def test_inv_rotation(self):
"""rotate two water molecules by random angles,
translate them in random space, one by oxygen other by center of mass
rotate them to standard orientation and center by mass"""
w1 = Water.get_standard()
w2 = Water.get_standard()
t1, t2, t3 = np.random.uniform( -np.pi, np.pi, [3] )
d1, d2, d3 = np.random.uniform( -np.pi, np.pi, [3] )
r1, r2 = np.random.uniform( -100, 100, [2,3] )
w1.translate_o( r1 )
w2.translate( r1 )
w1.rotate( t1, t2, t3 )
w2.rotate( d1, d2, d3 )
w1.inv_rotate( t3, t2, t1 )
w2.inv_rotate( d3, d2, d1 )
w1.center()
w2.center()
self.eq ( w1.com, w2.com )
def test_three_waters(self):
s = System()
ch1, ch2 = Chain(), Chain()
ch1.chain_id = 'A'
ch2.chain_id = 'B'
w1, w2 = Water.get_standard( AA = True ), Water.get_standard( AA = True )
ch1.add( w1 )
ch2.add( w2 )
#After rotating and translating both waters oxygen is 2 AA apart
w1.rotate( 0, np.pi/2, 0 )
w2.rotate( 0, -np.pi/2, 0 )
w1.t( -1, 0, 0 )
w2.t( 1, 0, 0 )
s.add( ch1 )
s.add( ch2 )
assert len( s.min_dist_atoms_separate_res_chain( 2.1 ) ) == 2
ch2.chain_id = 'A'
assert len( s.min_dist_atoms_separate_res_chain( 2.1 ) ) == 0
def test_dist_to_mol(self):
wat1, wat2 = Water.get_standard(), Water.get_standard()
wat1.translate([0, 0, 0])
wat2.translate([0, 0, 1])
self.eq(np.linalg.norm(wat1.dist_to_mol(wat2)), 1, decimal=7)
wat1.translate([0, 0, 0])
wat2.translate([1, 1, 1])
self.eq(np.linalg.norm(wat1.dist_to_mol(wat2)), np.sqrt(3), decimal=7)
def test_dipole(self):
w1 = Water.get_standard()
w2 = Water.get_standard()
w2.LoProp = True
w2.o.p.q -= 1.0
w2.translate_by_r(np.array([3, 3, 3]))
c = Cluster(w1, w2)
d1 = c.p.d.copy()
r = np.random.uniform(-10, 10, (3, ))
for i in c:
i.translate_by_r(r)
np.testing.assert_allclose(d1, c.p.d, atol=1e-7)
def test_reflection2(self):
w = Water.get_standard()
w.attach_properties(force_template=True)
q = w.p.q
d = w.p.d.copy()
Q = w.p.Q.copy()
a = w.p.a.copy()
b = w.p.b.copy()
w.rotate(
0,
np.pi / 2,
0,
)
w.reflect('zy')
w.rotate(
0,
np.pi / 2,
0,
)
np.testing.assert_allclose(q, w.p.q, atol=1e-7)
np.testing.assert_allclose(d, w.p.d, atol=1e-7)
np.testing.assert_allclose(Q, w.p.Q, atol=1e-7)
np.testing.assert_allclose(a, w.p.a, atol=1e-7)
np.testing.assert_allclose(b, w.p.b, atol=1e-7)
def test_add_mol(self):
a = len(self.c)
w = Water.get_standard()
self.assertNotIn(w, self.c)
self.c.add_mol(w)
self.assertEqual(len(self.c), (a + 1))
self.assertIn(w, self.c)
def test_rotate_dip(self):
w = Water.get_standard()
w.translate_o(np.zeros(3))
for at in w:
at.p = Property.from_template(
at.name,
Template().get(model='TIP3p', method='HF', basis='ANOPVDZ'))
w.LoProp = True
dip = 0.7870603
np.testing.assert_allclose(w.p.d, [0, 0, dip], atol=1e-7)
w.rotate(np.pi / 2, 0, 0)
self.eq(w.p.d, [0, 0, dip])
print "After 90 around Z-axis: counter-clock"
print w.p
w.rotate(0, np.pi / 2, 0)
self.eq(w.p.d, [-dip, 0, 0])
print "After 90 around Y-axis: clock"
print w.p.d
w.rotate(0, 0, np.pi / 2)
print "After 90 around Z-axis: counter-clock"
print w.p.d
t, r1, r2, r3 = utilz.center_and_xz(w.o.r,
