dihedral selection (phi,psi,omega,chi1) methods can handle empty grou…

…ps (#4529)

* Fixes #2879
* The AtomGroup methods phi_selections(), psi_selections(), omega_selections(), chi1_selections() 
  can now handle empty groups
  NOTE: Since the methods return a list of atom groups, the methods will also return an empty list
* add tests
* update AUTHORS and CHANGELOG

package/AUTHORS

@@ -236,11 +236,13 @@ Chronological list of authors
   2024
   - Aditya Keshari
   - Philipp Stärk
+  - Kai Niklas Spauszus
   - Sampurna Mukherjee
   - Leon Wehrhan
   - Valerij Talagayev
 
 
+
 External code
 -------------
 

package/CHANGELOG

@@ -16,13 +16,13 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
-         tyler.je.reddy, SampurnaM, leonwehrhan
-
+         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs
 
  * 2.8.0
 
 Fixes
- * Add support for TPR files produced by Gromacs 2024.1
+ * Atomname methods can handle empty groups (Issue #2879, PR #4529)
+ * Add support for TPR files produced by Gromacs 2024.1 (PR #4523)
  * Remove mutable data from ``progressbar_kwargs`` argument in ``AnalysisBase.run()``
    (PR #4459)
  * Fix ChainReader `__repr__()` method when sub-reader is MemoryReader 

package/MDAnalysis/core/topologyattrs.py

@@ -866,6 +866,9 @@ def phi_selections(residues, c_name='C', n_name='N', ca_name='CA'):
         .. versionadded:: 1.0.0
         """
 
+        if not residues:
+            return []
+
         u = residues[0].universe
         prev = u.residues[residues.ix-1]  # obv candidates first
         rsid = residues.segids
@@ -1062,6 +1065,10 @@ def psi_selections(residues, c_name='C', n_name='N', ca_name='CA'):
 
         .. versionadded:: 1.0.0
         """
+
+        if not residues:
+            return []
+
         results = np.array([None]*len(residues), dtype=object)
         nxtres = residues._get_next_residues_by_resid()
         rix = np.where(nxtres)[0]
@@ -1170,6 +1177,10 @@ def omega_selections(residues, c_name='C', n_name='N', ca_name='CA'):
 
         .. versionadded:: 1.0.0
         """
+
+        if not residues:
+            return []
+
         results = np.array([None]*len(residues), dtype=object)
         nxtres = residues._get_next_residues_by_resid()
         rix = np.where(nxtres)[0]
@@ -1267,6 +1278,10 @@ def chi1_selections(residues, n_name='N', ca_name='CA', cb_name='CB',
 
         .. versionadded:: 1.0.0
         """
+
+        if not residues:
+            return []
+
         results = np.array([None]*len(residues))
         names = [n_name, ca_name, cb_name, cg_name]
         keep = [all(sum(np.isin(r.atoms.names, n.split())) == 1

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -748,6 +748,10 @@ def test_phi_selections_single(self, GRO):
         assert_equal(phisel.residues.resids, [9, 10])
         assert_equal(phisel.residues.resnames, ['PRO', 'GLY'])
 
+    def test_phi_selections_empty(self, GRO):
+        rgsel = GRO.segments[0].residues[[]].phi_selections()
+        assert len(rgsel) == 0
+
     def test_phi_selections(self, resgroup):
         rgsel = resgroup.phi_selections()
         rssel = [r.phi_selection() for r in resgroup]
@@ -788,6 +792,10 @@ def test_psi_selections_single(self, GRO):
         assert_equal(psisel.residues.resids, [10, 11])
         assert_equal(psisel.residues.resnames, ['GLY', 'ALA'])
 
+    def test_psi_selections_empty(self, GRO):
+        rgsel = GRO.segments[0].residues[[]].psi_selections()
+        assert len(rgsel) == 0
+
     def test_psi_selections(self, resgroup):
         rgsel = resgroup.psi_selections()
         rssel = [r.psi_selection() for r in resgroup]
@@ -820,6 +828,10 @@ def test_omega_selection_name(self, GRO, kwargs, names):
         assert_equal(osel.residues.resids, [8, 9])
         assert_equal(osel.residues.resnames, ['ALA', 'PRO'])
 
+    def test_omega_selections_empty(self, GRO):
+        rgsel = GRO.segments[0].residues[[]].omega_selections()
+        assert len(rgsel) == 0
+
     def test_omega_selections_single(self, GRO):
         rgsel = GRO.segments[0].residues[[7]].omega_selections()
         assert len(rgsel) == 1
@@ -869,6 +881,10 @@ def test_chi1_selections_single(self, GRO):
         assert_equal(sel.residues.resids, [13])
         assert_equal(sel.residues.resnames, ['LYS'])
 
+    def test_chi1_selections_empty(self, GRO):
+        rgsel = GRO.segments[0].residues[[]].chi1_selections()
+        assert len(rgsel) == 0
+
     def test_chi1_selections(self, resgroup):
         rgsel = resgroup.chi1_selections()
         rssel = [r.chi1_selection() for r in resgroup]