Hi,
I just discovered that the atomic number of hydrogen atoms is null in the CDK.
After I load a simple benzene molecules (or any others), with atom
types configured, hydrogens added and converted to explicit, and
aromaticity detected, the following snippet:
for(int i = 0 ; i < iac.getAtomCount() ; i++) {
IAtom a = iac.getAtom(i) ;
System.out.println("Atom "+i+"/"+ iac.getAtomCount()+":
"+a.getAtomTypeName()+" "+a.getAtomicNumber());
}
Gives
Atom 0/12: C.sp2 6
Atom 1/12: C.sp2 6
Atom 2/12: C.sp2 6
Atom 3/12: C.sp2 6
Atom 4/12: C.sp2 6
Atom 5/12: C.sp2 6
Atom 6/12: H null
Atom 7/12: H null
Atom 8/12: H null
Atom 9/12: H null
Atom 10/12: H null
Atom 11/12: H null
Don't know if its a known issue... Anyway it does not seems normal :)
Cheers
Vincent
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