more 'matches' than the default which seems incorrect. Thank you Dennis

Hi Dennis,

if you want to run the screenmd with mentioned parameters, the following steps should be performed:
Change the following line in the config file (pharma-frag.xml):
    <ParametrizedMetric Name="Tanimoto" ActiveFamily="Generic" Metric="Tanimoto" Threshold="0.2"/>
Set 'Threshold' parameter to 0.3
Run the command:
    screenmd targets.sdf queries.sdf -g -k PF -c pharma-frag.xml -o mytable.table -M Tanimoto
   
   
Best regards,
Laszlo   
   

Laszlo

Thank you for the response, I will try this out.  Makes sense that the config file would override settings in the command line in this case.

 

Dennis