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libMCS clustering algorithm question
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Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Thu May 14, 2015 4:03 pmPost subject: libMCS clustering algorithm question Reply with quote

Dear Chemaxon,

I am using libMCS (9, normal) for clustering and in one of my clusters I have the following three molecules:

As you can see the three molecules in the white background, are quite dissimilar between them. My question is if you have a 9 atom MCS and you only see 6 in common, are the other 3 generic substituents or 'X' groups?

It will help me to understand more and better explain how the clusters have been formed.

Kind Regards,

Terry

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Wed Jun 03, 2015 3:48 pmPost subject: Reply with quote

Hi Terry, 

As you posted the same issue in the 

https://www.chemaxon.com/forum/ftopic14068.html

forum, let's continue the discussion of your LibMCS issues there, please. 

We try to follow the one issue, one topic system on our forums. 

Best regards, 

Daniel

Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Tue Jun 16, 2015 1:03 pmPost subject: Reply with quote

Dear Daniel,

I have another question please.

I used LibMCS (9, normal) for clustering. In the picture below you can see two clusters that contain two molecules each (top to bottom). In color is the cluster scaffold and in white background are the cluster molecules.

 

My questions are:

as I have set an MCS of 9, these two clusters should have joint in one cluster?

Does the clustering algorithm counts the hydrogens as well?

Many thanks,

Terry

Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Wed Jul 08, 2015 3:21 pmPost subject: Reply with quote

Dear  Daniel

I managed to understand my questions. When the smiles were converted to structures in Microsoft excel with the JChem add in, they were converted with hydrogens and saved to an sdf file, so the clustering algorithm took into account the Hs as well. This explain my questions and I want to apologize for any confusion I might have caused.

Is there any option, for converting smiles to structures, with the JChem extension in excel, with or without the Hs?

Kind Regards

Terry

Daniel
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Joined: 22 Jan 2012
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Link to postPosted: Wed Jul 15, 2015 1:07 pmPost subject: Reply with quote

Dear Terry, 

You can set the handling of explicit/implicit Hs in JChem For Excel using the Options window. Using that window you can set them the same way as in MarvinSketch. 

I hope this helps, 

Daniel

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