def get_molecule_status(name, autoflip=False):
mol = gjfwriter.NamedMolecule(name, autoflip=autoflip)
name_error = mol.get_name_error()
error_report = ErrorReport.objects.filter(molecule=name).exists() or None
new = not DataPoint.objects.filter(
exact_name=mol.get_exact_name()).exists()
return mol, name_error, error_report, new
def write_svg(request, molecule):
mol_form = MoleculeForm(request.REQUEST)
mol_form.is_valid()
mol_settings = dict(mol_form.cleaned_data)
out = gjfwriter.NamedMolecule(molecule, **mol_settings)
response = HttpResponse(out.get_svg(), content_type="image/svg+xml")
response['Content-Disposition'] = 'filename=%s.svg' % molecule
return response
def save_names(names):
for name in names:
struct = gjfwriter.NamedMolecule(
name,
keywords="opt B3LYP/6-31g(d,p)",
nprocshared=12,
memory=30,
)
with open(name + ".gjf", 'w') as f:
f.write(struct.get_gjf())
def write_mol2(request, molecule):
mol_form = MoleculeForm(request.REQUEST)
mol_form.is_valid()
add = "" if request.REQUEST.get("view") else "attachment; "
mol_settings = dict(mol_form.cleaned_data)
out = gjfwriter.NamedMolecule(molecule, **mol_settings)
response = HttpResponse(out.get_mol2(), content_type="text/plain")
response['Content-Disposition'] = add + 'filename=%s.mol2' % molecule
return response
def run_name(name):
from chemtools import gjfwriter
mol = gjfwriter.NamedMolecule(name).structure
links, tree = breadth_first_search(mol)
cycles, link_nodes = get_cycles(links, tree)
pruned_cycles = prune_cycles(cycles, link_nodes)
fused = get_fused_cycles(pruned_cycles)
sorted_cycles = sort_fused_cycles(fused)
temp = identify_cycle_types(mol, sorted_cycles)
noncycles = get_noncycles(mol, pruned_cycles)
pruned_noncycles = prune_noncycles(noncycles)
temp2 = identify_noncycle_types(pruned_noncycles)
return set(temp + temp2)
def run_standard_jobs(credential, string, mol_settings, job_settings):
results = {
"worked": [],
"failed": [],
"error": None,
}
# This is to catch invalid users early on
try:
results["cluster"] = credential.cluster.name
if not credential.user.is_staff:
results["error"] = "You must be a staff user to submit a job."
return results
except Exception as e:
results["error"] = "Invalid credential"
results["cluster"] = None
return results
names = []
gjfs = []
for mol in name_expansion(string):
try:
out = gjfwriter.NamedMolecule(mol, **mol_settings)
# This instantiation needs to be done here because of the errors
# in a structure are calculated lazily.
gjf = out.get_gjf()
names.append(mol)
gjfs.append(gjf)
except Exception as e:
logger.warn("Failed gjf write -- %s -- %s" % (mol, e))
results["failed"].append((mol, str(e)))
continue
if names:
settings = {
k: v
for k, v in job_settings.items() + mol_settings.items()
}
temp = run_jobs(credential, names, gjfs, **settings)
results["worked"] = temp["worked"]
results["failed"].extend(temp["failed"])
results["error"] = temp["error"]
return results
def wrapper(request, molecule, *args, **kwargs):
if request.REQUEST.get("autoflip"):
mol = gjfwriter.NamedMolecule(molecule, autoflip=True)
return redirect(wrapper, mol.name)
return f(request, molecule, *args, **kwargs)