def _parseUDCTokenList(self):
tokenizer = grrm.ListOutputTokenizer()
tokens = tokenizer.tokenize(self._filename)
current_molecule = None
header_found = False
for t in tokens:
if t.__class__ == tokentypes.HeaderDissociatedToken:
header_found = True
if t.__class__ == tokentypes.StructureHeaderToken:
if not header_found:
raise Exception("Header not found")
current_molecule = grrm2.BarrierlessDissociated.new(
self._graph,
rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
self._molecules.append(current_molecule)
grrm2.structureNumber(current_molecule).set(int(t.number()))
self._struct_label_to_molecule_mapper[(
"uDC", t.number())] = current_molecule
if t.__class__ == tokentypes.GeometryToken:
if not header_found:
raise Exception("Header not found")
grrm2.geometry(current_molecule).set(
helperfuncs.parseGeometryToken(t))
if t.__class__ == tokentypes.EnergyToken:
if not header_found:
raise Exception("Header not found")
grrm2.energy(current_molecule).set(
helperfuncs.parseEnergyToken(t))
if t.__class__ == tokentypes.SpinToken:
if not header_found:
raise Exception("Header not found")
grrm2.spin(current_molecule).set(
int(t.spin().rescale(units.hbar).magnitude))
if t.__class__ == tokentypes.ZPVEToken:
if not header_found:
raise Exception("Header not found")
grrm2.zeroPointVibrationalEnergy(current_molecule).set(
helperfuncs.parseZPVEToken(t))
if t.__class__ == tokentypes.NormalModesToken:
if not header_found:
raise Exception("Header not found")
grrm2.normalModesEigenvalues(current_molecule).set(
helperfuncs.parseNormalModesEigenvalues(t))
if t.__class__ == tokentypes.ConnectionToken:
if not header_found:
raise Exception("Header not found")
self._connections.append(
(("uDC", grrm2.structureNumber(current_molecule).get()),
("EQ", t.first())))
if t.__class__ == tokentypes.DissociationFragmentsToken:
if not header_found:
raise Exception("Header not found")
grrm2.fragments(current_molecule).set(t.fragments())
def grrmMoleculeInfoFilter(thing, data_list):
if not grrm2.Molecule.tryCast(thing):
return (thing, data_list)
mol = grrm2.Molecule.tryCast(thing)
energy = grrm2.energy(mol).get()
if energy:
for data in data_list:
data.grrm__energy = float(energy)
mass = grrm2.mass(mol).get()
if mass:
for data in data_list:
data.grrm__mass = float(mass)
geometry = grrm2.geometry(mol).get()
if geometry:
for data in data_list:
all_symbols = geometry["symbols"]
data.grrm__carbons = len(filter(lambda x: x == "C", all_symbols))
data.grrm__oxygens = len(filter(lambda x: x == "O", all_symbols))
data.grrm__hydrogens = len(filter(lambda x: x == "H", all_symbols))
data.grrm__nitrogens = len(filter(lambda x: x == "N", all_symbols))
smiles = grrm2.smiles(mol).get()
if smiles:
for data in data_list:
data.grrm__smiles_md5 = md5.md5(smiles).hexdigest()
inchi = grrm2.inchi(mol).get()
if inchi:
for data in data_list:
data.grrm__inchi_md5 = md5.md5(inchi).hexdigest()
return (thing, data_list)
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 dispatch(self, request, uri):
context = {}
graph = graphstore.graph()
try:
molecule = grrm2.Molecule.get(graph, uri)
except:
return None
if grrm2.fragments(molecule).get() is None:
return None
context["fragmentInfo"] = []
fragments = grrm2.fragments(molecule).get()
geometry = grrm2.geometry(molecule).get()
canost_planar = grrm2.fragmentsCanostPlanar(molecule).get()
canost_serial = grrm2.fragmentsCanostSerial(molecule).get()
canost_planar_canonical = grrm2.fragmentsCanostPlanarCanonical(
molecule).get()
canost_serial_canonical = grrm2.fragmentsCanostSerialCanonical(
molecule).get()
for i, frag in enumerate(fragments):
fragment_info = {}
fragment_info["index"] = i
fragment_info["atomIndices"] = str(frag)
symbols = [geometry["symbols"][j - 1] for j in frag]
fragment_info["hillFormula"] = str(chemistry.hillFormula(symbols))
try:
fragment_info["canostPlanar"] = "|".join(canost_planar[i])
except:
fragment_info["canostPlanar"] = None
try:
fragment_info["canostSerial"] = "|".join(canost_serial[i])
except:
fragment_info["canostSerial"] = None
try:
fragment_info[
"canostPlanarCanonical"] = canost_planar_canonical[i]