w.o.r + (w.h1.r - w.h2.r) / 2,
w.h1.r)
w.inv_rotate(r1, r2, r3)
def test_attach_both_ways(self):
c1 = Cluster([Water.get_standard() for i in range(2)])
c2 = Cluster([Water.get_standard() for i in range(2)])
for w1, w2 in zip(c1, c2):
t_vec, r_mat = np.random.random(3), np.random.random(3)
w1.rotate(*r_mat)
w2.rotate(*r_mat)
w1.t(t_vec)
w2.t(t_vec)
np.testing.assert_allclose(w1.o.r, w2.o.r)
c1.attach_properties(model='spc', force_template=True)
for wat in c2:
wat.attach_properties(model='spc', force_template=True)
np.testing.assert_allclose(c1.p.a, c2.p.a)
def test_both_loprop_and_none(self):
w1, w2, w3, w4 = [Water.get_standard() for i in range(4)]
c1 = Cluster(w1, w2.t(0, 0, 5))
c2 = Cluster(w3, w4.t(0, 0, 5))
c1.attach_properties(loprop=False)
c2.attach_properties(loprop=True)
np.testing.assert_allclose(c1.p.d, c2.p.d)
def test_read_template(self):
w1, w2 = Water.get_standard(), Water.get_standard()
model, method, loprop_false, loprop_true = 'tip3p', 'b3lyp', 0, 1
euler_f = lambda x: (x.o.r, (x.h1.r - x.h2.r) / 2.0 + x.h2.r, x.h1.r)
w1.attach_properties(
model=model,
method=method,
loprop=loprop_false,
euler_key=euler_f,
)
w2.attach_properties(
model=model,
method=method,
loprop=loprop_true,
euler_key=euler_f,
)
np.testing.assert_allclose(w1.p.d, w2.p.d)
def test_rotate_to_random(self):
w = Water.get_standard()
w.translate(self.w.com)
t1, t2, t3 = self.w.get_euler()
origin = w.com.copy()
w.translate_by_r(-w.com)
w.rotate(t1, t2, t3)
w.translate_by_r(origin)
self.eq(w.com, self.w.com)
def test_transform_by_inv_rotate(self):
w = Water.get_standard()
w.rotate(0, np.pi / 2, np.pi / 2)
w.o.p.d = np.array([0, -1.0, 0])
t, r1, r2, r3 = utilz.center_and_xz(w.o.r,
(w.h1.r - w.h2.r) / 2 + w.h2.r,
w.h1.r)
w.inv_rotate(r3, r2, r1)
np.testing.assert_allclose(w.o.p.d, np.array([0, 0, 1]), atol=1e-10)
def test_additive_pdlist(self):
"""Should give only props from oxygen to h2 since there is no bond from h1 to oxygen to oxygen"""
w1 = Water.get_standard()
w2 = Water.get_standard().t( 0, 0, 5 )
w3 = Water.get_standard()
w4 = Water.get_standard().t( 0, 0, 5 )
w1.props_from_targz( WATER_FILE_TARGZ, bonds = 0, maxl = 1)
w2.props_from_targz( WATER_FILE_TARGZ, bonds = 0, maxl = 1)
w3.props_from_targz( WATER_FILE_TARGZ, bonds = 1, maxl = 1)
w4.props_from_targz( WATER_FILE_TARGZ, bonds = 1, maxl = 1)
b1 = Cluster( w1, w2 ).get_pdlist( model = 'add', bonds = 0 ).beta( cython =1 )
b2 = Cluster( w3, w4 ).get_pdlist( model = 'add', bonds = 1 ).beta( cython =1 )
np.testing.assert_allclose( b1, b2 )
def test_rotate_around_z(self):
w = Water.get_standard()
w.translate(self.w.com)
self.eq(w.com, self.w.com)
origin = w.o.r.copy()
w.translate_by_r(-w.o.r)
w.rotate(np.pi / 2, 0, np.pi / 2)
w.translate_by_r(origin)
self.eq(w.com, self.w.com)
def setUp(self):
wat = Water.get_standard()
t1, t2, t3 = wat.get_euler()
kw_dict = Template().get(*("TIP3P", "HF", "ANOPVDZ", True, "0.0"))
for at in wat:
at.p = Property.from_template(at.name, kw_dict)
at.p = at.p.rotate(t1, t2, t3)
# will only test this quadrupole
at.Property["quadrupole"] = np.arange(6)
self.wat = wat
def test_y_rotation(self):
w = Water.get_standard()
#rotate around y axis by 90 degree, assert
w.translate(self.w.o.r)
w.rotate(0, np.pi / 2, 0)
w.rotate(0, np.pi / 2, 0)
w.center()
self.eq(w.h1.y, 0)
self.eq(w.h2.y, 0)
def setUp(self):
self.ut_alpha = np.random.random( (6, ) )
self.ut_beat = np.random.random( (10, ) )
self.g = Generator()
self.w = Water.get_standard()
self.w.translate_by_r( np.random.uniform( -10, 10, [3] ) )
self.t1 = np.random.uniform( 0, np.pi/2 )
self.t2 = np.random.uniform( 0, np.pi )
self.t3 = np.random.uniform( 0, np.pi/2 )
def test_center_water(self):
w = Water.get_standard()
#Move the water to random place
w.translate(np.random.uniform(-100, 100, [3]))
#Call center function
w.center()
#Assert that oxygen is in origo
self.eq(w.com, [0, 0, 0], decimal=7)
def test_rotate_inv_Z(self):
w = Water.get_standard()
self.eq(w.h1.y, 0)
self.eq(w.h2.y, 0)
self.eq(w.o.r, [0, 0, 0])
#rotate around z axis by 90 degree, both hydrogens now in zy plane
w.rotate(np.pi / 2, 0, 0)
self.eq(w.h1.x, 0)
self.eq(w.h2.x, 0)
self.eq(w.o.r, [0, 0, 0])
def test_moved_get_euler(self):
w = Water.get_standard()
w.translate([5,5,5])
t1, t2 ,t3 = w.get_euler( lambda x: (x.o.r, (x.h1.r-x.h2.r)/2.0 + x.h2.r, x.h1.r ))
w.center()
self.eq( [t1, t2, t3] , np.zeros(3) )
t1, t2 ,t3 = w.get_euler(lambda x: (x.o.r, (x.h1.r-x.h2.r)/2.0 + x.h2.r, x.h1.r ))
w.center()
self.eq( [t1, t2, t3] , np.zeros(3) )
def test_transform_by_matrix(self):
w = Water.get_standard()
w.rotate(0, np.pi / 2, np.pi / 2)
w.o.p.d = np.array([0, -1.0, 0])
t, r1, r2, r3 = utilz.center_and_xz(w.o.r,
(w.h1.r - w.h2.r) / 2 + w.h2.r,
w.h1.r)
R1 = utilz.R([0, 0, 1], np.pi / 2)
R2 = utilz.R([0, 1, 0], 3 * np.pi / 2)
for at in w:
at.p = at.p.transform_by_matrix(R1)
at.p = at.p.transform_by_matrix(R2)
np.testing.assert_allclose(w.o.p.d, np.array([0, 0, 1]), atol=1e-10)
def test_transfer_props_level_1(self):
w = Water.get_standard()
w.populate_bonds()
w.attach_properties()
p_ref = w.h1.p.copy_property()
bond = w.h1.bonds[0]
w.h1.transfer_props(level=1)
np.testing.assert_allclose(bond.p.q, p_ref.q)
np.testing.assert_allclose(bond.p.d, p_ref.d)
np.testing.assert_allclose(bond.p.a, p_ref.a)
np.testing.assert_allclose(bond.p.b, p_ref.b)
def test_translation(self):
w = Water.get_standard()
w.translate(self.w.o.r)
self.eq(w.com, self.w.o.r)
w.translate([1, 1, 1])
w.translate([0, 0, 0])
w.translate([1, 1, 1])
w.translate([1, 1, 1])
w.translate([2333, 1, 1])
w.translate([0, 0, 0])
self.eq(w.com, [0, 0, 0], decimal=7)
def test_centered_simple(self):
w = Water.get_standard()
w.attach_properties(loprop=0)
w.rotate(*np.random.random((3, )))
w.t(np.random.uniform(0, 5, (3, )))
p_ref = w.p.copy()
w.attach_properties(loprop=0)
np.testing.assert_allclose(w.p.d, p_ref['dipole'], atol=1e-7)
np.testing.assert_allclose(w.p.b, p_ref['beta'], atol=1e-7)
np.testing.assert_allclose(w.p.a, p_ref['alpha'], atol=1e-7)
def test_centered_simple(self):
w = Water.get_standard()
w.attach_properties( loprop = 0 )
w.rotate( *np.random.random( (3,) ))
w.t( np.random.uniform( 0, 5, (3,) ))
p_ref = w.p.copy()
w.attach_properties( loprop = 0 )
np.testing.assert_allclose( w.p.d, p_ref['dipole'], atol = 1e-7 )
np.testing.assert_allclose( w.p.b, p_ref['beta'], atol = 1e-7 )
np.testing.assert_allclose( w.p.a, p_ref['alpha'], atol = 1e-7 )
def test_attach_properties(self):
w = Water.get_standard()
t, r1, r2, r3 = utilz.center_and_xz(w.o.r,
(w.h1.r - w.h2.r) / 2.0 + w.h2.r,
w.h1.r)
w.o.pdb_name = 'OW'
w.h1.pdb_name = 'HW1'
w.h2.pdb_name = 'HW2'
w.attach_properties(model='TIP3P_PDB',
method='B3LYP',
basis='ANO631',
template_key=lambda x: x.pdb_name,
force_template=True)
np.testing.assert_allclose(w.p.q, 0.0, atol=1e-4)
def test_reflection(self):
"""docstring for test_reflection"""
w = Water.get_standard()
w.attach_properties( force_template = True)
w.rotate( 0, np.pi/3.0, 0 )
b_ref = w.p.b_proj.copy()
d_ref = w.p.d.copy()
w.reflect( plane = 'zy' )
np.testing.assert_allclose( w.p.q, 0.0, atol = 1e-7 )
np.testing.assert_allclose( w.p.b_proj, b_ref, atol = 1e-7 )
np.testing.assert_allclose( abs(w.p.d), abs( d_ref ), atol = 1e-5 )
def test_reflection(self):
"""docstring for test_reflection"""
w = Water.get_standard()
w.attach_properties(force_template=True)
w.rotate(0, np.pi / 3.0, 0)
b_ref = w.p.b_proj.copy()
d_ref = w.p.d.copy()
w.reflect(plane='zy')
np.testing.assert_allclose(w.p.q, 0.0, atol=1e-7)
np.testing.assert_allclose(w.p.b_proj, b_ref, atol=1e-7)
np.testing.assert_allclose(abs(w.p.d), abs(d_ref), atol=1e-5)
def test_attach_properties(self):
w = Water.get_standard()
t, r1, r2, r3 = utilz.center_and_xz( w.o.r, (w.h1.r - w.h2.r)/2.0 + w.h2.r, w.h1.r )
w.o.pdb_name = 'OW'
w.h1.pdb_name = 'HW1'
w.h2.pdb_name = 'HW2'
w.attach_properties(
model = 'TIP3P_PDB',
method = 'B3LYP',
basis ='ANO631',
template_key = lambda x: x.pdb_name,
force_template = True
)
np.testing.assert_allclose( w.p.q , 0.0, atol = 1e-4 )
def setUp(self):
np.random.seed(111)
self.ut_alpha = np.random.random((6, ))
self.ut_beat = np.random.random((10, ))
self.g = Generator()
r = np.random.uniform(-10, 10, [3])
self.w = Water.get_standard()
self.w.translate_o(r)
t1 = np.random.uniform(0, np.pi)
t2 = np.random.uniform(0, np.pi)
t3 = np.random.uniform(0, np.pi)
self.w.rotate(t1, t2, t3)
assert len(self.w) == 3
def test_reflection2(self):
w = Water.get_standard()
w.attach_properties( force_template = True )
q = w.p.q
d = w.p.d.copy()
Q = w.p.Q.copy()
a = w.p.a.copy()
b = w.p.b.copy()
w.rotate( 0, np.pi/2, 0, )
w.reflect( 'zy' )
w.rotate( 0, np.pi/2, 0, )
np.testing.assert_allclose( q, w.p.q, atol = 1e-7 )
np.testing.assert_allclose( d, w.p.d, atol = 1e-7 )
np.testing.assert_allclose( Q, w.p.Q, atol = 1e-7 )
np.testing.assert_allclose( a, w.p.a, atol = 1e-7 )
np.testing.assert_allclose( b, w.p.b, atol = 1e-7 )
def test_transfer_props(self):
w = Water.get_standard()
w.populate_bonds()
w.props_from_targz( WATER_FILE_TARGZ, bonds = 1, maxl = 1, pol = 22, hyp = 1 )
q_ref = w.p.q
a_ref = w.p.a.copy()
w.o.transfer_props( 2 )
np.testing.assert_allclose( w.h1.q, 0.0, atol = 1e-7 )
np.testing.assert_allclose( w.h2.q, 0.0, atol = 1e-7 )
