def testObjectProperty(self):
graph = rdflib.ConjunctiveGraph(getStore())
eq1 = grrm2.EquilibriumStructure.new(graph, "http://example.com/eq1")
ts1 = grrm2.TransitionState.new(graph, "http://example.com/ts1")
blessdiss1 = grrm2.BarrierlessDissociated.new(
graph, "http://example.com/blessdiss1")
bdiss1 = grrm2.BarrierDissociated.new(graph,
"http://example.com/bdiss1")
ic1 = grrm2.InterconversionStep.new(graph, "http://example.com/ic1")
iconv1 = grrm2.Interconversion.new(graph, "http://example.com/iconv1")
rundata1 = grrm2.RunData.new(graph, "http://example.com/rundata1")
run1 = grrm2.Run.new(graph, "http://example.com/run1")
mol1 = grrm2.Molecule.new(graph, "http://example.com/mol1")
runin1 = grrm2.RunInput.new(graph, "http://example.com/runin1")
runout1 = grrm2.RunOutput.new(graph, "http://example.com/runout1")
icres1 = grrm2.InterconversionResult.new(graph,
"http://example.com/icres1")
grrm2.runInput(run1).add(eq1)
grrm2.runInput(run1).add(ts1)
grrm2.runInput(run1).add(ic1)
grrm2.runInput(run1).add(blessdiss1)
grrm2.runInput(run1).add(bdiss1)
grrm2.runInput(run1).add(icres1)
grrm2.runInput(run1).add(mol1)
grrm2.runInput(run1).add(runin1)
grrm2.runInput(run1).add(rundata1)
self.assertRaises(Exception, grrm2.runInput(run1).add, iconv1)
self.assertRaises(Exception, grrm2.runInput(run1).add, runout1)
self.assertRaises(Exception, grrm2.runInput(run1).add, run1)
grrm2.runOutput(run1).add(eq1)
grrm2.runOutput(run1).add(ts1)
grrm2.runOutput(run1).add(ic1)
grrm2.runOutput(run1).add(blessdiss1)
grrm2.runOutput(run1).add(bdiss1)
grrm2.runOutput(run1).add(iconv1)
grrm2.runOutput(run1).add(icres1)
grrm2.runOutput(run1).add(mol1)
grrm2.runOutput(run1).add(runout1)
self.assertRaises(Exception, grrm2.runOutput(run1).add, runin1)
self.assertRaises(Exception, grrm2.runOutput(run1).add, rundata1)
self.assertRaises(Exception, grrm2.runOutput(run1).add, run1)
grrm2.interconversionStart(iconv1).set(eq1)
grrm2.interconversionEnd(iconv1).set(ts1)
self.assertRaises(Exception,
grrm2.interconversionStart(iconv1).set, run1)
self.assertRaises(Exception,
grrm2.interconversionEnd(iconv1).set, run1)
def _getInterconversionEnergy(self, request, uri, interconversion_uuid):
graph = graphstore.graph()
try:
route = grrm2.Interconversion.get(
graph, utils.uuidToUri(interconversion_uuid))
except:
raise http.Http404
output = {}
start = grrm2.interconversionStart(route).get()[0]
end = grrm2.interconversionEnd(route).get()[0]
energies = {}
for step in grrm2.interconversionStep(route).getAll():
step = step[0]
energies[grrm2.stepNumber(step).get()] = grrm2.energy(step).get()
energies[0] = grrm2.energy(start).get()
energies[max(energies.keys()) + 1] = grrm2.energy(end).get()
output["energies"] = energies
return http.HttpResponse(simplejson.dumps(output),
mimetype='application/javascript')
def dispatch(self, request, **args):
current_uri = args["uri"]
graph = graphstore.graph()
try:
iconv = grrm2.Interconversion.get(graph, current_uri)
except:
return None
ctx = {}
ctx["steps"] = []
ctx["start"] = ResultInfo()
ctx["end"] = ResultInfo()
start = grrm2.interconversionStart(iconv).get()[0]
ctx["start"].uri = start.uri()
ctx["start"].link = "/resources/%7B" + utils.uriToUuid(
start.uri()) + "%7D"
iconstorage = filestorage.ResourceIcon(
start, settings=settings.filestorage_settings)
ctx["start"].icon = iconstorage.url(filestorage.ResourceIcon.STATIC)
ctx["start"].energy = grrm2.energy(start).get()
ctx["start"].label = _getLabel(start)
end = grrm2.interconversionEnd(iconv).get()[0]
ctx["end"].uri = end.uri()
ctx["end"].link = "/resources/%7B" + utils.uriToUuid(end.uri()) + "%7D"
iconstorage = filestorage.ResourceIcon(
end, settings=settings.filestorage_settings)
