fixes and speedups for chi1_selection/chi1_selections

* Fixes #4108
* recognize additional atom names (CG1 OG OG1 SG ) for chi1_selections() so that it works for 
  amino acids CYS, ILE, SER, THR, VAL instead of returning None (Issue #4108)
* performance improvement: make chi1_selection() faster using np functions instead of select_atoms()
* add tests for new residues
* update AUTHORS
* update CHANGELOG

package/AUTHORS

@@ -216,6 +216,7 @@ Chronological list of authors
   - Xiaoxu Ruan
   - Egor Marin
   - Shaivi Malik
+  - Daniel J. Evans
 
 External code
 -------------

package/CHANGELOG

@@ -21,6 +21,8 @@ The rules for this file:
  * 2.5.0
 
 Fixes
+  * Fix chi1_selections() ignored atom names CG1 OG OG1 SG and incorrectly returned
+    None for amino acids CYS, ILE, SER, THR, VAL (Issue #4108)
   * Fix parsing of box vector in H5MD reader (Issue #4076)
   * Fix the misleading 'AtomGroup.guess_bonds()' docs and passed missing
     arguments (PR #4059)
@@ -37,6 +39,7 @@ Fixes
     (Issue #3336)
 
 Enhancements
+  * Improved speed of chi1_selection (PR #4109)
   * Add `progressbar_kwargs` parameter to `AnalysisBase.run` method, allowing to modify description, position etc of tqdm progressbars.
   * Add a nojump transformation, which unwraps trajectories so that particle
     paths are continuous. (Issue #3703, PR #4031)

package/MDAnalysis/core/topologyattrs.py

@@ -1233,15 +1233,16 @@ def chi1_selection(residue, n_name='N', ca_name='CA', cb_name='CB',
            faster atom matching with boolean arrays.
         """
         names = [n_name, ca_name, cb_name, cg_name]
-        ags = [residue.atoms.select_atoms(f"name {n}") for n in names]
+        atnames = residue.atoms.names
+        ags = [residue.atoms[np.in1d(atnames, n.split())] for n in names]
         if any(len(ag) != 1 for ag in ags):
             return None
         return sum(ags)
 
     transplants[Residue].append(('chi1_selection', chi1_selection))
 
     def chi1_selections(residues, n_name='N', ca_name='CA', cb_name='CB',
-                        cg_name='CG'):
+                        cg_name='CG CG1 OG OG1 SG'):
         """Select list of AtomGroups corresponding to the chi1 sidechain dihedral
         N-CA-CB-CG.
 
@@ -1266,13 +1267,13 @@ def chi1_selections(residues, n_name='N', ca_name='CA', cb_name='CB',
         """
         results = np.array([None]*len(residues))
         names = [n_name, ca_name, cb_name, cg_name]
-        keep = [all(sum(r.atoms.names == n) == 1 for n in names)
-                for r in residues]
+        keep = [all(sum(np.in1d(r.atoms.names, n.split())) == 1
+                    for n in names) for r in residues]
         keepix = np.where(keep)[0]
         residues = residues[keep]
 
         atnames = residues.atoms.names
-        ags = [residues.atoms[atnames == n] for n in names]
+        ags = [residues.atoms[np.in1d(atnames, n.split())] for n in names]
         results[keepix] = [sum(atoms) for atoms in zip(*ags)]
         return list(results)
 

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -874,6 +874,12 @@ def test_chi1_selections(self, resgroup):
         rssel = [r.chi1_selection() for r in resgroup]
         assert_equal(rgsel, rssel)
 
+    @pytest.mark.parametrize("resname", ["CYS", "ILE", "SER", "THR", "VAL"])
+    def test_chi1_selections_non_cg(self, resname, PSFDCD):
+        resgroup = PSFDCD.select_atoms(f"resname {resname}").residues
+        rgsel = resgroup.chi1_selections()
+        assert not any(sel is None for sel in rgsel)
+
     @pytest.mark.parametrize("resname", ["CYSH", "ILE", "SER", "THR", "VAL"])
     def test_chi1_selection_non_cg_gromacs(self, resname, TPR):
         resgroup = TPR.select_atoms(f"resname {resname}").residues