> >> 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)
> I have a CML file that I'm trying to convert to a LMPDAT format. The
> conversion appears to work,
…
Considering I don't know many people using LMPDAT it would really help to know
what the "correct" (e.g. your version) would look like.
I know that Albert wrote the code as a quick example that
Dear Noel,
Thank you for the answer.
I was able to actually remove all hydrogens, merge the two molecules and
reintroduce all the hydrogens.
Nevertheless, what I am getting is not methylbenzene (C7H8) but just the same
two molecules as before.
I believe I also created a new bond but I am pretty
Hi,
I have a CML file that I'm trying to convert to a LMPDAT format. The
conversion appears to work, but not particularly well. Some bonds appear to
be incorrect, and the atom coordinates are definitely not correct. The
command I'm using is:
babel -icml file.cml -olmpdat file.lmpdat
And
Use the Python keyword "next" on an iterator to get the next item:
mol1 = next(pybel.readfile()
You can add an OBMol to an existing one:
m1 += m2
I'd recommend writing it out as SMILES at this point, just to check the
structure:
print(pybel.Molecule(m1).write("smi"))
If the hydrogens are
Hello everyone,
I have two molecules (benzene and methane) in two separate xyz files.
I would like to create a methylbenzene molecule out of these and relax it
with a UFF.
I am new to pybel (and babel in general). I would like to:
- open the two files
- remove one hydrogen from the
