Fixes #4924 #4961
Fixes #4924 #4961
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… generate_kirchoff: fix residue_index_map generate to avoid use all atoms when select is 'name CA'
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4961 +/- ##
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- Coverage 93.42% 93.41% -0.02%
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Files 177 189 +12
Lines 21859 22925 +1066
Branches 3078 3078
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+ Hits 20422 21415 +993
- Misses 986 1059 +73
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Can you add a new test that shows that the bug has been fixed?
The test should FAIL without your fix and PASS with your fix.
The test should be added to testsuite/MDAnalysisTests/analysis/test_gnm.py.
…alysis - Add test case to verify correct behavior when selecting 'name CA' atoms - Ensure that all residues are included in the analysis, fixing the issue where only residues 0-14 were used - Validate the results against expected eigenvalues and Kirchhoff matrix
… readability - Improved code formatting and line breaks for better readability
I did not read the original paper on the algorithm, but I tried to optimize the code for speed and studied it in detail. I think it is because we get fewer contacts in a residue with selection Here are the diffrent values with different selections in the test case:
The value increases as the number of atoms increases. This fix also corrects the case in 'backbone'. |
… eigenvalue comparison
- Lowered precision in eigenvalue comparison to accommodate platform-specific results - Added comment about platform-specific results to explain the change in expected values
[… generate_kirchoff: fix residue_index_map generate to avoid use all atoms when select is 'name CA'](fix-bug: package/MDAnalysis/analysis/gnm.py: closeContactGNMAnalysis: generate_kirchoff: fix residue_index_map generate to avoid use all atoms when select is 'name CA')
Fixes #4924
Changes made in this Pull Request:
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📚 Documentation preview 📚: https://mdanalysis--4961.org.readthedocs.build/en/4961/