Missing GO term in networkx Graph

[vizkidd]

I get this error for some PDB files in a list

Traceback (most recent call last):
File "/home/vishvesh/DeepFRI/predict_fast.py", line 136, in <module>
predicted_goterms = explode_all_goterms(predicted_goterms)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vishvesh/DeepFRI/predict_fast.py", line 59, in explode_all_goterms
for parent in explode_goterm(goterm):
^^^^^^^^^^^^^^^^^^^^^^
File "/home/vishvesh/DeepFRI/predict_fast.py", line 49, in explode_goterm
tmp = list(networkx.predecessor(graph, goterm).keys())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<class 'networkx.utils.decorators.argmap'> compilation 4", line 3, in argmap_predecessor_1
File "/home/vishvesh/deepfri-env/lib/python3.11/site-packages/networkx/utils/backends.py", line 535, in _call_if_no_backends_installed
return self.orig_func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/vishvesh/deepfri-env/lib/python3.11/site-packages/networkx/algorithms/shortest_paths/unweighted.py", line 528, in predecessor
raise nx.NodeNotFound(f"Source {source} not in G")
networkx.exception.NodeNotFound: Source GO:0008022 not in G

I assume the missing GO terms to be at the tips.

Possible Solution:

To enclose the contents of explode_goterm() within a try-catch block and return and empty list for exceptions

def explode_goterm(goterm):
# get name of the GO term
try:
tmp = list(networkx.predecessor(graph, goterm).keys())
return tmp
except:
print(f"GO term {goterm} not found in the GO graph.")
return []