libMCS clustering algorithm question

User 6b694845c2

14-05-2015 15:03:45

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,


ChemAxon d51151248d

03-06-2015 14:48:47

Hi Terry, 

As you posted the same issue in the

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, 


User 6b694845c2

16-06-2015 12:03:37

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,


User 6b694845c2

08-07-2015 14:21:12

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


ChemAxon d51151248d

15-07-2015 12:07:33

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,