ctx["end"].icon = iconstorage.url(filestorage.ResourceIcon.STATIC)
ctx["end"].energy = grrm2.energy(end).get()
ctx["end"].label = _getLabel(end)
for s in grrm2.interconversionStep(iconv).getAll():
step = s[0]
iconstorage = filestorage.ResourceIcon(
step, settings=settings.filestorage_settings)
info = StepInfo()
info.link = "/resources/%7B" + utils.uriToUuid(step.uri()) + "%7D"
info.icon = iconstorage.url(filestorage.ResourceIcon.STATIC)
info.uri = step.uri()
info.energy = grrm2.energy(step).get()
info.number = grrm2.stepNumber(step).get()
ctx["steps"].append(info)
def cmpFunc(x, y):
return cmp(x.number, y.number)
ctx["steps"] = sorted(ctx["steps"], cmp=cmpFunc)
return ctx
def __init__(self, graph, parsers, mapper):
self._mapper = mapper
self._parsers = parsers
self._graph = graph
print "Resolving connections"
for routeinfo in self._mapper.allInterconversionAdditionalInfos():
start, end = routeinfo.startStructureLabel(
), routeinfo.endStructureLabel()
print "found " + str(start) + " - " + str(end)
route = routeinfo.interconversion()
try:
start_molecule = self._mapper.structureLabelToMolecule(start)
grrm2.interconversionStart(route).set(start_molecule)
except KeyError:
print "Unknown start molecule for interconversion " + str(
route)
try:
end_molecule = self._mapper.structureLabelToMolecule(end)
grrm2.interconversionEnd(route).set(end_molecule)
except KeyError:
print "Unknown end molecule for interconversion " + str(route)
def dispatch(self, request, **args):
current_uri = args["uri"]
graph = graphstore.graph()
try:
route = grrm2.Interconversion.get(graph, current_uri)
except:
return None
start = grrm2.interconversionStart(route).get()[0]
end = grrm2.interconversionEnd(route).get()[0]
iconstorage_start = filestorage.ResourceIcon(start, settings=settings.filestorage_settings)
iconstorage_end = filestorage.ResourceIcon(end, settings=settings.filestorage_settings)
iconstorage_route = filestorage.ResourceIcon(route, settings=settings.filestorage_settings)
ctx = {}
ctx["startUrl"] = "/resources/%7B"+utils.uriToUuid(start.uri())+"%7D"
ctx["endUrl"] = "/resources/%7B"+utils.uriToUuid(end.uri())+"%7D"
ctx["startIcon"] = iconstorage_start.url(filestorage.ResourceIcon.STATIC)
ctx["endIcon"] = iconstorage_end.url(filestorage.ResourceIcon.STATIC)
ctx["connectionRouteIcon"] = iconstorage_route.url(filestorage.ResourceIcon.ANIMATED)
ctx["startStructureLabel"] = _getLabel(start)
ctx["endStructureLabel"] = _getLabel(end)
energies = {}
for step in grrm2.interconversionStep(route).getAll():
step = step[0]
energies[grrm2.stepNumber(step).get()] = grrm2.energy(step).get()
energies[0] = grrm2.energy(start).get()
energies[max(energies.keys())+1] = grrm2.energy(end).get()
chart_query = http.QueryDict("").copy()
chart_query.update( {
"cht": "lxy",
"chs": "400x400",
"chd": "t:"+",".join([ str(x) for x in energies.keys()])+"|"+",".join( [str(x) for x in energies.values()]),
"chds": str(min(energies.keys()))+","+str(max(energies.keys()))+","+str(min(energies.values()))+","+str(max(energies.values())),
"chco": "3072F3,ff0000,00aaaa",
"chls": "2,4,1",
"chf": "bg,s,F0F0FF",
"chm": "s,FF0000,0,-1,5|s,0000ff,1,-1,5|s,00aa00,2,-1,5",
"chxt": "x,y",
"chxr": "0,"+str(min(energies.keys()))+","+str(max(energies.keys()))+"|1,"+str(min(energies.values()))+","+str(max(energies.values())),
} )
ctx["chartUrl"] = "http://chart.apis.google.com/chart?"+chart_query.urlencode()
return ctx
def dispatch(self, request, uri):
context = {}
graph = graphstore.graph()
try:
molecule = grrm2.Molecule.get(graph, uri)
except:
return None
context["moleculeInfo"] = self._getMoleculeInfo(molecule)
if context["moleculeInfo"].isInterconversionStep:
interconversion_step = grrm2.InterconversionStep.tryCast(molecule)
