def insert_elements(coll):
print("adding missing elements.")
for z in range(1, 19):
el = Element.from_Z(z)
r = coll.find(filter={"formula": "{}1".format(el.symbol)})
if r.count() == 0:
try:
clean_mol = Molecule([el], [[0, 0, 0]])
xyz = XYZ(clean_mol)
bb = BabelMolAdaptor.from_string(str(xyz), "xyz")
pbmol = pb.Molecule(bb.openbabel_mol)
smiles = pbmol.write("smi").split()[0]
can = pbmol.write("can").split()[0]
inchi = pbmol.write("inchi")
svg = pbmol.write("svg")
d = {"molecule": clean_mol.as_dict()}
comp = clean_mol.composition
d["pretty_formula"] = comp.reduced_formula
d["formula"] = comp.formula
d["composition"] = comp.as_dict()
d["elements"] = list(comp.as_dict().keys())
d["nelements"] = len(comp)
d["charge"] = 0
d["spin_multiplicity"] = clean_mol.spin_multiplicity
d["smiles"] = smiles
d["can"] = can
d["inchi"] = inchi
# d["names"] = get_nih_names(smiles)
d["svg"] = svg
d["xyz"] = str(xyz)
d["tags"] = ["G305 test set"]
coll.insert(d)
except Exception as ex:
print("Error in {}".format(el))
elif r.count() > 1:
print("More than 1 {} found. Removing...".format(el))
results = list(r)
for r in results[1:]:
print(r["_id"])
coll.remove({"_id": r["_id"]})
if __name__ == '__main__':
task1 = WritelammpsInputFromGaussian()
task2 = WritelammpsOutputTask()
task3 = ParselammpsProperties()
coords = []
sp = []
solvent_molecules_path = os.path.join(
rubicon.__path__[0], 'workflows/test_mols/solvent_molecules')
moleculelist = glob.glob(solvent_molecules_path + '/*.pdb')
for filename in moleculelist:
mol = Molecule.from_file(filename)
for site in mol:
coords.append([c for c in site.coords])
sp.append(site.specie.symbol)
mol2 = Molecule(
sp,
coords,
site_properties={"mol_name": [filename[48:-4]] * len(coords)})
fw1 = Firework([task1],
name='Run Lammps',
spec={"molecules": [mol2.as_dict()]},
fw_id=1)
fw2 = Firework([task2], name='Lammps Log Parsing', fw_id=2)
fw3 = Firework([task3], name='Lammps Properties Parser', fw_id=3)
depen = {1: [2, 3]}
wf = Workflow([fw1, fw2, fw3], name="LAMMPS", links_dict=depen)
lp = LaunchPad.auto_load()
lp.add_wf(wf)
