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_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 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_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_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_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_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_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_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) )
def test_get_mol(self):
w = Water.get_standard()
self.assertIsInstance( w, Molecule )
