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Kappa-Dev / KAMI

Bio-curation library for modelling cellular signalling
MIT License
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No edge from Residue to Site (or Region) when creating a Binding #5

Closed slegare2 closed 6 years ago

slegare2 commented 6 years ago

I want to create interaction: GRB2 binds EGFR through GRB2's Region SH2 and EGFR's Site motif1092 if EGFR Residue Y1092 is phosphorylated. I use the following Kami interaction: 

b = Binding(
    [SiteActor(gene=Gene(uniprotid="P00533", hgnc_symbol="EGFR",
                         residues=[Residue("Y", 1092, state=State("phosphorylation", True))]),
               site=Site(name="motif1092", start=1088, end=1096))],
    [RegionActor(gene=Gene("P62993",  hgnc_symbol="GRB2"), region=sh2)]
)

Everything works as expected, except that there is no edge between Residue Y1092 and Site motif1092.

This issue does not happen with Modification and is independent of whether the anatomizer is used or not.