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 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 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 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 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 browsedb(request,dbname):
try:
db = DBAccess.DBAccess(os.path.join(settings.DB_PATH, dbname))
except:
raise Http404
molecule_list = []
all = db.retrieveAll()
molecule_list = []
for graph in all:
molecule={}
code = graph.getInfosets(infoset_type=InfosetType.getMoleculeCodeType())
if len(code) == 0:
continue
else:
molecule["code"] = code[0].value(graph)
name = graph.getInfosets(infoset_type=InfosetType.getConventionalMoleculeNameType())
if len(name) == 0:
molecule["name"] = molecule["code"]
else:
molecule["name"] = name[0].value(graph)
elements = graph.getInfosets(infoset_type=InfosetType.getElementType())
if len(elements) == 0:
continue
else:
molecule["num_of_atoms"] = elements[0].size()
molecule["brute_formula"] = Utilities.hillFormula(map(lambda x: x[1], elements[0].allValues()))
hf_energy = graph.getInfosets(infoset_type=InfosetType.getHFEnergyType())
if len(hf_energy) == 0:
continue
else:
molecule["hf_energy"] = hf_energy[0].value(graph)
#molecule["uuid"] = graph.uuid()
molecule_list.append(molecule)
database = { "name": dbname }
return render_to_response("application/browsedb.html", { "database" : database, "molecule_list" : molecule_list })
def searchdb(request):
if request.method == "POST" and request.POST:
db_name = request.POST["db_name"]
page = int(request.POST['page'])
rows_per_page = int(request.POST['rp'])
sortname = request.POST['sortname']
sortorder = request.POST['sortorder']
else:
raise Http404
try:
db = DBAccess.DBAccess(os.path.join(settings.DB_PATH, db_name))
except:
raise Http404
all = db.retrieveAll()
json_response = {"page": page, "total": len(all), "rows": []}
rows = []
for id, graph in enumerate(all):
molecule = {}
code = graph.getInfosets(
infoset_type=InfosetType.getMoleculeCodeType())
if len(code) == 0:
continue
else:
# FIXME possible danger of injection of db_name by the user
molecule["code"] = "<a href=\"/browsedb/" + db_name + "/" + code[
0].value(graph) + "\">" + code[0].value(graph) + "</a>"
name = graph.getInfosets(
infoset_type=InfosetType.getConventionalMoleculeNameType())
if len(name) == 0:
molecule["name"] = molecule["code"]
else:
molecule["name"] = name[0].value(graph)
elements = graph.getInfosets(infoset_type=InfosetType.getElementType())
if len(elements) == 0:
continue
else:
molecule["num_of_atoms"] = elements[0].size()
molecule["brute_formula"] = Utilities.hillFormula(
map(lambda x: x[1], elements[0].allValues()))
hf_energy = graph.getInfosets(
infoset_type=InfosetType.getHFEnergyType())
if len(hf_energy) == 0:
molecule["hf_energy"] = ""
else:
molecule["hf_energy"] = hf_energy[0].value(graph).value()
row = {}
row["id"] = molecule["code"]
row["cell"] = [
molecule["code"], molecule["name"], molecule["brute_formula"],
molecule["num_of_atoms"], molecule["hf_energy"], ""
]
rows.append(row)
json_response["rows"].extend(
sortAndTrim(rows, page, rows_per_page, sortname, sortorder))
json_response = {
"total":
3,
"page":
1,
"rows": [{
"cell": ["foo", "bar"]
}, {
"cell": ["foo", "bar"]
}, {
"cell": ["foo", "bar"]
}]
}
return HttpResponse(simplejson.dumps(json_response),
mimetype='application/javascript')