Just to add that "addh" and "removeh" don't add and remove hydrogens, they convert the hydrogens that are explicit in the molecular graph into implicit hydrogens. I appreciate that the names are misleading, but it's hard to change them at this point. To actually delete an explicit hydrogen, you need to use OBMol.DeleteAtom(). To change the number of implicit hydrogens you would instead use OBAtom.SetImplicitHCount().
To check whether something is correct, you can just write out the SMILES string. On Thu, 9 Apr 2020 at 17:31, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > >> m1 = mol1.OBMol > >> m2 = mol2.OBMol > > > You'll want to count the number of atoms in each molecule before you do > the addition. > > >> m1 += > m2 > #merging the two molecules > >> m1.AddBond(1,2,1) > ## how do I give the right > indices here? > > > You just added a bond between atom 1 and atom 2. Most likely these are > both in mol1. > > If you have benzene as m1 and methane as m2, then you have 6 atoms in m1 > and 1 atom in m2, so you want to link atom 1 and atom 7. > > Moreover I would like to check whether the bond I have inserted is correct. > > > Probably you want to do this in a Jupyter notebook and depict the molecule. > > Certainly, you can get properties from the bond (e.g., start and end atom > index) but those will be exactly what you specified. > > Personally, if you're trying to grow a molecule, I do this all in SMILES > and generate 3D coordinates later. > > 'c1ccccc1' + 'C' = 'c1ccccc1C' # toluene > > Now you don't always have the SMILES in the right atom order, but you can > always abuse SMILES syntax: > > 'c1%99c[C]cccc1' + '.C%99' # new bond created to the atom I want... > > Hope that helps, > -Geoff > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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