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Which fingerprint in LibMCS? MinimumCS?
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Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Wed May 20, 2015 12:32 pmPost subject: Which fingerprint in LibMCS? MinimumCS? Reply with quote

Dear ChemAxon,

I would like to ask what is the fingerprint that is being used in LibMCS for clustering?

Also on LibMCS, I would to ask if there is a MinimumCS as a preset, no matter what you can set as a MaximumCS?

Many Thanks,

Terry

Daniel
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Link to postPosted: Thu May 21, 2015 4:07 pmPost subject: Reply with quote

Dear Terry, 

The libmcs is a structure-based clustering tool, so it is basically does not use fingerprints for clustering. However, internally it uses the Chemical Hashed Fingerprints to speed up the structural search. 

Please see the following manual for detailed description of the libmcs:

https://docs.chemaxon.com/display/jklustor/Library+MCS+%28LibMCS%29+clustering

Best regards, 

Daniel

Eleftherios

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Link to postPosted: Mon Jun 01, 2015 1:28 pmPost subject: Reply with quote

Hi Daniel,

 

Thank you very much!

I still do not understand the difference between the hashed fingerprints and fingerprints?

 

Regards

Daniel
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Link to postPosted: Mon Jun 01, 2015 1:43 pmPost subject: Reply with quote

Dear Terry, 

We have many fingerprints to use, Chemical Hashed Fingerpint is one of them. The Chemical Hashed Fingerprint is basically a linear fingerprint that uses hashing to create the binary representation of the fingerprint. You can find a very detailed explanation of how we generate it in the following manual:

https://docs.chemaxon.com/display/CD/Chemical+Hashed+Fingerprint

I hope this helps to clarify your problem. Feel free to ask if not.

Daniel 

Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Tue Jun 02, 2015 4:51 pmPost subject: Reply with quote

Dear Daniel,

Thank you very much for the information, my understanding is better now!

I also have another question!

I did my clustering with LibMCS and set the minimum component substructure to 9, but two of my clusters have been created with a common substructure of 7 atoms

I would like to ask if there is an explanations for this as it is confusing.? Normally these three molecules should be singletons.

Regards

Terry

Daniel
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Link to postPosted: Wed Jun 03, 2015 3:43 pmPost subject: Reply with quote

Hi Terry, 

Can you send us the data necessary for us to reproduce this issue? The molecule set, and the settings of the clustering. We would need further data to investigate this issue. 

Thanks, 

Daniel

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