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_angle_tg_creation_notype(self, PSFDCD):
vals = np.array([[0, 5, 10], [5, 10, 15]])
tg = TopologyGroup(vals, PSFDCD)
assert tg.btype == 'angle'
assert_equal(tg[0].indices, (0, 5, 10))
assert_equal(tg[1].indices, (5, 10, 15))
def test_TG_getitem_fancy(self, PSFDCD):
tg = PSFDCD.atoms.bonds[:10]
tg2 = tg[[1, 4, 5]]
manual = TopologyGroup(tg.indices[[1, 4, 5]], tg.universe, tg.btype)
assert list(tg2) == list(manual)
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_dihedral_tg_creation_notype(self):
vals = np.array([[0, 2, 4, 6], [5, 7, 9, 11]])
tg = TopologyGroup(vals, self.universe)
assert_(tg.btype == 'dihedral')
assert_array_equal(tg[0].indices, (0, 2, 4, 6))
assert_array_equal(tg[1].indices, (5, 7, 9, 11))
def test_TG_getitem_fancy(self):
tg = self.universe.bonds[:10]
tg2 = tg[[1, 4, 5]]
manual = TopologyGroup([tg[i] for i in [1, 4, 5]])
assert_equal(list(tg2), list(manual))
def test_dihedral_tg_creation_notype(self, PSFDCD):
vals = np.array([[0, 2, 4, 6], [5, 7, 9, 11]])
tg = TopologyGroup(vals, PSFDCD)
assert tg.btype == 'dihedral'
assert_equal(tg[0].indices, (0, 2, 4, 6))
assert_equal(tg[1].indices, (5, 7, 9, 11))
def test_TG_getitem_fancy(self):
tg = self.universe.atoms.bonds[:10]
tg2 = tg[[1, 4, 5]]
manual = TopologyGroup(tg.indices[[1, 4, 5]], tg.universe, tg.btype)
assert_equal(list(tg2), list(manual))
def test_angle_tg_creation_notype(self):
vals = np.array([[0, 5, 10], [5, 10, 15]])
tg = TopologyGroup(vals, self.universe)
assert_(tg.btype == 'angle')
assert_array_equal(tg[0].indices, (0, 5, 10))
assert_array_equal(tg[1].indices, (5, 10, 15))
def manual(topg, atomg):
if len(atomg) == 1: # hack for Atom input
atomg = [atomg]
man = []
for b in topg.bondlist:
if all(a in atomg for a in b.atoms):
man.append(b)
if len(man) > 0:
return TopologyGroup(man)
else:
return None
def test_create_empty_TG(self):
tg = TopologyGroup([])
def check(a):
if a:
return True
else:
return False
assert_equal(check(tg), False)
assert_equal(len(tg), 0)
assert_equal(tg.toptype, None)
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_verticalTG(self):
b1 = self.universe.atoms[0].dihedrals[0]
b2 = self.universe.atoms[20].dihedrals[0]
TG = TopologyGroup([b1, b2])
forwards = [AtomGroup([b1[i], b2[i]]) for i in range(4)]
backwards = [AtomGroup([b2[i], b1[i]]) for i in range(4)]
verts = [TG.atom1, TG.atom2, TG.atom3, TG.atom4]
# the lists might be in one of two formats, but always in a strict order
# ie any(1234 or 4321) but not (1324)
assert_equal(
any([
all(list(x) == list(y) for x, y in zip(forwards, verts)),
all(list(x) == list(y) for x, y in zip(backwards, verts))
]), True)
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)
def test_create_guessed_tg_2(self):
vals = np.array([[0, 10], [5, 15]])
tg = TopologyGroup(vals, self.universe, guessed=False)
assert_array_equal(tg._guessed, np.array([[False], [False]]))
def test_nobonds_warns(self):
self.u.bonds = TopologyGroup([])
assert_warns(UserWarning, self.u.select_atoms,
'type 2 and bonded name N')
def manual(topg, atomg):
man = []
for b in topg.bondlist:
if any(a in atomg for a in b.atoms):
man.append(b)
return TopologyGroup(man)
def test_create_guessed_tg_2(self, PSFDCD):
vals = np.array([[0, 10], [5, 15]])
tg = TopologyGroup(vals, PSFDCD, guessed=False)
assert_equal(tg._guessed, np.array([[False], [False]]))
def test_tg_creation_bad_btype(self, PSFDCD):
vals = np.array([[0, 10], [5, 15]])
with pytest.raises(ValueError):
TopologyGroup(vals, PSFDCD, btype='apple')
def test_bad_creation_TG(self):
"""Test making a TopologyGroup out of nonsense"""
inputlist = ['a', 'b', 'c']
with pytest.raises(TypeError):
TopologyGroup(inputlist)
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)
