bugfix: run Molck before any selection statement

Corrupt residues may have some properties missing => Select("peptide=true")
may give an empty view.

modules/mol/alg/pymod/scoring.py

@@ -130,11 +130,29 @@ class Scorer:
                  molck_settings = None, naive_chain_mapping_thresh=12,
                  cad_score_exec = None, custom_mapping=None):
 
-        model = model.Select("peptide=True or nucleotide=True")
-        self._model = mol.CreateEntityFromView(model, False)
+        if isinstance(model, mol.EntityView):
+            model = mol.CreateEntityFromView(model, False)
+        else:
+            model = model.Copy()
 
-        target = target.Select("peptide=True or nucleotide=True")
-        self._target = mol.CreateEntityFromView(target, False)
+        if isinstance(target, mol.EntityView):
+            target = mol.CreateEntityFromView(target, False)
+        else:
+            target = target.Copy()
+
+        if molck_settings is None:
+            molck_settings = MolckSettings(rm_unk_atoms=True,
+                                           rm_non_std=False,
+                                           rm_hyd_atoms=True,
+                                           rm_oxt_atoms=True,
+                                           rm_zero_occ_atoms=False,
+                                           colored=False,
+                                           map_nonstd_res=True,
+                                           assign_elem=True)
+        Molck(model, conop.GetDefaultLib(), molck_settings)
+        Molck(target, conop.GetDefaultLib(), molck_settings)
+        self._model = model.Select("peptide=True or nucleotide=True")
+        self._target = target.Select("peptide=True or nucleotide=True")
 
         # catch models which have empty chain names
         for ch in self._model.chains:
@@ -174,17 +192,6 @@ class Scorer:
                                        "must be strictly increasing if "
                                        "resnum_alignments are enabled")
 
-        if molck_settings is None:
-            molck_settings = MolckSettings(rm_unk_atoms=True,
-                                           rm_non_std=False,
-                                           rm_hyd_atoms=True,
-                                           rm_oxt_atoms=True,
-                                           rm_zero_occ_atoms=False,
-                                           colored=False,
-                                           map_nonstd_res=True,
-                                           assign_elem=True)
-        Molck(self._model, conop.GetDefaultLib(), molck_settings)
-        Molck(self._target, conop.GetDefaultLib(), molck_settings)
         self.resnum_alignments = resnum_alignments
         self.naive_chain_mapping_thresh = naive_chain_mapping_thresh
         self.cad_score_exec = cad_score_exec