from kami.entities import (Gene, Region, Site, Residue, State, RegionActor,
SiteActor)
from kami.interactions import (Binding, Unbinding, Modification,
TransModification, AutoModification,
AnonymousModification)
from kami.hierarchy import (KamiHierarchy)
from regraph import print_graph
inter = AnonymousModification(
substrate=Gene(uniprotid="P06239",
hgnc_symbol="LCK"),
target=Residue(aa="Y", loc=394,
state=State("phosphorylation", True)),
value=False,
rate=0.01
)
print(inter)
hierarchy = KamiHierarchy()
hierarchy.add_interaction(inter, anatomize=False)
print("printing nugget_1")
print_graph(hierarchy.graph['nugget_1'])
i get this error:
AnonymousModification:
Substrate: P06239
Mod target: Y394
Value: False
Rate: 0.01
Traceback (most recent call last):
File "anonymousmod.py", line 21, in <module>
hierarchy.add_interaction(inter, anatomize=False)
File "/home/slegare/ENS/venv_meta_update/lib/python3.6/site-packages/kami-1.2-py3.6.egg/kami/hierarchy.py", line 840, in add_interaction
nugget, nugget_type = generator.generate(interaction)
File "/home/slegare/ENS/venv_meta_update/lib/python3.6/site-packages/kami-1.2-py3.6.egg/kami/aggregation/generators.py", line 456, in generate
nugget, mod.enzyme)
File "/home/slegare/ENS/venv_meta_update/lib/python3.6/site-packages/kami-1.2-py3.6.egg/kami/aggregation/generators.py", line 399, in _generate_actor
"Unkown type of a PPI actor: '%s'" % type(actor)
kami.exceptions.NuggetGenerationError: Unkown type of a PPI actor: '<class 'NoneType'>'
With the following script:
i get this error: