add test case if idr regions but no secstruct.

- need to modify create_sys_all_attrs so cgsecstruct not always written
- remove duplicate annotation in annotate_idrs.py

vermouth/processors/annotate_idrs.py

@@ -41,7 +41,6 @@ def annotate_disorder(molecule, id_regions, annotation="cgidr"):
             molecule.nodes[key][annotation] = True
             if "cgsecstruct" in molecule.nodes[key]:
                 molecule.nodes[key]["cgsecstruct"] = "C"
-            molecule.nodes[key][annotation] = True  # ???
         else:
             molecule.nodes[key][annotation] = False
 

vermouth/tests/helper_functions.py

@@ -85,7 +85,7 @@ def find_in_path(names=('martinize2', 'martinize2.py')):
             if os.path.isfile(fullpath):
                 return fullpath
 
-def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs):
+def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs, write_secstruct=True):
     """
     Generate a test system from a molecule
     with all attributes set and blocks in
@@ -138,7 +138,8 @@ def create_sys_all_attrs(molecule, moltype, secstruc, defaults, attrs):
         resid = res_graph.nodes[node]['resid']
         # assign secondary structure
         for mol_node in mol_nodes:
-            molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid]
+            if write_secstruct:
+                molecule.nodes[mol_node]['cgsecstruct'] = secstruc[resid]
             block.add_node(molecule.nodes[mol_node]['atomname'],
                            atype=molecule.nodes[mol_node]['atype'])
 

vermouth/tests/test_annotate_idrs.py

@@ -59,20 +59,28 @@ def test_make_disorder_string(test_molecule,
             result.append(False)
     assert result == expected
 
-@pytest.mark.parametrize('idr_regions, expected',(
+@pytest.mark.parametrize('idr_regions, write_sec, expected',(
         ([(1, 4)],
+         True,
          {0: "C", 1: "C", 2: "C",
           3: "C", 4: "C",
           5: "C",
           6: "C", 7: "C", 8: "C"}),
         ([(1, 2)],
+         True,
          {0: "C", 1: "C", 2: "C",
           3: "C", 4: "C",
           5: "H",
           6: "H", 7: "H", 8: "H"}),
+        ([(1, 2)],
+         False,
+         {0: None, 1: None, 2: None,
+          3: None, 4: None,
+          5: None,
+          6: None, 7: None, 8: None})
 
 ))
-def test_ss_reassign(test_molecule, idr_regions, expected):
+def test_ss_reassign(test_molecule, idr_regions, write_sec, expected):
     secstruc = {1: "H", 2: "H", 3: "H", 4: "H"}
     resnames = {0: "A", 1: "A", 2: "A",
                 3: "B", 4: "B",
@@ -82,20 +90,16 @@ def test_ss_reassign(test_molecule, idr_regions, expected):
               3: "SP1", 4: "C1",
               5: "TP1",
               6: "P1", 7: "SN3a", 8: "SP4"}
-    cgsectruc = {0: "H", 1: "H", 2: "H",
-                 3: "H", 4: "H",
-                 5: "H",
-                 6: "H", 7: "H", 8: "H"}  # i.e. all ss is H to begin
 
     system = create_sys_all_attrs(test_molecule,
                                   moltype="molecule_0",
                                   secstruc=secstruc,
                                   defaults={"chain": "A"},
                                   attrs={"resname": resnames,
-                                         "atype": atypes,
-                                         "cgsecstruct": cgsectruc})
+                                         "atype": atypes},
+                                  write_secstruct=write_sec)
 
     AnnotateIDRs(id_regions=idr_regions).run_system(system)
 
     for key, node in system.molecules[0].nodes.items():
-        assert system.molecules[0].nodes[key]["cgsecstruct"] == expected[key]
+        assert system.molecules[0].nodes[key].get("cgsecstruct", None) == expected[key]