Modify graphs.py to handle insertions when {'insertions': True}
#223
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Codecov ReportBase: 40.27% // Head: 47.93% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #223 +/- ##
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+ Coverage 40.27% 47.93% +7.66%
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Files 48 85 +37
Lines 2811 5411 +2600
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+ Hits 1132 2594 +1462
- Misses 1679 2817 +1138
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Reference Issues/PRs
The centroid coordinates of protein graphs contain NaN values when the PDB file contains at least one insertion and when
{'insertions': True}is provided to ProteinGraphConfigWhat does this implement/fix? Explain your changes
Adding the
insertionidentifier in the node_id and in the centroid atom grouping function solves the problemWhat testing did you do to verify the changes in this PR?
Graph creation for 1i7z.
ex:
before modifications: ['A:ASP:1', 'A:LEU:2', 'A:PRO:95', 'A:TRP:96', ...]
G.coords #=> contains NaNsafter modifications:before modifications: ['A:ASP:1', 'A:LEU:2', 'A:PRO:95', 'A:TRP:96', ...]
G.coords #=> no NaNPull Request Checklist
./CHANGELOG.mdfile (if applicable)./graphein/tests/*directories (if applicable)./notebooks/(if applicable)python -m py.test tests/and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,python -m py.test tests/protein/test_graphs.py)black .andisort .