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 moleculeCode(self): # fold>>
element_part = []
element_infoset = self._graph.getInfosets(infoset_type=InfosetType.getElementType())[0]
coords_infoset = self._graph.getInfosets(infoset_type=InfosetType.getCoordsType())[0]
element_part= sorted([y.atomicNumber() for x,y in element_infoset.allValues() ])
geometry_part = []
for node_id, element in element_infoset.allValues():
coordinate = coords_infoset.value(node_id).asUnit(Units.bohr).value()
geometry_part.append("%d %15.10f %15.10f %15.10f" % (element.atomicNumber(), coordinate[0], coordinate[1], coordinate[2]))
return "AA-"+_encode("\n".join([ str(x) for x in element_part]))+"-"+_encode("\n".join(geometry_part))
def fromGraph(graph):
elements = graph.getInfosets(infoset_type=InfosetType.getElementType())
coords = graph.getInfosets(infoset_type=InfosetType.getCoordsType())
if len(elements) == 0 or len(coords) == 0:
return None
atom_list = []
for id, value in elements[0].allValues():
atom_list.append( (elements[0].value(id), coords[0].value(id)))
return XYZMolecule(atom_list)
def _createXYZFile(mol):
cache_dir = os.path.join(os.path.dirname(__file__),"..","..","cache","jmol")
uuid = mol.uuid()
element = mol.getInfosets(infoset_type=InfosetType.getElementType())[0]
coords = mol.getInfosets(infoset_type=InfosetType.getCoordsType())[0]
f = file(os.path.join(cache_dir,str(uuid)+".xyz"), "w")
num_atoms = len(element.allValues())
f.write(str(num_atoms)+"\n\n")
for node, element in element.allValues():
coordinates = coords.value(node).asUnit(Units.angstrom).value()
f.write( "%s %16.10f %16.10f %16.10f\n" % (element.symbol(), coordinates[0], coordinates[1], coordinates[2]) )
f.close()
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 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')