def test_villin_folded(self):
# one folded, one unfolded
f = mda.Universe(contacts_villin_folded, dt=1.0)
u = mda.Universe(contacts_villin_unfolded, dt=1.0)
sel = "protein and not name H*"
grF = f.select_atoms(sel)
grU = u.select_atoms(sel)
q = contacts.Contacts(
(grU, grU), refs=(grF, grF), method="soft_cut").run()
results = soft_cut(f, u, sel, sel)
assert_almost_equal(q.timeseries[:, 1], results[:, 1])
def _run_Contacts(self,
universe,
start=None,
step=None,
stop=None,
n_blocks=1,
**kwargs):
acidic = universe.select_atoms(self.sel_acidic)
basic = universe.select_atoms(self.sel_basic)
return contacts.Contacts(
(acidic, basic), (acidic, basic), radius=6.0, **kwargs).run(
start=start, stop=stop, step=step, n_blocks=n_blocks)