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.
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.
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?
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?
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,