def test_3(self):
atoms = [
topology.Atom(name="N", element="N", xyz=(11.498, 10.510, 10.231)),
topology.Atom(name="CA", element="C",
xyz=(12.730, 11.073, 10.769)),
topology.Atom(name="C", element="C", xyz=(13.674, 9.966, 11.221)),
topology.Atom(name="O", element="O", xyz=(13.739, 8.902, 10.605)),
topology.Atom(name="CB", element="C",
xyz=(12.421, 12.004, 11.944)),
topology.Atom(name="CG", element="C",
xyz=(11.478, 13.179, 11.661)),
topology.Atom(name="CD1",
element="C",
xyz=(11.043, 13.834, 12.963)),
topology.Atom(name="CD2",
element="C",
xyz=(12.126, 14.201, 10.736)),
]
compound = topology.Compound.from_structure(atoms=atoms, tolerance=0.1)
self.assertEqual(
set(frozenset([l.name, r.name]) for (l, r) in compound.bonds),
set([
frozenset(["N", "CA"]),
frozenset(["CA", "C"]),
frozenset(["C", "O"]),
frozenset(["CA", "CB"]),
frozenset(["CB", "CG"]),
frozenset(["CG", "CD1"]),
frozenset(["CG", "CD2"]),
]))
def test_2(self):
m = topology.Compound.create()
a1 = topology.Atom()
a2 = topology.Atom()
m.add_atom( atom = a1 )
m.add_atom( atom = a2 )
self.assertEqual( set( m.atoms ), set( [ a1, a2 ] ) )
self.assertEqual( len( m.atom_for ), 2 )
self.assertTrue( a1 in m.atom_for.values() )
self.assertTrue( a2 in m.atom_for.values() )
self.assertEqual( len( m.descriptor_for ), 2 )
self.assertTrue( a1 in m.descriptor_for )
self.assertTrue( a2 in m.descriptor_for )
self.assertEqual( len( list( m.graph.vertices() ) ), 2 )
self.assertEqual( len( list( m.graph.edges() ) ), 0 )
self.assertEqual( m.distances_from( atom = a1 ), { a1: 0, a2: None } )
self.assertEqual( m.distances_from( atom = a2 ), { a2: 0, a1: None } )
self.assertEqual(
set( frozenset( s ) for s in m.connected_segments() ),
set( [ frozenset( [ a1 ] ), frozenset( [ a2 ] ) ] ),
)
m.add_bond( left = a1, right = a2 )
self.assertEqual( len( list( m.graph.vertices() ) ), 2 )
self.assertEqual( len( list( m.graph.edges() ) ), 1 )
self.assertEqual( m.distances_from( atom = a1 ), { a1: 0, a2: 1 } )
self.assertEqual( m.distances_from( atom = a2 ), { a2: 0, a1: 1 } )
self.assertEqual(
set( frozenset( s ) for s in m.connected_segments() ),
set( [ frozenset( [ a1, a2 ] ) ] ),
)
ss1 = m.subset( atoms = [ a1 ] )
self.assertEqual( len( ss1.atom_for ), 1 )
self.assertTrue( a1 in ss1.atom_for.values() )
self.assertEqual( len( ss1.descriptor_for ), 1 )
self.assertTrue( a1 in ss1.descriptor_for )
self.assertEqual( len( list( ss1.graph.vertices() ) ), 1 )
self.assertEqual( len( list( ss1.graph.edges() ) ), 0 )
ss2 = m.subset( atoms = [ a2 ] )
self.assertEqual( len( ss2.atom_for ), 1 )
self.assertTrue( a2 in ss2.atom_for.values() )
self.assertEqual( len( ss2.descriptor_for ), 1 )
self.assertTrue( a2 in ss2.descriptor_for )
self.assertEqual( len( list( ss2.graph.vertices() ) ), 1 )
self.assertEqual( len( list( ss2.graph.edges() ) ), 0 )
def test_1(self):
foo = object()
bar = object()
a = topology.Atom( foo = foo, bar = bar )
self.assertEqual( a.foo, foo )
self.assertEqual( a.bar, bar )
def test_2(self):
m = topology.Molecule()
a1 = topology.Atom()
a2 = topology.Atom()
m.add( atom = a1, xyz = ( 0, 0, 0 ) )