except:
fragment_info["canostPlanarCanonical"] = None
try:
fragment_info[
"canostSerialCanonical"] = canost_serial_canonical[i]
except:
fragment_info["canostSerialCanonical"] = None
context["fragmentInfo"].append(fragment_info)
return context
def _parseInput(self):
input_tokenizer = grrm.InputTokenizer()
token_list = input_tokenizer.tokenize(self._filename)
molecule_dict = {}
run_dict = {}
for t in token_list:
if t.__class__ == tokentypes.InputGeometryToken:
molecule_dict["charge"] = int(t.charge())
molecule_dict["spin_multiplicity"] = int(t.spinMultiplicity())
molecule_dict["geometry"] = helperfuncs.parseGeometryToken(t)
elif t.__class__ == tokentypes.CommandDirectiveToken:
run_dict["job"] = t.jobString()
run_dict["method"] = t.methodString()
run_dict["basis_set"] = t.basisSetString()
molecule = grrm2.Molecule.new(
self._graph, rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
grrm2.geometry(molecule).set(molecule_dict["geometry"])
grrm2.spinMultiplicity(molecule).set(
molecule_dict["spin_multiplicity"])
grrm2.charge(molecule).set(molecule_dict["charge"])
rundata = grrm2.RunData.new(
self._graph, rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
grrm2.job(rundata).set(run_dict["job"])
grrm2.method(rundata).set(run_dict["method"])
grrm2.basisSet(rundata).set(run_dict["basis_set"])
run = grrm2.Run.new(self._graph,
rdflib.URIRef("urn:uuid:" + str(uuid.uuid4())))
grrm2.runInput(run).add(rundata)
grrm2.runInput(run).add(molecule)
self._run = run
self._molecule = molecule
def testDataProperty(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")
all_results = [eq1, ts1, blessdiss1, bdiss1, icres1]
all_not_results = [iconv1, rundata1, run1, runin1, ic1, mol1, runout1]
all_molecules = all_results + [ic1, mol1]
all_not_molecules = [iconv1, rundata1, run1, runin1, runout1]
all_runin = [runin1] + all_molecules
all_runout = [runout1] + all_molecules
for r in all_results:
grrm2.zeroPointVibrationalEnergy(r).set(12.3)
self.assertRaises(Exception,
grrm2.zeroPointVibrationalEnergy(r).set, "hello")
for r in all_not_results:
self.assertRaises(Exception, grrm2.zeroPointVibrationalEnergy, r)
for r in all_results:
grrm2.structureNumber(r).set(1)
self.assertRaises(Exception, grrm2.structureNumber(r).set, "hello")
for r in all_not_results:
self.assertRaises(Exception, grrm2.structureNumber, r)
for r in [ic1]:
grrm2.stepNumber(r).set(1)
self.assertRaises(Exception, grrm2.stepNumber(r).set, "hello")
for r in [
eq1, ts1, blessdiss1, bdiss1, icres1, iconv1, rundata1, run1,
runin1, mol1, runout1
]:
self.assertRaises(Exception, grrm2.stepNumber, r)
for r in all_molecules:
grrm2.spinMultiplicity(r).set(1)
self.assertRaises(Exception,
grrm2.spinMultiplicity(r).set, "hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.spinMultiplicity, r)
for r in all_molecules:
grrm2.spin(r).set(1.4)
self.assertRaises(Exception, grrm2.spin(r).set, "hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.spin, r)
for r in all_molecules:
grrm2.smiles(r).set("hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.smiles, r)
for r in all_molecules:
grrm2.normalModesEigenvalues(r).set([1, 2, 3])
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.normalModesEigenvalues, r)
for r in [rundata1]:
grrm2.method(r).set("hello")
for r in [
eq1, ts1, blessdiss1, bdiss1, ic1, iconv1, run1, mol1, runin1,
runout1, icres1
]:
self.assertRaises(Exception, grrm2.method, r)
for r in all_molecules:
grrm2.mass(r).set(1.4)
self.assertRaises(Exception, grrm2.mass(r).set, "hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.mass, r)
for r in [rundata1]:
grrm2.job(r).set("hello")
for r in [
eq1, ts1, blessdiss1, bdiss1, ic1, iconv1, run1, mol1, runin1,
runout1, icres1
]:
self.assertRaises(Exception, grrm2.job, r)
for r in all_molecules:
grrm2.inchi(r).set("hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.inchi, r)
for r in all_molecules:
grrm2.hillFormula(r).set("hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.hillFormula, r)
for r in all_molecules:
grrm2.geometry(r).set({})
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.geometry, r)