prev_step = grrm2.prevInterconversionStep(
interconversion_step).get()
next_step = grrm2.nextInterconversionStep(
interconversion_step).get()
interconversion = grrm2.interconversionStepOf(
interconversion_step).get()
if interconversion and interconversion[0]:
start_structure = grrm2.interconversionStart(
interconversion[0]).get()
if start_structure and start_structure[0]:
start_structure = start_structure[0]
end_structure = grrm2.interconversionEnd(
interconversion[0]).get()
if end_structure and end_structure[0]:
end_structure = end_structure[0]
if prev_step and prev_step[0]:
context["prevStepInfo"] = self._getMoleculeInfo(prev_step[0])
else:
context["prevStepInfo"] = self._getMoleculeInfo(
start_structure)
if next_step and next_step[0]:
context["nextStepInfo"] = self._getMoleculeInfo(next_step[0])
else:
context["nextStepInfo"] = self._getMoleculeInfo(end_structure)
else:
context["isInterconversion"] = False
context["fromRoutes"] = self._getFromRoutesContext(molecule)
context["toRoutes"] = self._getToRoutesContext(molecule)
return context
def _getToRoutesContext(self, molecule):
icres = grrm2.InterconversionResult.tryCast(molecule)
context = []
iconvs = grrm2.interconversionStartOf(icres).getAll()
if iconvs is None:
return context
for iconv in iconvs:
iconv = iconv[0]
end = grrm2.interconversionEnd(iconv).get()[0]
route_info = RouteInfo()
route_info.link = "/resources/%7B" + utils.uriToUuid(
iconv.uri()) + "%7D"
route_info.targetLink = "/resources/%7B" + utils.uriToUuid(
end.uri()) + "%7D"
route_info.targetIcon = filestorage.ResourceIcon(
end, settings=settings.filestorage_settings).url(
filestorage.ResourceIcon.STATIC)
struct_number = grrm2.structureNumber(end).get()
if grrm2.EquilibriumStructure.tryCast(end):
struct_type = "EQ"
elif grrm2.TransitionState.tryCast(end):
struct_type = "TS"
elif grrm2.BarrierlessDissociated.tryCast(end):
struct_type = "DDC"
elif grrm2.BarrierDissociated.tryCast(end):
struct_type = "UDC"
route_info.targetStructureLabel = struct_type + str(struct_number)
route_info.targetEnergy = grrm2.energy(end).get()
route_info.energyDifference = grrm2.energy(
end).get() - grrm2.energy(molecule).get()
route_info.icon = filestorage.ResourceIcon(
iconv, settings=settings.filestorage_settings).url(
filestorage.ResourceIcon.ANIMATED)
context.append(route_info)
return context
def foo():
end = grrm2.interconversionEnd(route).get()[0]
iconstorage_start = filestorage.ResourceIcon(
start, settings=settings.filestorage_settings)
iconstorage_end = filestorage.ResourceIcon(
end, settings=settings.filestorage_settings)
iconstorage_route = filestorage.ResourceIcon(
route, settings=settings.filestorage_settings)
ctx = {}
ctx["startUrl"] = "/resources/%7B" + utils.uriToUuid(start.uri()) + "%7D"
ctx["endUrl"] = "/resources/%7B" + utils.uriToUuid(end.uri()) + "%7D"
ctx["startIcon"] = iconstorage_start.url(filestorage.ResourceIcon.STATIC)
ctx["endIcon"] = iconstorage_end.url(filestorage.ResourceIcon.STATIC)
ctx["connectionRouteIcon"] = iconstorage_route.url(
filestorage.ResourceIcon.ANIMATED)
ctx["startStructureLabel"] = _getLabel(start)
ctx["endStructureLabel"] = _getLabel(end)
def dispatch(self, request, **args):
current_uri = args["uri"]
graph = graphstore.graph()
try:
transition_state = grrm2.TransitionState.get(graph, current_uri)
except:
return None
ctx = {}
iconv_start_tuple_list = grrm2.interconversionStartOf(
transition_state).getAll() or []
iconv_end_tuple_list = grrm2.interconversionEndOf(
transition_state).getAll() or []
if len(iconv_start_tuple_list) + len(iconv_end_tuple_list) != 2:
return None # we have a problem... a transition state must have two links
if len(iconv_start_tuple_list) == 2:
iconv_left = iconv_start_tuple_list[0][0]
