Fix bug breaking ala and gly rotamer ensembels when eval_clash = True

src/chilife/RotamerEnsemble.py

@@ -462,7 +462,7 @@ def protein_setup(self):
             raise RuntimeError('Both `minimize` and `eval_clash` options have been selected, but they are incompatible.'
                                'Please select only one. Also note that minimize performs its own clash evaluations so '
                                'eval_clash is not necessary.')
-        elif self.eval_clash:
+        elif self.eval_clash and len(self.side_chain_idx):
             self.evaluate()
 
         elif self._minimize:

src/chilife/__init__.py

@@ -44,4 +44,4 @@
 # SpinLabel = SpinLabel.SpinLabel
 # dSpinLabel = dSpinLabel.dSpinLabel
 
-__version__ = "1.2.4"
+__version__ = "1.2.5"

src/chilife/io.py

@@ -432,7 +432,9 @@ def read_bbdep(res: str, Phi: int, Psi: int) -> Dict:
 
     else:
         lib["weights"] = np.array([1])
-        lib["dihedrals"], lib["sigmas"], dihedral_atoms = [], [], []
+        lib["dihedrals"] = np.zeros((1, 0))
+        lib["sigmas"] = np.zeros((1, 0))
+        dihedral_atoms = []
         coords = ICs.to_cartesian()[None, ...]
         internal_coords = ICs.copy()
 

tests/test_ProteinUtils.py

@@ -179,6 +179,15 @@ def test_mutate3():
     assert len(labeled_protein.atoms) != len(protein.atoms)
 
 
+def test_mutate_ala_gly_eval_clash():
+    protein = mda.Universe("test_data/1omp_H.pdb").select_atoms("protein")
+    D41G = chilife.RotamerEnsemble("GLY", 41, protein=protein)
+    S238A = chilife.RotamerEnsemble("ALA", 238, protein=protein)
+    mPro = chilife.mutate(protein, D41G, S238A, add_missing_atoms=False)
+    assert mPro.select_atoms("resnum 41").residues[0].resname == "GLY"
+    assert mPro.select_atoms("resnum 238").residues[0].resname == "ALA"
+
+
 def test_mutate4():
     protein = mda.Universe("test_data/1omp_H.pdb").select_atoms("protein")
     D41G = chilife.RotamerEnsemble("GLY", 41, protein=protein, eval_clash=False)