how to calculate a similarity matrix in command line

Hi,

I want to obtain a similarity matrix between a set of molecules. I am using the following command in cmd

screenmd file1.sdf file2.sdf -t:i:1 -o output.txt

but it doesn't work, could you please let me know what I am doing wrong?

Thanks!

Hi, 

The screenmd can only generate dissimilarity values currently. To get the similarity matrix you should calculate 1-dissim. values. 

Does this help?

Daniel

Dear Daniel.

Thank you very much for your reply. It is very logical what you say about the dissimilarity score.

The problem is the command I have written is not doing anything and I am looking for some help in to making it work.

Kind Regards,

Terry

Hi Terry, 

I highly suggest that you take a look at the user manual of the screenmd tool. If you use options of other command line tools with screenmd, it could easily happen that it won't work. 

To get a fully detailed list of options of screenmd with many examples, please type

screenmd -x

I also link the full written manual of the tool to help you with your work:

https://docs.chemaxon.com/display/screen/ScreenMD

Daniel

Dear Daniel,

Great! Thank you very much!

Terry