Multiple mutate fixes

.gitignore

@@ -17,3 +17,5 @@ htmlcov
 doc/build
 doc/source/api
 doc/source/.doctrees
+
+.idea/

vermouth/data/quotes.txt

@@ -35,3 +35,5 @@ Happiness is a dry martini and a good woman... or a bad woman. -- George Burns
 A classical Martini is made without Vermouth, although it is better with. -- Peter C Kroon
 
 A classical Martini is made with up to 2 sizes of olives, although newer variants can contain up to three sizes of olives. -- Peter C Kroon
+
+So I said 'I must get out of these wet clothes, and into a dry Martini' -- Homer Simpson

vermouth/processors/annotate_mut_mod.py

@@ -176,6 +176,22 @@ def _format_resname(res):
     out += res.get('insertion_code', '')
     return out
 
+def _resiter(mod, residue_graph, resspec, library, key, molecule):
+    mod_found = False
+    for res_idx in residue_graph:
+        if residue_matches(resspec, residue_graph, res_idx):
+            mod_found = True
+            if mod != 'none' and mod not in library:
+                raise NameError('{} is not known as a {} for '
+                                'force field {}'
+                                ''.format(mod, key, molecule.force_field.name))
+            res = residue_graph.nodes[res_idx]
+            LOGGER.debug('Annotating {} with {} {}',
+                         _format_resname(res), key, mod)
+            for node_idx in res['graph']:
+                molecule.nodes[node_idx][key] = molecule.nodes[node_idx].get(key, []) + [mod]
+    return mod_found
+
 
 def annotate_modifications(molecule, modifications, mutations):
     """
@@ -219,39 +235,14 @@ def annotate_modifications(molecule, modifications, mutations):
         for resspec, mod in mutmod:
             # Ie. the target residue is chain specific
             if (resspec.get('chain') is not None) and (resspec.get('chain') == chain):
-                mod_found = False
-                for res_idx in residue_graph:
-                    if residue_matches(resspec, residue_graph, res_idx):
-                        mod_found = True
-                        if mod != 'none' and mod not in library:
-                            raise NameError('{} is not known as a {} for '
-                                            'force field {}'
-                                            ''.format(mod, key, molecule.force_field.name))
-                        res = residue_graph.nodes[res_idx]
-                        LOGGER.debug('Annotating {} with {} {}',
-                                     _format_resname(res), key, mod)
-                        for node_idx in res['graph']:
-                            molecule.nodes[node_idx][key] = molecule.nodes[node_idx].get(key, []) + [mod]
+                mod_found = _resiter(mod, residue_graph, resspec, library, key, molecule)
                 if mod_found == False:
                     LOGGER.warning('Mutation "{}" not found. '
                                    'Check target resid!'
                                    ''.format(_format_resname(resspec)))
             # If instead we're targeting all residues in the chain
             elif resspec.get(chain) == None:
-                for res_idx in residue_graph:
-                    if residue_matches(resspec, residue_graph, res_idx):
-                        mod_found = True
-                        if mod != 'none' and mod not in library:
-                            raise NameError('{} is not known as a {} for '
-                                            'force field {}'
-                                            ''.format(mod, key, molecule.force_field.name))
-                        res = residue_graph.nodes[res_idx]
-                        LOGGER.debug('Annotating {} with {} {}',
-                                     _format_resname(res), key, mod)
-                        for node_idx in res['graph']:
-                            molecule.nodes[node_idx][key] = molecule.nodes[node_idx].get(key, []) + [mod]
-
-
+                _resiter(mod, residue_graph, resspec, library, key, molecule)
 
 class AnnotateMutMod(Processor):
     """
@@ -283,8 +274,5 @@ def run_molecule(self, molecule):
         annotate_modifications(molecule, self.modifications, self.mutations)
         return molecule
     def run_system(self, system):
-        mols = []
-        for molecule in system.molecules:
-            mols.append(self.run_molecule(molecule))
-        system.molecules = mols
+        super().run_system(system)