def test_0(self):
m = topology.Molecule()
self.assertEqual( m.size(), 0 )
self.assertEqual( m.atoms, [] )
self.assertEqual( m.atom_for, {} )
self.assertEqual( m.descriptor_for, {} )
self.assertEqual( list( m.graph.vertices() ), [] )
self.assertEqual( list( m.graph.edges() ), [] )
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_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 )