molecule matching

hi guys,


i wanted to ask ,is there a library/tool in marvin where i can compare molecules with each other,and print diffrences?


thanx

Yes we have many tools for comparing molecular structures. But I am not sure, how would you like to print out the differences? Atom indices, colored images, using API, a command line tool, a desktop or a web GUI?

Hi Gyri thanks for replying,


i want to use the api ,and i want to be able to compare 2 molecules and see the diffrences in atom indices and diffrent bounds.is there a class for canonicalization or is it integrated in the molecule matching?


thnx

I assume, that you need the MolSearch class of the JChem toolkit. One molecule is the query, the other is the target and it returns the indices of the matching atoms. It has lots of options for matching.





Only very basic canonicalization is done autmatically: aromaticity and handling explicit/implicit hydrogens.





If you need advanced canonicalization features (tautomers, mesomers, counterions, etc.) you should use the Standardizer class.

Hi Gyri,


thank you for your very much for your reply,so far ive succesfully,integrated the molsearch class in to my programm.But i dont find the method that i need.What i have to calculate ist wether to graph(molecules) matches or not.The result shoult be boolean.

It is the isMatching function.

Hi Gyuri thank you very much so far ,you helped me very much.I got a further question though.


can i check if a single atom is maching and what kind of numbering ist given in the hits[][] numbering ,is its the rearranged numbering (canonicalized) or the numbering of the orginal mol/sdf files?