Thank you both,
@Geoff: I could draw the molecule and use a Jupyter notebook
I think I could get the right bond with
$ m1.AddBond(1,13,1)
But instead of getting 'C1=CC=CC=C1C' I get 'c1(ccccc1)C'. Are these equivalent?
Actually this is an easy case and I know that the atom to be bound is the
central C in the methane, but in reality I have many different molecules to
bind, and I would like to iterate over all atoms in the molecule which do not
belong to the ring (as below).
@Noel
What argument should I pass to DeleteAtom()?
I am stuck on a NotImplementedError: Wrong number or type of arguments for
overloaded function 'OBMol_DeleteAtom'.
Specifically,
$ import pybel as pb
$ import openbabel as ob
$ benz_pyb = next(pb.readfile('xyz', 'benzene.xyz')) #pybel object
$ benz_obm = benz_pyb.OBMol #openbabel
object
$ print(benz_pyb.atoms)
>> [<pybel.Atom object at 0x10e02a6a0>, <pybel.Atom object at 0x10e02aa58>,
>> <pybel.Atom object at 0x10e02aa90>, <pybel.Atom object at 0x10e042b70>,
>> <pybel.Atom object at 0x10e042c88>, <pybel.Atom object at 0x10e042cf8>,
>> <pybel.Atom object at 0x10e042e10>, <pybel.Atom object at 0x10e042978>,
>> <pybel.Atom object at 0x10e0429e8>, <pybel.Atom object at 0x10e042ef0>,
>> <pybel.Atom object at 0x10e5f4c50>, <pybel.Atom object at 0x10e5f4cc0>]
$ print(benz_obm.GetAtom)
>> <bound method OBMol_GetAtom of <openbabel.OBMol; proxy of <Swig Object of
>> type 'OpenBabel::OBMol *' at 0x106b441b0> >>
But then either
$ ob.OBMol.DeleteAtom(benz_pyb.atoms[0])
or
$ ob.OBMol.DeleteAtom(benz_obm.GetAtom)
Give me the same error
>> NotImplementedError: Wrong number or type of arguments for overloaded
>> function 'OBMol_DeleteAtom'.
>> Possible C/C++ prototypes are:
>> OpenBabel::OBMol::DeleteAtom(OpenBabel::OBAtom *,bool)
>> OpenBabel::OBMol::DeleteAtom(OpenBabel::OBAtom *)
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