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 _getEnergies(iconv):
energies = {}
for step in grrm2.interconversionStep(iconv).getAll():
step = step[0]
energies[grrm2.stepNumber(step).get()] = grrm2.energy(step).get()
return energies
def _parseUDCAnalysis(self):
tokenizer = grrm.UDCAnalysisOutputTokenizer()
tokens = tokenizer.tokenize(self._filename)
steepest_header_found = False
m_uDC = re.search("_uDC(\d+)\.log", self._filename)
route = grrm2.Interconversion.new(
self._graph, rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
self._route = route
self._route_additional_infos = InterconversionAdditionalInfo.InterconversionAdditionalInfo(
route)
self._route_additional_infos.setStartStructureLabel(
("uDC", int(m_uDC.group(1))))
steps = {}
for t in tokens:
if t.__class__ == tokentypes.SteepestDescentHeaderToken:
steepest_header_found = True
if t.__class__ == tokentypes.IRCStepToken:
if not steepest_header_found:
raise Exception("Steepest Header not found")
molecule = grrm2.InterconversionStep.new(
self._graph,
rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
self._route_steps.append(molecule)
grrm2.energy(molecule).set(t.energy().rescale(
units.hartree).magnitude)
grrm2.spin(molecule).set(t.spin().rescale(
units.hbar).magnitude)
grrm2.geometry(molecule).set(helperfuncs.parseGeometryToken(t))
grrm2.stepNumber(molecule).set(t.step())
grrm2.interconversionStep(route).add(molecule)
steps[t.step()] = molecule
if t.step() != 1:
grrm2.prevInterconversionStep(molecule).set(
steps[t.step() - 1])
if t.__class__ == tokentypes.DownhillWalkingResultToken:
self._route_additional_infos.setEndStructureLabel(t.result())
def testTSAnalysis(self):
graph = rdflib.ConjunctiveGraph()
p = parsinghelpers.TSAnalysisParser(
graph,
os.path.join(os.path.dirname(__file__), "formaldehyde-newnames",
"grrm_HCHO_TS3.log"))
self.assertEqual(
p._forward_route_additional_infos.startStructureLabel(), ("TS", 3))
self.assertEqual(p._forward_route_additional_infos.endStructureLabel(),
("UDC", 1))
self.assertEqual(
len(grrm2.interconversionStep(p._forward_route).getAll()), 17)
self.assertEqual(
p._backward_route_additional_infos.startStructureLabel(),
("TS", 3))
self.assertEqual(
p._backward_route_additional_infos.endStructureLabel(), ("UDC", 2))
self.assertEqual(
len(grrm2.interconversionStep(p._backward_route).getAll()), 19)
print graph.serialize()
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 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
_usage()
sys.exit(1)
graph = Graph(graphstore.store(),
identifier=rdflib.URIRef("urn:uuid:" +
str(options.submission_uuid)))
for iconv in grrm2.Interconversion.all(graph):
print "Generating xyz for interconversion " + iconv.uri()
res_storage = filestorage.ResourceStorage(
iconv, web_accessible=True, settings=settings.filestorage_settings)
all_files = []
step_tuples = []
for s in grrm2.interconversionStep(iconv).getAll():
step = s[0]
fs = filestorage.ResourceStorage(
step, web_accessible=True, settings=settings.filestorage_settings)
step_xyz = fs.path("geometry", "xyz")
step_number = grrm2.stepNumber(step).get()
step_tuples.append((step_number, step_xyz))
def cmpFunc(x, y):
return cmp(x[0], y[0])
for step, file in sorted(step_tuples, cmp=cmpFunc):
all_files.append(file)
if len(all_files) != 0:
os.system("cat " + " ".join(all_files + list(reversed(all_files))) +
def _parseTSAnalysis(self):
tokenizer = grrm.TSAnalysisOutputTokenizer()
tokens = tokenizer.tokenize(self._filename)
status = Anon()
status.header_found = False
status.doing_forward = False
status.doing_backward = False
m_TS = re.search("_TS(\d+)\.log", self._filename)
forward_route = grrm2.Interconversion.new(self._graph,rdflib.URIRef("urn:uuid:"+str(uuid.uuid4())))
backward_route = grrm2.Interconversion.new(self._graph,rdflib.URIRef("urn:uuid:"+str(uuid.uuid4())))
self._forward_route = forward_route
self._backward_route = backward_route
forward_steps = {}
backward_steps = {}
self._forward_route_additional_infos = InterconversionAdditionalInfo.InterconversionAdditionalInfo(forward_route)
self._forward_route_additional_infos.setStartStructureLabel( ( "TS", int(m_TS.group(1)) ) )
self._backward_route_additional_infos = InterconversionAdditionalInfo.InterconversionAdditionalInfo(backward_route)
self._backward_route_additional_infos.setStartStructureLabel( ( "TS", int(m_TS.group(1)) ) )
for t in tokens:
if t.__class__ == tokentypes.IRCHeaderToken:
status.header_found = True
if t.__class__ == tokentypes.ForwardIRCHeaderToken:
if not status.header_found:
raise Exception("Header not found")
status.doing_forward = True
status.doing_backward = False
if t.__class__ == tokentypes.BackwardIRCHeaderToken:
if not status.header_found:
raise Exception("Header not found")
status.doing_forward = False
status.doing_backward = True
if t.__class__ == tokentypes.IRCStepToken:
molecule = grrm2.InterconversionStep.new(self._graph, rdflib.URIRef("urn:uuid:"+str(uuid.uuid4())))
grrm2.energy(molecule).set(t.energy().rescale(units.hartree).magnitude)
grrm2.spin(molecule).set(t.spin().rescale(units.hbar).magnitude)
grrm2.geometry(molecule).set(helperfuncs.parseGeometryToken(t))
grrm2.stepNumber(molecule).set(t.step())
if status.doing_forward:
grrm2.interconversionStep(forward_route).add(molecule)
self._forward_steps.append(molecule)
forward_steps[t.step()] = molecule
if t.step() != 1:
grrm2.prevInterconversionStep(molecule).set(forward_steps[t.step()-1])
elif status.doing_backward:
grrm2.interconversionStep(backward_route).add(molecule)
self._backward_steps.append(molecule)
backward_steps[t.step()] = molecule
if t.step() != 1:
grrm2.prevInterconversionStep(molecule).set(backward_steps[t.step()-1])
else:
raise Exception("found IRCStepToken but no idea who it belongs to")
if t.__class__ == tokentypes.IRCFollowingResultsToken:
self._forward_route_additional_infos.setEndStructureLabel(_properNaming(t.forward()))
self._backward_route_additional_infos.setEndStructureLabel(_properNaming(t.backward()))
