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how to calculate a similarity matrix in command line
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Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Sun May 10, 2015 5:59 pmPost subject: how to calculate a similarity matrix in command line Reply with quote

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!

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Wed May 13, 2015 1:51 pmPost subject: Reply with quote

Hi, 

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

Does this help?

Daniel

Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Thu May 14, 2015 3:20 pmPost subject: Reply with quote

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

Daniel
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Link to postPosted: Sat May 16, 2015 9:19 amPost subject: Reply with quote

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

Eleftherios

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Link to postPosted: Mon May 18, 2015 12:02 pmPost subject: Reply with quote

Dear Daniel,

Great! Thank you very much!

Terry

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