def test_TG_without_bondclass(self):
ag = self.universe.atoms
tg = TopologyGroup.from_indices([(0, 1), (1, 2), (2, 3)], ag)
assert_(len(tg) == 3)
assert_(type(tg[0]) == Bond)
tg = TopologyGroup.from_indices([(0, 1, 2), (1, 2, 3), (2, 3, 4)], ag)
assert_(len(tg) == 3)
assert_(type(tg[0]) == Angle)
tg = TopologyGroup.from_indices([(0, 1, 2, 3), (1, 2, 3, 4)], ag)
assert_(len(tg) == 2)
assert_(type(tg[0]) == Dihedral)
def test_TG_without_bondclass(self):
ag = self.universe.atoms
tg = TopologyGroup.from_indices([(0, 1), (1, 2), (2, 3)], ag)
assert_(len(tg) == 3)
assert_(type(tg[0]) == Bond)
tg = TopologyGroup.from_indices([(0, 1, 2), (1, 2, 3), (2, 3, 4)],
ag)
assert_(len(tg) == 3)
assert_(type(tg[0]) == Angle)
tg = TopologyGroup.from_indices([(0, 1, 2, 3), (1, 2, 3, 4)],
ag)
assert_(len(tg) == 2)
assert_(type(tg[0]) == Dihedral)
def test_from_indices_nonglobal_idx(self):
idx = [(0, 1), (4, 5)]
ag = self.universe.atoms[100:]
tg = TopologyGroup.from_indices(idx, ag)
b1 = self.universe.atoms[[100, 101]].bond
b2 = self.universe.atoms[[104, 105]].bond
assert_(b1 in tg)
assert_(b2 in tg)
def test_from_indices_nonglobal_idx(self):
idx = [(0, 1), (4, 5)]
ag = self.universe.atoms[100:]
tg = TopologyGroup.from_indices(idx, ag)
b1 = self.universe.atoms[[100, 101]].bond
b2 = self.universe.atoms[[104, 105]].bond
assert_(b1 in tg)
assert_(b2 in tg)
def test_TG_indices_creation(self):
"""Create a TG from indices"""
bonds = [(0, 1), (1, 2)]
tg = TopologyGroup.from_indices(bonds, self.universe.atoms,
bondclass=Bond)
assert_equal(len(tg), 2)
b1 = self.universe.atoms[[0, 1]].bond
b2 = self.universe.atoms[[1, 2]].bond
assert_(b1 in tg)
assert_(b2 in tg)
assert_equal(bonds, tg.to_indices())
def test_TG_from_indices_roundtrip(self):
"""Round trip check of dumping indices then recreating"""
tg = self.universe.bonds[:10]
idx = tg.to_indices()
tg2 = TopologyGroup.from_indices(idx, self.universe.atoms,
bondclass=Bond)
# This doesn't work as it uses set operation and .from_indices
# has created new Bond instances
# assert_equal(tg, tg2)
# instead...
assert_equal(len(tg), len(tg2))
assert_equal(tg.to_indices(), tg2.to_indices())
def test_TG_indices_creation(self):
"""Create a TG from indices"""
bonds = [(0, 1), (1, 2)]
tg = TopologyGroup.from_indices(bonds,
self.universe.atoms,
bondclass=Bond)
assert_equal(len(tg), 2)
b1 = self.universe.atoms[[0, 1]].bond
b2 = self.universe.atoms[[1, 2]].bond
assert_(b1 in tg)
assert_(b2 in tg)
assert_equal(bonds, tg.to_indices())
def test_TG_from_indices_roundtrip(self):
"""Round trip check of dumping indices then recreating"""
tg = self.universe.bonds[:10]
idx = tg.to_indices()
tg2 = TopologyGroup.from_indices(idx,
self.universe.atoms,
bondclass=Bond)
# This doesn't work as it uses set operation and .from_indices
# has created new Bond instances
# assert_equal(tg, tg2)
# instead...
assert_equal(len(tg), len(tg2))
assert_equal(tg.to_indices(), tg2.to_indices())
def test_force_bondclass(self):
# Make a TG of improper dihedral
tg = TopologyGroup.from_indices([(0, 1, 2, 3), (2, 3, 4, 6)],
self.universe.atoms,
bondclass=ImproperDihedral)
assert_(type(tg[0]) == ImproperDihedral)
def _load_bonds(self):
# Load some bonds into Universe, not required for all tests
bondlist = [(0, 1), (1, 2), (1, 3), (1, 4), (4, 5), (4, 6), (4, 7)]
tg = TopologyGroup.from_indices(bondlist, self.u.atoms, bondclass=Bond)
self.u.bonds = tg
def _load_bonds(self):
# Load some bonds into Universe, not required for all tests
bondlist = [(0, 1), (1, 2), (1, 3), (1, 4), (4, 5), (4, 6), (4, 7)]
tg = TopologyGroup.from_indices(bondlist, self.u.atoms, bondclass=Bond)
self.u.bonds = tg
def test_force_bondclass(self):
# Make a TG of improper dihedral
tg = TopologyGroup.from_indices([(0, 1, 2, 3), (2, 3, 4, 6)],
self.universe.atoms,
bondclass=ImproperDihedral)
assert_(type(tg[0]) == ImproperDihedral)