iconv_right = iconv_start_tuple_list[1][0]
energies_left = _getEnergies(iconv_left)
energies_right = _getEnergies(iconv_right)
energies = {}
energies[0] = grrm2.energy(transition_state).get()
for k, v in sorted(map(lambda x:
(-x[0], x[1]), energies_left.items()) +
energies_right.items(),
key=lambda x: x[0]):
print k
energies[k] = v
end_left = grrm2.interconversionEnd(iconv_left).get()[0]
end_right = grrm2.interconversionEnd(iconv_right).get()[0]
energies[min(energies.keys()) - 1] = grrm2.energy(end_left).get()
energies[max(energies.keys()) + 1] = grrm2.energy(end_right).get()
else:
return None
chart_query = http.QueryDict("").copy()
chart_query.update({
"cht":
"lxy",
"chs":
"400x400",
"chd":
"t:" + ",".join([
str(x[0]) for x in sorted(energies.items(), key=lambda x: x[0])
]) + "|" + ",".join([
str(x[1]) for x in sorted(energies.items(), key=lambda x: x[0])
]),
"chds":
str(min(energies.keys())) + "," + str(max(energies.keys())) + "," +
str(min(energies.values())) + "," + str(max(energies.values())),
"chco":
"3072F3,ff0000,00aaaa",
"chls":
"2,4,1",
"chf":
"bg,s,F0F0FF",
"chm":
"s,FF0000,0,-1,5|s,0000ff,1,-1,5|s,00aa00,2,-1,5",
"chxt":
"x,y",
"chxr":
"0," + str(min(energies.keys())) + "," +
str(max(energies.keys())) + "|1," + str(min(energies.values())) +
"," + str(max(energies.values())),
})
ctx["chartUrl"] = "http://chart.apis.google.com/chart?" + chart_query.urlencode(
)
iconstorage = filestorage.ResourceIcon(
transition_state, settings=settings.filestorage_settings)
if iconstorage.readable(filestorage.ResourceIcon.STATIC):
icon_url = iconstorage.url(filestorage.ResourceIcon.STATIC)
elif iconstorage.readable(filestorage.ResourceIcon.ANIMATED):
icon_url = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
else:
icon_url = None
ctx["transitionStateIcon"] = icon_url
iconstorage = filestorage.ResourceIcon(
end_left, settings=settings.filestorage_settings)
if iconstorage.readable(filestorage.ResourceIcon.STATIC):
icon_url = iconstorage.url(filestorage.ResourceIcon.STATIC)
elif iconstorage.readable(filestorage.ResourceIcon.ANIMATED):
icon_url = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
else:
icon_url = None
ctx["leftEndIcon"] = icon_url
iconstorage = filestorage.ResourceIcon(
end_right, settings=settings.filestorage_settings)
if iconstorage.readable(filestorage.ResourceIcon.STATIC):
icon_url = iconstorage.url(filestorage.ResourceIcon.STATIC)
elif iconstorage.readable(filestorage.ResourceIcon.ANIMATED):
icon_url = iconstorage.url(filestorage.ResourceIcon.ANIMATED)
else:
icon_url = None
ctx["rightEndIcon"] = icon_url
ctx["leftEndUrl"] = "/resources/%7B" + utils.uriToUuid(
end_left.uri()) + "%7D"
ctx["rightEndUrl"] = "/resources/%7B" + utils.uriToUuid(
end_right.uri()) + "%7D"
return ctx
if len(runs) != 1:
raise Exception("Run length != 1")
storage = filestorage.ResourceStorage(runs[0], web_accessible=True, settings=settings.filestorage_settings)
print "writing file : "+storage.path("connectivity","csv")
f=file(storage.path("connectivity","csv"),"w")
for icresult in grrm2.InterconversionResult.all(graph):
label=_getLabel(icresult)
f.write("v,"+label+","+utils.uriToUuid(icresult.uri())+"\n")
for iconv in grrm2.Interconversion.all(graph):
start = grrm2.interconversionStart(iconv).get()[0]
if grrm2.interconversionStart(iconv).get() is not None:
start = grrm2.interconversionStart(iconv).get()[0]
else:
continue
if grrm2.interconversionEnd(iconv).get() is not None:
end = grrm2.interconversionEnd(iconv).get()[0]
else:
continue
start_energy = grrm2.energy(start).get()
end_energy = grrm2.energy(end).get()
f.write("e,"+str(end_energy-start_energy)+","+_getLabel(start)+","+_getLabel(end)+","+utils.uriToUuid(iconv.uri())+"\n")
f.close()
