GNMAnalysis fixes #4924 (#4961)

* fix #4924
* 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'
* docs(AUTHORS): add BHM-Bob G to the list of authors
* test(gnm): add test case for 'name CA' selection in closeContactGNMAnalysis
* 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

* test(gnm): reformat test_closeContactGNMAnalysis_select_CA for better readability

- Improved code formatting and line breaks for better readability

* test(gnm): Update the test to use a higher precision (decimal=17) for eigenvalue comparison

* docs(changelog): Add fix for bug in `analysis/gnm.py` in `closeContactGNMAnalysis`

* test(gnm): relax precision in CloseContactGNMAnalysis eigenvalue test

- Lowered precision in eigenvalue comparison to accommodate platform-specific results
- Added comment about platform-specific results to explain the change in expected values

* test(gnm): fit linters / black

---------

Co-authored-by: Oliver Beckstein <[email protected]>

Author: BHM-Bob

package/AUTHORS

@@ -250,6 +250,7 @@ Chronological list of authors
   - Joshua Raphael Uy 
   - Namir Oues
   - Lexi Xu
+  - BHM-Bob G    
 
 External code
 -------------

package/CHANGELOG

@@ -14,12 +14,15 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, orbeckst
+??/??/?? IAlibay, orbeckst, BHM-Bob
 
 
  * 2.10.0
 
 Fixes
+ * Fixes bug in `analysis/gnm.py`: `closeContactGNMAnalysis`: correct the
+   `residue_index_map` generation when selection is not `protein`.
+   (Issue #4924, PR #4961)
 
 Enhancements
 

package/MDAnalysis/analysis/gnm.py

@@ -458,11 +458,7 @@ def __init__(
     def generate_kirchoff(self):
         nresidues = self.ca.n_residues
         positions = self.ca.positions
-        residue_index_map = [
-            resnum
-            for [resnum, residue] in enumerate(self.ca.residues)
-            for atom in residue.atoms
-        ]
+        residue_index_map = self.ca.resindices.copy()
         matrix = np.zeros((nresidues, nresidues), dtype=np.float64)
         cutoffsq = self.cutoff**2
 

testsuite/MDAnalysisTests/analysis/test_gnm.py

@@ -175,3 +175,47 @@ def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis):
         ]
     )
     # fmt: on
+
+
+def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis):
+    # Issue #4924 fix the bug of CA selection
+    gnm = mda.analysis.gnm.closeContactGNMAnalysis(
+        universe, "name CA", weights=None
+    )
+    gnm.run(stop=2, **client_GNMAnalysis)
+    result = gnm.results
+    assert len(result.times) == 2
+    assert_almost_equal(gnm.results.times, (0, 100), decimal=4)
+    # without Issue #4924 fix, eigenvalues are [3.20010632e-16, 4.27574601e-16]
+    # but use big totolerance to make sure PASS in each platform
+    assert_almost_equal(
+        gnm.results.eigenvalues,
+        [3.57984776e-16, 3.53892581e-16],
+    )
+    gen = gnm.generate_kirchoff()
+    # without Issue #4924 fix, gnm only use 0~14 residues for this data
+    assert np.abs(gen[15]).sum() > 0
+    # fmt: off
+    assert_almost_equal(
+        gen[0],
+        [
+            1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+            0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+        ]
+    )
+    # fmt: on