Closed bobleesj closed 1 month ago
The problem is fixed when the minimum number of points for polyhedron is 5 in src/cifkit/coordination/filter.py
within the function of find_best_polyhedron
.
# Only if there are 5 or more points in the polyhedron
if len(connection_data) > 4:
for connection in connection_data:
polyhedron_points.append(connection[3])
else:
continue
It appears that the issue is not solved.
The following error message is acquired with a different size value.
Processing 1421162.cif with 1782 atoms (134/152)
Error computing polyhedron metrics: index 6 is out of bounds for axis 0 with size 6
The problem is not observed during my pytest
run in my local machine: https://github.com/bobleesj/cif-bond-analyzer/actions/runs/9824087665/job/27122684319
but it appears that the issue occurs in CI
.
This needs a further investigation.
Another file:
3795 1831430.cif CN values: 12 Error computing polyhedron metrics: index 7 is out of bounds for axis 0 with size 7
Fixed the problem! In src/cifkit/coordination/filter.py
, the issue was that when there is a problem with computing the polyhedron metrics with a specific method, it returns None
. Now, I have added continue
for the None
case and it skips the method to be considered as one of the best methods.
# Returns none if ther eis any error
polyhedron_metrics = compute_polyhedron_metrics(
polyhedron_points, hull
)
# If there is no metrics, then skip the mthod
if polyhedron_metrics is None:
continue
Checklist
Describe the bug
Currently, I am investigating what the issue is