100% similarity versus exact

Hello,


What is the difference between 100% similarity threshold (or 0% dissimilarity threshold) and an exact search. Recently, I did a search on a library and got a hit for an 'Exact Search' which registered itself at 77% similarity when I did a similarity search. I was wondering as to how is that possible.

Hi,

Quote:

What is the difference between 100% similarity threshold (or 0% dissimilarity threshold) and an exact search.

These are different conceptions for different tasks.





-Exact search is a graph search algorithm that requires a full graph match.


You can use query features (e.g. any atom, or atom list, etc.) in this search mode.





-Similarity search uses Chemical Hashed Fingerprints, and the distance is calculated from the Tanimoto distance of the fingerprints.


Similarity search only makes sense for comparing actual molecules (without query features).





You can read more on fingerprints here:





http://www.chemaxon.com/jchem/doc/user/fingerprint.html





Tanimoto and other dissimilarity metrics are discussed here:





http://www.chemaxon.com/jchem/doc/user/ScreenMD.html width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> Quote: on a library and got a hit for an 'Exact Search' which registered itself at 77% similarity when I did a similarity search. I was wondering as to how is that possible. Probably your query was not an actual molecule, but a structure with query features (R-groups, atom list, query atom type, query bond type, etc.). In this case the dissimilarity may be other than 0, while exact search provides a hit.





Best regards,





Szilard

Does the jcman utility regard salt forms as duplicates? If I have Compound 2 that is a salt form of Compound 1, does the default standardizer treat them as seperate compounds; or are the considered duplicates?

I am assuming that jcman does not 'wash' salt forms as it imports them into a standard JChem table.

 

Does the jcman utility regard salt forms as duplicates?

No, the default standardization does not remove salts.

https://www.chemaxon.com/jchem/doc/guide/dbconcepts/index.html#standardizerintegration