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?
The screenmd can only generate dissimilarity values currently. To get the similarity matrix you should calculate 1-dissim. values.
Does this help?
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.
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
I also link the full written manual of the tool to help you with your work:
Great! Thank you very much!