for r in all_molecules:
grrm2.energy(r).set(1.4)
self.assertRaises(Exception, grrm2.energy(r).set, "hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.energy, r)
for r in all_molecules:
grrm2.charge(r).set(1.4)
self.assertRaises(Exception, grrm2.charge(r).set, "hello")
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.charge, r)
for r in all_molecules:
grrm2.canostSerial(r).set(["foo"])
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.canostSerial, r)
for r in all_molecules:
grrm2.canostPlanar(r).set(["foo"])
for r in all_not_molecules:
self.assertRaises(Exception, grrm2.canostPlanar, r)
for r in [rundata1]:
grrm2.basisSet(r).set("hello")
for r in [
eq1, ts1, blessdiss1, bdiss1, ic1, iconv1, run1, mol1, runin1,
runout1, icres1
]:
self.assertRaises(Exception, grrm2.basisSet, r)
print error
print ""
options = Options(sys.argv)
graph = Graph(graphstore.store(),
identifier=rdflib.URIRef("urn:uuid:" +
str(options.submission_uuid)))
for mol in grrm2.Molecule.all(graph):
fs = filestorage.ResourceStorage(mol,
web_accessible=True,
settings=settings.filestorage_settings)
data = grrm2.geometry(mol).get()
elements = data["symbols"]
coords = data["coordinates"]
f = file(fs.path("geometry", "xyz"), "w")
num_atoms = len(elements)
f.write(str(num_atoms) + "\n\n")
for element, coord in zip(elements, coords):
f.write("%s %16.10f %16.10f %16.10f\n" %
(element, coord[0], coord[1], coord[2]))
f.close()
fragments = grrm2.fragments(mol).get()
if fragments:
def dispatch(self, request, uri):
context = {}
graph = graphstore.graph()
try:
molecule = grrm2.Molecule.get(graph, uri)
except:
return None
context["moleculeInfo"] = []
context["moleculeInfo"].append(
("Formula", grrm2.hillFormula(molecule).get(), None))
context["moleculeInfo"].append(
("Molecular Mass", grrm2.mass(molecule).get(), None))
context["moleculeInfo"].append(
("InChi", grrm2.inchi(molecule).get(), None))
context["moleculeInfo"].append(
("SMILES", grrm2.smiles(molecule).get(), None))
context["moleculeInfo"].append(
("Energy", grrm2.energy(molecule).get(), None))
context["moleculeInfo"].append(
("Charge", grrm2.charge(molecule).get(), None))
context["moleculeInfo"].append(
("Spin", grrm2.spin(molecule).get(), None))
context["moleculeInfo"].append(
("Structure Type", _getStructureType(molecule), None))
result = grrm2.InterconversionResult.tryCast(molecule)
if result:
context["moleculeInfo"].append(
("Structure Number", grrm2.structureNumber(result).get(),
None))
context["moleculeInfo"].append(
("Zero Point Vibrational Energy",
grrm2.zeroPointVibrationalEnergy(result).get(), None))
step = grrm2.InterconversionStep.tryCast(molecule)
if step:
context["moleculeInfo"].append(
("Interconversion Step", grrm2.stepNumber(step).get(), None))
context["moleculeInfo"].append(
("Belongs to interconversion",
grrm2.interconversionStepOf(step).get()[0].uri(),
"/resources/%7B" + utils.uriToUuid(
grrm2.interconversionStepOf(step).get()[0].uri()) +
"%7D"))
context["moleculeInfo"].append(
("CANOST canonical planar",
grrm2.canostSerialCanonical(molecule).get(), None))
context["moleculeInfo"].append(
("CANOST canonical serial",
grrm2.canostPlanarCanonical(molecule).get(), None))
context["moleculeInfo"].append(
("CANOST planar codes", grrm2.canostPlanar(molecule).get(), None))
context["moleculeInfo"].append(
("CANOST serial codes", grrm2.canostSerial(molecule).get(), None))
fragment_strings = []
if grrm2.fragments(molecule).get() is not None:
geometry = grrm2.geometry(molecule).get()
for fragment in grrm2.fragments(molecule).get():
symbols = [geometry["symbols"][i - 1] for i in fragment]
fragment_strings.append(chemistry.hillFormula(symbols))
context["moleculeInfo"].append(
("Fragments", "/".join(fragment_strings), None))
try:
run = grrm2.runOutputOf(molecule).get()[0]
context["moleculeInfo"].append(
("Run", run.uri(),
"/resources/%7B" + utils.uriToUuid(run.uri()) + "%7D"))
except Exception, e:
pass
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()))
def generateFormula(mol):
data = grrm2.geometry(mol).get()
formula = chemistry.hillFormula(data["symbols"])
return formula