def _getMoleculeByMoleculeCode(db, molecule_code):
molecules = [x for x in db.retrieveAll()]
for m in molecules:
molecule_code_infoset = m.getInfosets(infoset_type=InfosetType.getMoleculeCodeType())
if len(molecule_code_infoset) != 1:
continue
if molecule_code_infoset[0].value(None) == molecule_code:
return m
return None
def browsemol(request, dbname, mol_code):
try:
db = DBAccess.DBAccess(os.path.join(settings.DB_PATH, dbname))
except:
raise Http404
mol = _getMoleculeByMoleculeCode(db, mol_code)
if mol is None:
raise Http404
infosets = mol.getInfosets()
_createXYZFile(mol)
render_data = { "dbname" : dbname,
"molname" : str(mol.uuid()),
"uuid" : str(mol.uuid())
}
render_data["molecule"] = {}
render_data["grrm"] = {}
render_data["unrecognized"] = []
for i in infosets:
if i.type() == InfosetType.getMoleculeCodeType():
render_data["molecule"]["MoleculeCode"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"StructureType":
render_data["grrm"]["StructureType"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"Spin":
render_data["grrm"]["Spin"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"HFEnergy":
render_data["grrm"]["HFEnergy"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"ZeroPointVibrationalEnergy":
render_data["grrm"]["ZeroPointVibrationalEnergy"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"NormalModesEigenvalues":
render_data["grrm"]["NormalModesEigenvalues"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"ReactionConnectivityMarker":
render_data["grrm"]["ReactionConnectivityMarker"] = i.value(None)
elif i.typeURI() == InfosetTypeURI.INFOSET_TYPE_URI_BASE+"ReactionConnectivityCodes":
render_data["grrm"]["ReactionConnectivityCodes"] = i.value(None)
render_data["grrm"]["first_code"] = i.value(None)[0]
render_data["grrm"]["second_code"] = i.value(None)[1]
else:
render_data["unrecognized"].append( ( i.typeURI(), i.dimensionality()))
return render_to_response("application/browsemol.html", render_data )
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 browsemol(request, dbname, mol_code):
try:
db = DBAccess.DBAccess(os.path.join(settings.DB_PATH, dbname))
except:
raise Http404
molecules = [x for x in db.retrieveAll()]
mol = None
for m in molecules:
molecule_code_infoset = m.getInfosets(
infoset_type=InfosetType.getMoleculeCodeType())
if len(molecule_code_infoset) != 1:
continue
if molecule_code_infoset[0].value(None) == mol_code:
mol = m
break
if mol is None:
raise Http404
infosets = mol.getInfosets()
_createXYZFile(mol)
infosets_data = []
graph_infosets_data = []
angle_data = []
for i in infosets:
if i.dimensionality() == 0:
graph_infosets_data.append((i.uuid(), i.value(None), i.typeURI()))
else:
infosets_data.append(
(i.uuid(), i.dimensionality(), i.typeURI(), i.size()))
return render_to_response(
"application/browsemol.html", {
"dbname": dbname,
"molname": str(mol.uuid()),
"uuid": str(mol.uuid()),
"graph_infosets_data": graph_infosets_data,
"infosets_data": infosets_data,
"angle_data": angle_data
})
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')