Hi there
#read in protein
model = IMP. Model()
mhd = IMP.atom.read_pdb(pdb_name, model,
IMP.atom.NonWaterNonHydrogenPDBSelector())
ff = IMP.atom.get_heavy_atom_CHARMM_parameters()
top = ff.create_topology(mhd)
top.add_atom_types(mhd)
bonds = top.add_bonds(mhd)
angles = ff.create_angles(bonds)
dihedrals = ff.create_dihedrals(bonds)
Why is this last line so much slower than the others? It's sad, because
it takes up most of the time in the construction of a protein hierarchy.
thanks!
Yannick