def get_single_cif(request: Request,
entry_id: str,
params: SingleEntryQueryParams = Depends()):
from optimade.adapters import Structure
response = get_single_entry(
collection=structures_coll,
entry_id=entry_id,
request=request,
params=params,
response=StructureResponseOne,
)
adapter = Structure(response.data.dict())
filename = entry_id.replace("/", "_") + ".cif"
headers = {
"Content-Type": "text/plain",
"Content-Disposition": f"attachment;filename={filename};",
}
cif_list = adapter.as_cif.split("\n")
num_lines = len(cif_list)
cif_generator = (f"{line}\n" if ind != num_lines - 1 else line
for ind, line in enumerate(cif_list))
return StreamingResponse(
cif_generator,
media_type="text/plain",
headers=headers,
)
def get_single_structure(request: Request,
entry_id: str,
params: SingleEntryQueryParams = Depends()):
return get_single_entry(
collection=structures_coll,
entry_id=entry_id,
response=StructureResponseOne,
request=request,
params=params,
)
def get_single_reference(
request: Request,
entry_id: str,
params: SingleEntryQueryParams = Depends()
) -> ReferenceResponseOne:
return get_single_entry(
collection=references_coll,
entry_id=entry_id,
response=ReferenceResponseOne,
request=request,
params=params,
)
def get_single_structure(request: Request,
entry_id: str,
params: SingleEntryQueryParams = Depends()):
response = get_single_entry(
collection=structures_coll,
entry_id=entry_id,
request=request,
params=params,
response=StructureResponseOne,
)
context = {"request": request, "entry_id": entry_id}
if response.meta.data_returned < 1:
return TEMPLATES.TemplateResponse("structure_not_found.html", context)
stoichiometry = get_stoich_from_formula(
response.data.attributes.chemical_formula_descriptive)
for ind, (elem, num) in enumerate(stoichiometry):
if num - int(num) > 1e-5:
raise RuntimeError("Unable to cast formula to correct format")
stoichiometry[ind][1] = int(num)
context.update({
"odbx_title": "odbx",
"odbx_blurb": "the open database of xtals",
"odbx_about":
'odbx is a public database of crystal structures from the group of <a href="https://ajm143.github.io">Dr Andrew Morris</a> at the University of Birmingham.',
"odbx_cif_string": optimade_to_basic_cif(response.data),
"structure_info": dict(response),
"cif_link": str(request.url).replace("structures/", "cif/"),
"stoichiometry": stoichiometry,
})
return TEMPLATES.TemplateResponse("structure.html", context)