I experience a strange behaviour regarding getBondOrderSum. This method
lives in two classes: cdk.AtomType (double getBondOrderSum()) and
cdk.AtomContainer (double getBondOrderSum(Atom atom)).
Have a look at the following code:
// read in molecule from sd file or SMILES (not shown)
// query the bond order sum of atom1
Atom atom1 = molecule.getAtomAt(0);
double bondOrderSum_one = molecule.getBondOrderSum(atom1);
double bondOrderSum_two = atom1.getBondOrderSum();
bondOrderSum_one holds the correct value, whereas bondOrderSum_two is
always 0. Is it supposed to work that way? What kind of information can
be queried by the methods of AtomType?