np.testing.assert_allclose( w.p.q, q_ref, atol = 1e-7 )
np.testing.assert_allclose( w.p.a, a_ref, atol = 1e-7 )
def test_property_beta_proj(self):
w = Water.get_standard()
w.translate_by_r(np.random.uniform(-10, 10, (3, )))
w.rotate(*np.random.uniform(-10, 10, (3, )))
w[0].p.d = np.random.random(3)
w[0].p.b = np.random.random(10)
w[1].p.d = np.random.random(3)
w[1].p.b = np.random.random(10)
w[2].p.d = np.random.random(3)
w[2].p.b = np.random.random(10)
BP = w.p.b_proj
t, r1, r2, r3 = utilz.center_and_xz(w[0].r,
w[0].r + (w.h1.r - w.h2.r) / 2,
w.h1.r)
w.translate_by_r(t)
w.inv_rotate(r1, r2, r3)
np.testing.assert_allclose(BP, w.p.b_proj, atol=1e-7)
def test_isotropic_alpha(self):
w = Water.get_standard()
w.translate_by_r(np.random.uniform(-10, 10, (3, )))
w.rotate(*np.random.uniform(-10, 10, (3, )))
w[0].p.d = np.random.random(3)
w[0].p.b = np.random.random(10)
w[1].p.d = np.random.random(3)
w[1].p.b = np.random.random(10)
w[2].p.d = np.random.random(3)
w[2].p.b = np.random.random(10)
iso_a = np.einsum('ii', utilz.ut2s(w.p.a)) / 3
t, r1, r2, r3 = utilz.center_and_xz(w[0].r,
w[0].r + (w.h1.r - w.h2.r) / 2,
w.h1.r)
w.translate_by_r(t)
w.inv_rotate(r1, r2, r3)
np.testing.assert_allclose(iso_a,
np.einsum('ii', utilz.ut2s(w.p.a)) / 3,
atol=1e-7)
def test_transfer_props_asymm(self):
"""Should give only props from oxygen to h2 since there is no bond from h1 to oxygen to oxygen"""
w = Water.get_standard()
w.populate_bonds()
w.props_from_targz( WATER_FILE_TARGZ, bonds = 1, maxl = 1, pol = 22, hyp = 1 )
w.h1._res_id = 2
q_ref = w.p.q
q_h2_ref = w.o.p.q
q_o_ref = w.h2.p.q
a_ref = w.p.a.copy()
w.o.transfer_props( 2 )
np.testing.assert_allclose( w.h2.q, q_h2_ref + q_o_ref , atol = 1e-7 )
np.testing.assert_allclose( w.p.q, q_ref, atol = 1e-7 )
np.testing.assert_allclose( w.p.a, a_ref, atol = 1e-7 )
def test_transfer_props_level_2(self):
w = Water.get_standard()
w.populate_bonds()
w.attach_properties()
p_ref_o = w.o.p.copy_property()
p_ref_h1 = w.h1.p.copy_property()
w.h1.transfer_props(level=2)
np.testing.assert_allclose(w.o.p.q, (p_ref_o + p_ref_h1).q)
np.testing.assert_allclose(w.o.p.d, (p_ref_o + p_ref_h1).d)
np.testing.assert_allclose(w.o.p.a, (p_ref_o + p_ref_h1).a)
np.testing.assert_allclose(w.o.p.b, (p_ref_o + p_ref_h1).b)
np.testing.assert_allclose(np.zeros(3, ), w.h1.p.d)
np.testing.assert_allclose(np.zeros(6, ), w.h1.p.a)
np.testing.assert_allclose(np.zeros(3, ), w.h1.bonds[0].p.d)
np.testing.assert_allclose(np.zeros(6, ), w.h1.bonds[0].p.a)
np.testing.assert_allclose(np.zeros(3, ), w.o.bonds[0].p.d)
np.testing.assert_allclose(np.zeros(6, ), w.o.bonds[0].p.a)
def test_get_mol(self):
w = Water.get_standard()
self.assertIsInstance( w, Molecule )
def test_populate_bonds(self):
w = Water.get_standard()
w.populate_bonds()
assert len(w.o.bonds) == 2
assert len(w.h1.bonds) == 1
assert len(w.h2.bonds) == 1
def test_center_get_euler(self):
w = Water.get_standard()
t1, t2, t3 = w.get_euler( lambda x: (x.o.r, (x.h1.r-x.h2.r)/2.0 + x.h2.r, x.h1.r ))
self.eq( [t1, t2, t3] , np.zeros(3) )