def test_pack_molecule(self):
from mogli import Molecule, LGFIOConfig, pack_molecule, unpack_molecule
mol1 = Molecule()
mol2 = Molecule()
config = LGFIOConfig('label', 'atomType')
config.add_string_node_prop("label2")\
.add_bool_node_prop("isC")\
.add_int_node_prop("iNum")\
.add_double_node_prop("dNum")
mol1.read_lgf(ETHANE_PROPS, config)
mol2 = unpack_molecule(pack_molecule(mol1))
self.assertEqual(mol1.get_atom_count(), mol2.get_atom_count())
def s(e):
id1 = mol1.get_id(mol1.get_u(e))
id2 = mol1.get_id(mol1.get_v(e))
return (id1, id2) if id1 < id2 else (id2, id1)
edges1 = sorted([s(e) for e in mol1.get_edge_iter()])
edges2 = sorted([s(e) for e in mol2.get_edge_iter()])
self.assertEqual(edges1, edges2)
props = mol2.get_properties()
self.assertIn('label2', props)
self.assertIn('isC', props)
self.assertIn('iNum', props)
self.assertIn('dNum', props)
for v1 in mol1.get_node_iter():
v2 = mol2.get_node_by_id(mol1.get_id(v1))
self.assertEqual(mol1.get_property(v1, 'label2'),
mol2.get_property(v2, 'label2'))
self.assertEqual(mol1.get_property(v1, 'isC'),
mol2.get_property(v2, 'isC'))
self.assertEqual(mol1.get_property(v1, 'iNum'),
mol2.get_property(v2, 'iNum'))
self.assertEqual(mol1.get_property(v1, 'dNum'),
mol2.get_property(v2, 'dNum'))
def test_read_lgf(self):
from mogli import Molecule
mol = Molecule()
mol.read_lgf(ETHANE_1)
self.assertEqual(mol.get_atom_count(), 8)
c1 = mol.get_node_by_id(0)
c2 = mol.get_node_by_id(1)
props = mol.get_properties()
self.assertIn('label2', props)
self.assertEqual(mol.get_property(c1, 'label2'), 'C1')
self.assertEqual(mol.get_property(c2, 'label2'), 'C2')
c1_edges = {(0, 1), (0, 2), (0, 3), (0, 4)}
c2_edges = {(0, 1), (1, 5), (1, 6), (1, 7)}
edges = c1_edges | c2_edges
for e in mol.get_inc_edge_iter(c1):
id1 = mol.get_id(mol.get_u(e))
id2 = mol.get_id(mol.get_v(e))
edge = (id1, id2) if id1 < id2 else (id2, id1)
self.assertIn(edge, c1_edges)
for e in mol.get_inc_edge_iter(c2):
id1 = mol.get_id(mol.get_u(e))
id2 = mol.get_id(mol.get_v(e))
edge = (id1, id2) if id1 < id2 else (id2, id1)
self.assertIn(edge, c2_edges)
for e in mol.get_edge_iter():
id1 = mol.get_id(mol.get_u(e))
id2 = mol.get_id(mol.get_v(e))
edge = (id1, id2) if id1 < id2 else (id2, id1)
self.assertIn(edge, edges)
def test_read_lgf_properties(self):
from mogli import LGFIOConfig, Molecule
config = LGFIOConfig("label", "atomType")
config.add_string_node_prop("label2")\
.add_bool_node_prop("isC")\
.add_int_node_prop("iNum")\
.add_double_node_prop("dNum")
mol = Molecule()
mol.read_lgf(ETHANE_PROPS, config)
self.assertEqual(mol.get_atom_count(), 8)
props = mol.get_properties()
self.assertEqual(len(props), 4)
self.assertIn("label2", props)
self.assertIn("isC", props)
self.assertIn("iNum", props)
self.assertIn("dNum", props)
v = mol.get_node_by_id(0)
self.assertEqual(mol.get_property(v, "label2"), "C1")
self.assertTrue(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 1)
self.assertEqual(mol.get_property(v, "dNum"), 1.0)
v = mol.get_node_by_id(1)
self.assertEqual(mol.get_property(v, "label2"), "C2")
self.assertTrue(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 2)
self.assertEqual(mol.get_property(v, "dNum"), 2.0)
v = mol.get_node_by_id(2)
self.assertEqual(mol.get_property(v, "label2"), "H3")
self.assertFalse(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 3)
self.assertEqual(mol.get_property(v, "dNum"), 3.0)
v = mol.get_node_by_id(3)
self.assertEqual(mol.get_property(v, "label2"), "H4")
self.assertFalse(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 4)
self.assertEqual(mol.get_property(v, "dNum"), 4.0)
v = mol.get_node_by_id(4)
self.assertEqual(mol.get_property(v, "label2"), "H5")
self.assertFalse(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 5)
self.assertEqual(mol.get_property(v, "dNum"), 5.0)
v = mol.get_node_by_id(5)
self.assertEqual(mol.get_property(v, "label2"), "H6")
self.assertFalse(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 6)
self.assertEqual(mol.get_property(v, "dNum"), 6.0)
v = mol.get_node_by_id(6)
self.assertEqual(mol.get_property(v, "label2"), "H7")
self.assertFalse(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 7)
self.assertEqual(mol.get_property(v, "dNum"), 7.0)
v = mol.get_node_by_id(7)
self.assertEqual(mol.get_property(v, "label2"), "H8")
self.assertFalse(mol.get_property(v, "isC"))
self.assertEqual(mol.get_property(v, "iNum"), 8)
self.assertEqual(mol.get_property(v, "dNum"), 8.0)