Adapt code to make links add interactions per batch, removing overlap…

…ping interactions

Fixes #584

vermouth/molecule.py

@@ -577,7 +577,7 @@ def get_interaction(self, type_):
         """
         return self.interactions[type_]
 
-    def remove_interaction(self, type_, atoms, version=0):
+    def remove_interaction(self, type_, atoms, version=None):
         """
         Removes the specified interaction.
 
@@ -587,25 +587,27 @@ def remove_interaction(self, type_, atoms, version=0):
             The type of interaction, such as 'bonds' or 'angles'.
         atoms: collections.abc.Sequence
             The atoms that are involved in this interaction.
-        version: int
+        version: Optional[int]
             Sometimes there can be multiple distinct interactions between the
             same group of atoms. This is reflected with their `version` meta
             attribute.
+            If None, the version is not taken into account.
 
         Raises
         ------
         KeyError
             If the specified interaction could not be found
         """
-        idx = 0
+        to_remove = []
         for idx, interaction in enumerate(self.interactions[type_]):
-            if interaction.atoms == atoms and interaction.meta.get('version', 0) == version:
-                break
-        else:  # no break
+            if interaction.atoms == atoms and (version is None or interaction.meta.get('version', 0) == version):
+                to_remove.append(idx)
+        if not to_remove:
             msg = ("Can't find interaction of type {} between atoms {} "
                    "and with version {}")
             raise KeyError(msg.format(type_, atoms, version))
-        del self.interactions[type_][idx]
+        for idx in reversed(to_remove):
+            del self.interactions[type_][idx]
         if not self.interactions[type_]:
             del self.interactions[type_]
 

vermouth/processors/do_links.py

@@ -313,8 +313,15 @@ def run_molecule(self, molecule):
                         except ValueError:
                             pass
                 for inter_type, interactions in link.interactions.items():
+                    interactions_to_add = []
                     for interaction in interactions:
                         interaction = _build_link_interaction_from(molecule, interaction, match)
+                        interactions_to_add.append(interaction)
+                        try:
+                            molecule.remove_interaction(inter_type, interaction.atoms, version=None)
+                        except KeyError:
+                            pass
+                    for interaction in interactions_to_add:
                         molecule.add_or_replace_interaction(inter_type, *interaction, link.citations)
 
                 for loglevel, entries in link.log_entries.items():