Yes you are correct hcount is 0 i used it null it was mistake.
Actually i don't see the value of hcount during the programm run so i thought in mind it is null.
 
Most file formats do not have implicit Hs (mol for
example), so it is 0, since the parser doesn't set it (but it could if it is
in file). You can run HydrogenAdder to have implicit Hs.
Total H should be implicit + explicit. Since both are in, I would not keep
another value (most likely to get inconsistent).
 
Actually i have added the TOTAL_H_COUNT in cdkconstants but the information you have
provided is  really helpful.
Also i found that having this constant is not useful if one read the molecule from smile.
In that case again the totalHcount will remain 0.
 
I will experiment with HydrogenAdder and make a new function as soon as this work. 
"Total H should ==implicit + explicit"
 
and remove the constant.
 
thanks 
 
 
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sushil ronghe
Center of Pharmacoinformatics
India
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