Hi,
I would like to use the pybel
"hyb<http://openbabel.org/docs/2.3.1/UseTheLibrary/Python_PybelAPI.html>"
attribute (corresponding to
OBAtom::GetHyb()<http://openbabel.org/dev-api/classOpenBabel_1_1OBAtom.shtml#a4f510d8274d4d2a835c7c438aa794e57>)
Docs says that it gives the hybridization of the atom: 1 for sp, 2 for sp2,
3 for sp3, ...
But some sp3 atoms have 2 or 0 for hyb. (Using Open Babel 2.3.1)
mol = pybel.readstring( "smi", "C(Cl)NC(=O)C")
for a in mol.atoms:
print "Atom %d" % a.idx, a.OBAtom.GetAtomicNum(), a.hyb
Output :
Atom 1 6 3 # sp3, correct
Atom 2 17 0 # sp3, incorrect
Atom 3 7 2 # sp3, incorrect
Atom 4 6 2 # sp2, correct
Atom 5 8 2 # sp2, correct
Atom 6 6 3 # sp3, correct
But with C(Cl)NCC(=O)C :
Atom 1 6 3
Atom 2 17 0
Atom 3 7 3 # different, now 3 instead of 2
Atom 4 6 3 # sp3, correct
Atom 5 6 2
Atom 6 8 2
Atom 7 6 3
Do I misinterpret something?
Thanks,
Regards,
Pascal
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