Kappa-Dev / KAMI

Bio-curation library for modelling cellular signalling
MIT License
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kinase activity notation not updated #14

Closed slegare2 closed 6 years ago

slegare2 commented 6 years ago

For kinase activity state nodes, I still get {'activity': {True}} instead of {'name': {'activity'}, 'test': {'true'}}

import json
import pickle
from kami.entities import (Gene, Region, Site, Residue, State, RegionActor, SiteActor)
from kami.interactions import (Binding, Modification)
from kami.hierarchy import (KamiHierarchy)
from kami.export.old_kami import get_studio_v1
from regraph import print_graph

b1 = Binding(
        left=SiteActor(gene=Gene(uniprotid="P00533",
                                 hgnc_symbol="EGFR"),
                       site=Site(name="pY",
                                 residues=[Residue(aa="Y", loc=1092, 
                                           state=State("phosphorylation", "true"))],
                                 start=1088, end=1096)),
        right=RegionActor(gene=Gene(uniprotid="P62993",
                                    hgnc_symbol="GRB2"),
                          region=Region(name="SH2"))
)

print(b1)

hierarchy = KamiHierarchy()
hierarchy.add_interaction(b1, anatomize=True)

print_graph(hierarchy.graph['action_graph'])
print('---')
print(hierarchy.graph['action_graph']
               .node['P00533_region_Ser-Thr/Tyr_kinase_cat_dom Prot_kinase_'
                     'dom Tyr_kinase_cat_dom_IPR001245-IPR000719-IPR020635_'
                     '712_979_Tyr_kinase_activity'])
slegare2 commented 6 years ago

Ok, this seems to work now