def testStoreAndRetrieve(self):
reinitdb()
graph = Graph.Graph()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
labels = Infoset.Infoset(graph, InfosetType.getAtomLabelType())
bondtypes = Infoset.Infoset(graph, InfosetType.getBondTypeType())
energy = Infoset.Infoset(graph, InfosetType.getHFEnergyType())
angles = Infoset.Infoset(graph, InfosetType.getAngleType())
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
link = graph.createEntity((node1, node2))
angle = graph.createEntity((node1, node2, node3))
coords.setValue(node1, (10.0, 0.0, 0.0))
coords.setValue(node2, (10.0, 2.0, 0.0))
coords.setValue(node3, (10.0, 2.0, 3.0))
bondtypes.setValue(link, 2)
angles.setValue(angle, Measure.Measure(45, Units.degrees))
db = DBAccess.DBAccess(os.path.join(moduleDir(), "testdb"))
db.store(graph)
molecule_list = db.retrieveAll()
self.assertEqual(len(molecule_list), 1)
def testSearch(self):
reinitdb()
db = DBAccess.DBAccess(os.path.join(moduleDir(), "testdb"))
for i in xrange(1, 90):
graph = Graph.Graph()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
labels = Infoset.Infoset(graph, InfosetType.getAtomLabelType())
bondtypes = Infoset.Infoset(graph, InfosetType.getBondTypeType())
energy = Infoset.Infoset(graph, InfosetType.getHFEnergyType())
angles = Infoset.Infoset(graph, InfosetType.getAngleType())
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
link = graph.createEntity((node1, node2))
angle = graph.createEntity((node1, node2, node3))
coords.setValue(node1, (10.0, 0.0, 0.0))
coords.setValue(node2, (10.0, 2.0, 0.0))
coords.setValue(node3, (10.0, 2.0, 3.0))
bondtypes.setValue(link, 2)
angles.setValue(angle, Measure.Measure(float(i), Units.degrees))
db.store(graph)
def testEntityDeletionCascade(self): # fold>>
graph = Graph.Graph()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
labels = Infoset.Infoset(graph, InfosetType.getAtomLabelType())
bondtypes = Infoset.Infoset(graph, InfosetType.getBondTypeType())
angles = Infoset.Infoset(graph, InfosetType.getAngleType())
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
link = graph.createEntity((node1, node2))
angle_entity = graph.createEntity((node1, node2, node3))
coords.setValue(node1, (10.0, 0.0, 0.0))
coords.setValue(node2, (10.0, 2.0, 0.0))
coords.setValue(node3, (10.0, 2.0, 3.0))
bondtypes.setValue(link, 2)
angles.setValue(angle_entity, 45.0)
graph.deleteEntity(node1)
self.assertEqual(coords.size(), 2)
self.assertEqual(labels.size(), 2)
self.assertEqual(bondtypes.size(), 0)
self.assertEqual(angles.size(), 0)
def __init__(self, atom_list): # fold>>
self._graph = Graph.Graph()
self._elements = Infoset.Infoset(self._graph, InfosetType.getElementType())
self._coords = Infoset.Infoset(self._graph, InfosetType.getCoordsType())
for atom in atom_list:
entity = self._graph.createEntity()
self._elements.setValue(entity, atom[0])
self._coords.setValue(entity, atom[1])
def testFromGraph(self):
g = Graph.Graph()
elements = Infoset.Infoset(g, InfosetType.getElementType())
coords = Infoset.Infoset(g, InfosetType.getCoordsType())
e = g.createEntity()
elements.setValue(e, PeriodicTable.C)
coords.setValue(e,Measure.Measure( ( 0.0000000000,8.5886187987,0.1625164475 ), Units.bohr))
e = g.createEntity()
elements.setValue(e, PeriodicTable.C)
coords.setValue(e,Measure.Measure( ( 0.0000000000,8.5886187987,0.1625164475 ), Units.bohr))
mol = XYZMolecule.fromGraph(g)
self.assertEqual(mol.__class__, XYZMolecule.XYZMolecule)
def testSearch(self):
reinitdb()
db = DBAccess.DBAccess(os.path.join(moduleDir(), "testdb"))
for i in xrange(1, 90):
graph = Graph.Graph()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
labels = Infoset.Infoset(graph, InfosetType.getAtomLabelType())
bondtypes = Infoset.Infoset(graph, InfosetType.getBondTypeType())
energy = Infoset.Infoset(graph, InfosetType.getHFEnergyType())
angles = Infoset.Infoset(graph, InfosetType.getAngleType())
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
link = graph.createEntity((node1, node2))
angle = graph.createEntity((node1, node2, node3))
coords.setValue(node1, (10.0, 0.0, 0.0))
coords.setValue(node2, (10.0, 2.0, 0.0))
coords.setValue(node3, (10.0, 2.0, 3.0))
bondtypes.setValue(link, 2)
angles.setValue(angle, Measure.Measure(float(i), Units.degrees))
db.store(graph)
class Search:
def __init__(self, angle):
self._angle = angle
def satisfiedBy(self, graph):
infoset = graph.getInfosets(
infoset_type=InfosetType.getAngleType())[0]
if infoset is None:
return False
#if infoset.value(angle).value() > 45.0 and infoset.value(angle).value() < 48.0:
# return True
if infoset.value(angle).value() % 2 == 0:
return True
return False
results = db.search(Search(angle))
#self.assertEqual(len(results), 2)
for i in results:
print i.getInfosets(
infoset_type=InfosetType.getAngleType())[0].value(angle)
def testGraphInfoset(self): # fold>>
graph = Graph.Graph()
energy = Infoset.Infoset(graph, InfosetType.getHFEnergyType())
energy.setValue(None, Measure.Measure(10.4, Units.hartree))
self.assertEqual(energy.dimensionality(), 0)
self.assertEqual(energy.size(), 1)
self.assertEqual(energy.value(None).value(), 10.4)
self.assertEqual(energy.value(None).unit(), Units.hartree)
def testInfoset2(self): # fold>>
graph = Graph.Graph()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
labels = Infoset.Infoset(graph, InfosetType.getAtomLabelType())
bondtypes = Infoset.Infoset(graph, InfosetType.getBondTypeType())
angles = Infoset.Infoset(graph, InfosetType.getAngleType())
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
link = graph.createEntity((node1, node2))
angle_entity = graph.createEntity((node1, node2, node3))
coords.setValue(node1, (10.0, 0.0, 0.0))
coords.setValue(node2, (10.0, 2.0, 0.0))
self.assertEqual(coords.hasNone(), True)
coords.setValue(node3, (10.0, 2.0, 3.0))
self.assertEqual(coords.hasNone(), False)
self.assertEqual(coords.value(node1), (10.0, 0.0, 0.0))
self.assertEqual(coords.value(node2), (10.0, 2.0, 0.0))
self.assertEqual(coords.value(node3), (10.0, 2.0, 3.0))
bondtypes.setValue(link, 2)
self.assertEqual(bondtypes.value(link), 2)
self.assertEqual(bondtypes.hasNone(), False)
angles.setValue(angle_entity, Measure.Measure(45.0, Units.degrees))
self.assertEqual(angles.hasNone(), False)
self.assertEqual(
angles.value(angle_entity).value(),
Measure.Measure(45.0, Units.degrees).value())
graph.deleteEntity(node1)
self.assertEqual(coords.size(), 2)
self.assertEqual(labels.size(), 2)
self.assertEqual(bondtypes.size(), 0)
self.assertEqual(angles.size(), 0)
def testGetInfoset(self): # fold>>
graph = Graph.Graph()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
coords2 = Infoset.Infoset(graph, InfosetType.getCoordsType())
labels = Infoset.Infoset(graph, InfosetType.getAtomLabelType())
bondtypes = Infoset.Infoset(graph, InfosetType.getBondTypeType())
angles = Infoset.Infoset(graph, InfosetType.getAngleType())
energy = Infoset.Infoset(graph, InfosetType.getHFEnergyType())
self.assertEqual(len(graph.getInfosets()), 6)
self.assertEqual(len(graph.getInfosets(dimensionality=0)), 1)
self.assertEqual(len(graph.getInfosets(dimensionality=1)), 3)
self.assertEqual(len(graph.getInfosets(dimensionality=2)), 1)
self.assertEqual(len(graph.getInfosets(dimensionality=3)), 1)
self.assertEqual(len(graph.getInfosets(dimensionality=4)), 0)
self.assertEqual(len(graph.getInfosets(uuid=coords.uuid())), 1)
self.assertEqual(len(graph.getInfosets(uuid=labels.uuid())), 1)
self.assertEqual(len(graph.getInfosets(uuid=uuid.uuid4())), 0)
self.assertEqual(
len(graph.getInfosets(infoset_type=InfosetType.getCoordsType())),
2)
self.assertEqual(
len(graph.getInfosets(infoset_type=InfosetType.getHFEnergyType())),
1)
self.assertEqual(len(graph.getInfosets(infoset_type=list)), 0)
self.assertEqual(
len(graph.getInfosets(uuid=labels.uuid(), dimensionality=1)), 1)
self.assertEqual(
len(graph.getInfosets(uuid=labels.uuid(), dimensionality=2)), 0)
def testInfoset(self): # fold>>
graph = Graph.Graph()
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
self.assertTrue(isinstance(coords, Infoset.Infoset))
self.assertEqual(coords.graph(), graph)
self.assertNotEqual(coords.uuid(), None)
self.assertEqual(coords.typeURI(),
InfosetType.getCoordsType().typeURI())
self.assertEqual(coords.dimensionality(),
InfosetType.getCoordsType().dimensionality())
self.assertEqual(coords.size(), 3)
self.assertEqual(coords.hasNone(), True)
def testReification(self): # fold>>
graph = Graph.Graph()
node1 = graph.createEntity()
node2 = graph.createEntity()
node3 = graph.createEntity()
coords = Infoset.Infoset(graph, InfosetType.getCoordsType())
self.assertEqual(len(coords.getReifications()), 0)
id = coords.reify(ReificationTypeURI.COMMENT_REIFICATION_TYPE_URI,
"hello")
type_uri, value = coords.getReifications(id=id)
self.assertEqual(type_uri,
ReificationTypeURI.COMMENT_REIFICATION_TYPE_URI)
self.assertEqual(value, "hello")
self.assertEqual(len(coords.getReifications()), 1)