def test_combine(self):
plmd = PLUMEDInterface(self.topology)
phi_pl = PLUMEDCV("phi", plmd, "TORSION ATOMS=5,7,9,15")
psi_pl = PLUMEDCV("psi", plmd, "TORSION ATOMS=7,9,15,17")
sum_pl = phi_pl(self.trajectory) + psi_pl(self.trajectory)
comb_pl = PLUMEDCV("sum", plmd, "COMBINE ARG=phi,psi PERIODIC=NO")
np.testing.assert_almost_equal(sum_pl,
comb_pl(self.trajectory),
decimal=6)
def test_group(self):
plmd = PLUMEDInterface(self.topology)
tor_pl = PLUMEDCV("tor", plmd, "TORSION ATOMS=7,9,15,17")
plmd.set("group", "GROUP ATOMS=7,9,15,17")
tor_group_pl = PLUMEDCV("tor_group", plmd, "TORSION ATOMS=group")
np.testing.assert_almost_equal(tor_pl(self.trajectory),
tor_group_pl(self.trajectory),
decimal=6)
def test_components(self):
plmd = PLUMEDInterface(self.topology)
dist_pl = PLUMEDCV("dist", plmd, "DISTANCE ATOMS=7,9")
comp_pl = PLUMEDCV("comp",
plmd,
"DISTANCE ATOMS=7,9 COMPONENTS",
components=["x", "y", "z"])
comp_dist_pl = (comp_pl(self.trajectory)[:, 0]**2 +
comp_pl(self.trajectory)[:, 1]**2 +
comp_pl(self.trajectory)[:, 2]**2)**0.5
np.testing.assert_almost_equal(dist_pl(self.trajectory),
comp_dist_pl,
decimal=6)
def test_torsion_vs_mdtraj(self):
plmd = PLUMEDInterface(self.topology)
tor_md = paths.MDTrajFunctionCV("tor_md",
md.compute_dihedrals,
self.topology,
indices=[[6, 8, 14, 16]])
tor_pl = PLUMEDCV("tor_pl", plmd, "TORSION ATOMS=7,9,15,17")
np.testing.assert_almost_equal(tor_md(self.trajectory),
tor_pl(self.trajectory),
decimal=3)
def test_angle_vs_mdtraj(self):
plmd = PLUMEDInterface(self.topology)
ang_md = paths.MDTrajFunctionCV("ang_md",
md.compute_angles,
self.topology,
angle_indices=[[4, 6, 8]])
ang_pl = PLUMEDCV("ang_pl", plmd, "ANGLE ATOMS=5,7,9")
np.testing.assert_almost_equal(ang_md(self.trajectory),
ang_pl(self.trajectory),
decimal=3)
def test_distance_vs_mdtraj(self):
plmd = PLUMEDInterface(self.topology)
dist_md = paths.MDTrajFunctionCV("dist_md",
md.compute_distances,
self.topology,
atom_pairs=[[6, 8]])
dist_pl = PLUMEDCV("dist_pl", plmd, "DISTANCE ATOMS=7,9")
np.testing.assert_almost_equal(dist_md(self.trajectory),
dist_pl(self.trajectory),
decimal=3)
def test_molinfo(self):
plmd = PLUMEDInterface(self.topology,
molinfo=data_filename("plumed_wrapper/" +
"AD_initial_frame.pdb"))
tor_md = paths.MDTrajFunctionCV("tor_md",
md.compute_dihedrals,
self.topology,
indices=[[6, 8, 14, 16]])
tor_pl = PLUMEDCV("tor_pl", plmd, "TORSION ATOMS=@psi-2")
np.testing.assert_almost_equal(tor_md(self.trajectory),
tor_pl(self.trajectory),
decimal=3)
def test_storage(self):
plmd = PLUMEDInterface(self.topology)
dist = PLUMEDCV("dist", plmd, "DISTANCE ATOMS=7,9")
store = paths.Storage("test.nc", "w")
store.save(self.trajectory[:2])
store.save(dist)
store.sync()
store.close()
store2 = paths.Storage('test.nc', 'r')
dist2 = store2.cvs[dist.name]
store2.close()
np.testing.assert_almost_equal(dist(self.trajectory),
dist2(self.trajectory),
decimal=6)
def test_rmsd_vs_mdtraj(self):
plmd = PLUMEDInterface(self.topology)
rmsd_ref_file = data_filename(
os.path.join("plumed_wrapper", "AD_plumed_rmsd.pdb"))
md_ref = md.load(rmsd_ref_file)
rmsd_md = paths.MDTrajFunctionCV("rmsd_md",
md.rmsd,
self.topology,
reference=md_ref,
frame=0,
atom_indices=range(22))
rmsd_pl = PLUMEDCV("rmsd_pl", plmd,
"RMSD REFERENCE=" + rmsd_ref_file + " TYPE=OPTIMAL")
np.testing.assert_almost_equal(rmsd_md(self.trajectory),
rmsd_pl(self.trajectory),
decimal=3)