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exporting dendrogram of MCS lib to excel & centromere
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Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Wed Apr 29, 2015 12:05 pmPost subject: Reply with quote

Dear All,

I have two questions:

1) is there a way of exporting the dendrogram of the MCS library clustering to excel (for structure visualisation of every molecule)?

2) is there a way of selecting a centromere (most representative molecule) form each cluster?

Any help will be much appreciated!

Many Thanks,

Terry

Daniel
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Link to postPosted: Thu Apr 30, 2015 2:53 pmPost subject: Reply with quote

Hi, 

The answers for your questions:

1. The only way you can export the cluster data to Excel is to export it into an SD file in libmcs. This SD file will contain all clustering data, which you can put in JChem For Excel.

2. You can't select the centroid in libmcs, because the representation does not allow that. You should use Sphere Exclusion clustering instead. It that case centroid can be easily selected.

I hope this helps.

Daniel 

Eleftherios

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Link to postPosted: Fri May 01, 2015 4:29 pmPost subject: Reply with quote

Hi,

Thank you very much for the reply. What is this Sphere exclusion clustering? Is it in JChem? Could you please give me some more info cause I am new to the software?

Many Thanks,

Terry

Eleftherios

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Link to postPosted: Fri May 01, 2015 5:09 pmPost subject: Reply with quote

I have finished with clustering in libmcs. I now want to find centroids from the large clusters. As I think I about it, I have to import the molecule of each clusters and find centroid. Is there any guide for this please?

Daniel
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Link to postPosted: Mon May 04, 2015 1:01 pmPost subject: Reply with quote

Hi, 

As I wrote earlier you can't get the centroids from the libmcs clustering. You should use the Sphere Exclusion clustering in JKlustor to have that.

I link here the user guide of the Sphere Exclusion clustering that will help you get started:

https://docs.chemaxon.com/display/jklustor/Sphere+Exclusion+clustering

I hope this helps. 

Daniel

Eleftherios

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Link to postPosted: Fri May 08, 2015 6:00 pmPost subject: Reply with quote

Thank you very much for your reply!

It took me a while to reply because of heavy schedule.

I confused the centroid with the 'most representative molecule ' of a cluster. So what I need to find is the most representative molecule for each of my clusters. I discovered that you can a get a similarity/dissimilarity matrix for the molecules of a cluster by using the command line.

I am using this command: jcsearch -q [file name] -f [output file name] -t:i:1

but I get an error message that is not recognizing .smiles or .sdf files. What kind of file extension I need to use please?

Any advises on how to finish this task please?

Eleftherios

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Link to postPosted: Sun May 10, 2015 6:00 pmPost subject: 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
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Link to postPosted: Mon May 18, 2015 9:49 amPost subject: Reply with quote

Dear Terry, 

For clustering I highly recommend that you use our command line tool jklustor. You can use the Sphere Exclusion clustering algorithm with that, which will hopefully suit your needs.

To get the full manual of jklustor under the command line, type

 jklustor -h

I also link here the official JKlustor manual:

https://docs.chemaxon.com/display/jklustor/Home

Answering your question regarding the screenmd, you used a wrong option with the command. Please see my answers regarding that in my previous answers for you.

Daniel

Eleftherios

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Link to postPosted: Mon May 18, 2015 12:04 pmPost subject: Reply with quote

Dear Daniel,

Thank you!

The link is not working?

Terry

Daniel
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Link to postPosted: Mon May 18, 2015 12:41 pmPost subject: Reply with quote

Hi Terry, 

It works. However, I rather put the homepage of the manual to help you get through it:

https://docs.chemaxon.com/pages/viewpage.action?pageId=28410252

Daniel

Eleftherios

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Link to postPosted: Mon May 18, 2015 4:30 pmPost subject: Reply with quote

Dear Daniel,

Thank you very much!

Terry

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