def setUp(self):
lib = Library(name="JBS")
lib.save()
for frag_code in ["j001", "j002"]:
frag = Fragment(library=lib, code=frag_code, smiles="C")
frag.save()
def setUp(self):
mylib = Library(name="FragMAXlib")
mylib.save()
frag = Fragment(library=mylib,
code="VT00249",
smiles="O=C1N[C@@H](CO1)C1=CC=CC=C1")
frag.save()
def test_frag_svg(self):
"""
check that we can generate valid SVG for a simple fragment
"""
lib = Library(name="ZeLib")
lib.save()
frag = Fragment(library=lib, code="F1", smiles="C")
frag.save()
resp = self.client.get(reverse("fragment_svg", args=(frag.id, )))
self.assertEqual(200, resp.status_code)
self.assertEqual(resp["Content-Type"], "image/svg+xml")
self._assert_svg(resp.content)
def get_fragment_by_id(fragment_id: str) -> Fragment:
try:
fragment = Fragment.get_by_id(fragment_id)
except Fragment.DoesNotExist:
raise Http404(f"no fragment with id '{fragment_id}' exist")
return fragment
def get_crystals_fragment(crystal) -> Optional[Fragment]:
"""
get Crystal's Fragment, returns None for apo crystals
"""
if crystal.is_apo():
return None
return Fragment.get_by_id(crystal.fragment_id)
def get_fragment_id(crystal: Crystal) -> Optional[str]:
fragment = crystal.get_fragment()
if fragment is None:
# pony ORM uses empty string as 'None'
return ""
db_frag = Fragment.get(fragment.library, fragment.code)
return str(db_frag.id)
def _create_library(lib_desc: Dict):
lib_name = lib_desc["name"]
# check if this library already exist
if Library.objects.filter(name=lib_name).exists():
raise CommandError(
f"Fragments library '{lib_name}' already exists, refusing to overwrite."
)
lib = Library(name=lib_name)
lib.save()
for code, smiles in lib_desc["fragments"].items():
frag = Fragment(library=lib, code=code, smiles=smiles)
frag.save()
num_frags = len(lib_desc["fragments"].keys())
print(f"added library '{lib_name}' with {num_frags} fragments")
def get_project_libraries(project: Project) -> Set[Library]:
libs = set()
for crystal in project.get_crystals():
if crystal.is_apo():
continue
frag = Fragment.get_by_id(crystal.fragment_id)
libs.add(frag.library)
return libs
def _setup_frags_lib(self):
library = Library(name="TSLib")
library.save()
for n in range(3):
Fragment(library=library, code=f"T{n}", smiles="C").save()
def setUp(self):
mylib = Library(name="MyLib")
mylib.save()
frag = Fragment(library=mylib, code="VT000", smiles="CN1CCCC1CO")
frag.save()