> Specifically I want to take as input a protein pdb file, and a small molecule
> as sdf input, then output a pdb containing both structures.
That's pretty easy:
from openbabel import pybel
protein = next(pybel.readfile("pdb", "filename.pdb"))
print(len(protein.atoms))
small = pybel.readfile("mol", "filename.sdf")
print(len(small.atoms))
protein.OBMol += small.OBMol
print(len(protein.atoms)) # more atoms
protein.write('pdb', 'new_file.pdb', overwrite=False)
Hope that helps,
-Geoff
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