m.add( atom = a2, xyz = ( 1, 1, 1 ) )
self.assertEqual( m.size(), 2 )
self.assertEqual( set( m.atoms ), set( [ a1, a2 ] ) )
self.assertEqual( len( m.atom_for ), 2 )
self.assertTrue( a1 in m.atom_for.values() )
self.assertTrue( a2 in m.atom_for.values() )
self.assertEqual( len( m.descriptor_for ), 2 )
self.assertTrue( a1 in m.descriptor_for )
self.assertTrue( a2 in m.descriptor_for )
self.assertEqual( len( list( m.graph.vertices() ) ), 2 )
self.assertEqual( len( list( m.graph.edges() ) ), 1 )
edge = m.graph.edges().next()
self.assertAlmostEqual( m.graph.edge_weight( edge = edge ), 1.73205, 5 )
def test_asn_leu(self):
l_ca = topology.Atom( label = "CA" )
l_cb = topology.Atom( label = "C" )
l_cg = topology.Atom( label = "C" )
l_cd1 = topology.Atom( label = "C" )
l_cd2 = topology.Atom( label = "C" )
leu = topology.Molecule()
leu.add( atom = l_ca, xyz = ( -1.0085, -0.590773, 0.814318 ) )
leu.add( atom = l_cb, xyz = ( 0.0275, -0.557773, -0.314682 ) )
leu.add( atom = l_cg, xyz = ( 1.2335, 0.374227, -0.138682 ) )
leu.add( atom = l_cd1, xyz = ( 2.3065, 0.046227, -1.16768 ) )
leu.add( atom = l_cd2, xyz = ( 0.8395, 1.84323, -0.230682 ) )
a_ca = topology.Atom( label = "CA" )
a_cb = topology.Atom( label = "C" )
a_cg = topology.Atom( label = "C" )
a_od1 = topology.Atom( label = "C" )
a_nd2 = topology.Atom( label = "C" )
asn = topology.Molecule()
asn.add( atom = a_ca, xyz = ( -1.03327, -0.544348, 0.860946 ) )
asn.add( atom = a_cb, xyz = ( 0.10486, -0.548357, -0.164901 ) )
asn.add( atom = a_cg, xyz = ( 0.990984, 0.682823, -0.070521 ) )
asn.add( atom = a_od1, xyz = ( 1.39496, 1.24684, -1.08724 ) )
asn.add( atom = a_nd2, xyz = ( 1.29745, 1.10599, 1.15228 ) )
m = topology.GreedyMatch(
molecule1 = leu,
molecule2 = asn,
vertex_equality = lambda l, r: l.label == r.label,
edge_equality = lambda l, r: abs( l - r ) <= 0.1,
)
self.assertEqual( m.count(), 1 )
self.assertEqual( m.length(), 3 )
mapping = m.remapped()[0]
self.assertEqual( len( mapping ), 3 )
self.assertTrue( ( l_ca, a_ca ) in mapping )
self.assertTrue( ( l_cb, a_cb ) in mapping )
self.assertTrue( ( l_cg, a_cg ) in mapping )
self.assertTrue( ( l_cd1, a_od1 ) not in mapping )
def test_1(self):
m = topology.Molecule()
a = topology.Atom()
m.add( atom = a, xyz = ( 0, 0, 0 ) )
self.assertEqual( m.size(), 1 )
self.assertEqual( m.atoms, [ a ] )
self.assertEqual( len( m.atom_for ), 1 )
self.assertTrue( a in m.atom_for.values() )
self.assertEqual( len( m.descriptor_for ), 1 )
self.assertTrue( a in m.descriptor_for )
self.assertEqual( len( list( m.graph.vertices() ) ), 1 )
self.assertEqual( list( m.graph.edges() ), [] )
def test_1(self):
m = topology.Compound.create()
a = topology.Atom()
m.add_atom( atom = a )
self.assertEqual( m.atoms, [ a ] )
self.assertEqual( len( m.atom_for ), 1 )
self.assertTrue( a in m.atom_for.values() )
self.assertEqual( len( m.descriptor_for ), 1 )
self.assertTrue( a in m.descriptor_for )
self.assertEqual( len( list( m.graph.vertices() ) ), 1 )
self.assertEqual( list( m.graph.edges() ), [] )
self.assertEqual( m.distances_from( atom = a ), { a: 0 } )
self.assertEqual( m.connected_segments(), [ [ a ] ] )
