from __future__ import absolute_import, division, print_function from mmtbx.geometry import topology import unittest class TestAtom(unittest.TestCase): 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 ) class TestMolecule(unittest.TestCase): 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_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 = next(m.graph.edges()) self.assertAlmostEqual( m.graph.edge_weight( edge = edge ), 1.73205, 5 ) class TestCompound(unittest.TestCase): def test_0(self): m = topology.Compound.create() 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_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 ] ] ) 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_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" ] ), ] ) ) class TestMcGregorMatch(unittest.TestCase): 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 ) ) res = topology.McGregorMatch( molecule1 = leu, molecule2 = asn, is_valid = lambda match: any( m.label == "CA" for m in match ), vertex_equality = lambda l, r: l.label == r.label, edge_equality = lambda l, r: abs( l - r ) < 0.1 ) self.assertEqual( res.length(), 3 ) mapping = res.remapped() 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 ) class TestRascalMatch(unittest.TestCase): 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.RascalMatch( 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 ) class TestGreedyMatch(unittest.TestCase): 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 ) suite_atom = unittest.TestLoader().loadTestsFromTestCase( TestAtom ) suite_molecule = unittest.TestLoader().loadTestsFromTestCase( TestMolecule ) suite_compound = unittest.TestLoader().loadTestsFromTestCase( TestCompound ) suite_mcgregor_match = unittest.TestLoader().loadTestsFromTestCase( TestMcGregorMatch ) suite_rascal_match= unittest.TestLoader().loadTestsFromTestCase( TestRascalMatch ) suite_greedy_match= unittest.TestLoader().loadTestsFromTestCase( TestGreedyMatch ) alltests = unittest.TestSuite( [ suite_atom, suite_molecule, suite_compound, suite_mcgregor_match, suite_rascal_match, suite_greedy_match, ] ) def load_tests(loader, tests, pattern): return alltests if __name__ == "__main__": unittest.TextTestRunner( verbosity = 2 ).run( alltests )