reset_labels kwarg to force_overlap, new method reset_labels

mbuild/compound.py

@@ -1013,14 +1013,14 @@ def add(
                     "outside of the defined simulation box"
                 )
 
-    def remove(self, objs_to_remove, reset_labels=True):
+    def remove(self, objs_to_remove, reset_labels=False):
         """Remove children from the Compound cleanly.
 
         Parameters
         ----------
         objs_to_remove : mb.Compound or list of mb.Compound
             The Compound(s) to be removed from self
-        reset_labels : bool
+        reset_labels : bool, optional, default=False
             If True, the Compound labels will be reset
         """
         # Preprocessing and validating input type
@@ -1087,51 +1087,55 @@ def _check_if_empty(child):
 
         # Reorder labels
         if reset_labels:
-            new_labels = OrderedDict()
-            hoisted_children = {
-                key: val
-                for key, val in self.labels.items()
-                if (
-                    not isinstance(val, list)
-                    and val.parent is not None
-                    and id(self) != id(val.parent)
-                )
-            }
-            new_labels.update(hoisted_children)
-            children_list = {
-                id(val): [key, val]
-                for key, val in self.labels.items()
-                if (not isinstance(val, list))
-            }
-            for child in self.children:
-                label = (
-                    children_list[id(child)][0]
-                    if "[" not in children_list[id(child)][0]
-                    else None
-                )
-                if label is None:
-                    if "Port" in child.name:
-                        label = [
-                            key
-                            for key, x in self.labels.items()
-                            if id(x) == id(child)
-                        ][0]
-                        if "port" in label:
-                            label = "port[$]"
-                    else:
-                        label = f"{child.name}[$]"
-
-                if label.endswith("[$]"):
-                    label = label[:-3]
-                    if label not in new_labels:
-                        new_labels[label] = []
-                    label_pattern = label + "[{}]"
-
-                    count = len(new_labels[label])
-                    new_labels[label].append(child)
-                    label = label_pattern.format(count)
-                new_labels[label] = child
-            self.labels = new_labels
+            self.reset_labels()
+
+    def reset_labels(self):
+        """Reset Compound labels so that substituents and ports are renumbered, indexed from port[0] to port[N], where N-1 is the number of ports."""
+        new_labels = OrderedDict()
+        hoisted_children = {
+            key: val
+            for key, val in self.labels.items()
+            if (
+                not isinstance(val, list)
+                and val.parent is not None
+                and id(self) != id(val.parent)
+            )
+        }
+        new_labels.update(hoisted_children)
+        children_list = {
+            id(val): [key, val]
+            for key, val in self.labels.items()
+            if (not isinstance(val, list))
+        }
+        for child in self.children:
+            label = (
+                children_list[id(child)][0]
+                if "[" not in children_list[id(child)][0]
+                else None
+            )
+            if label is None:
+                if "Port" in child.name:
+                    label = [
+                        key
+                        for key, x in self.labels.items()
+                        if id(x) == id(child)
+                    ][0]
+                    if "port" in label:
+                        label = "port[$]"
+                else:
+                    label = "{0}[$]".format(child.name)
+
+            if label.endswith("[$]"):
+                label = label[:-3]
+                if label not in new_labels:
+                    new_labels[label] = []
+                label_pattern = label + "[{}]"
+
+                count = len(new_labels[label])
+                new_labels[label].append(child)
+                label = label_pattern.format(count)
+            new_labels[label] = child
+        self.labels = new_labels
 
     def _prune_ghost_ports(self):
         """Worker for remove(). Remove all ports whose anchor has been deleted."""

mbuild/coordinate_transform.py

@@ -16,7 +16,9 @@
 ]
 
 
-def force_overlap(move_this, from_positions, to_positions, add_bond=True):
+def force_overlap(
+    move_this, from_positions, to_positions, add_bond=True, reset_labels=False
+):
     """Move a Compound such that a position overlaps with another.
 
     Computes an affine transformation that maps the from_positions to the
@@ -33,6 +35,8 @@ def force_overlap(move_this, from_positions, to_positions, add_bond=True):
     add_bond : bool, optional, default=True
         If `from_positions` and `to_positions` are `Ports`, create a bond
         between the two anchor atoms.
+    reset_labels : bool, optional, default=False
+        If True, the Compound labels will be reset, renumbered using the Compound.reset_labels methods
     """
     from mbuild.port import Port
 
@@ -67,8 +71,12 @@ def force_overlap(move_this, from_positions, to_positions, add_bond=True):
                 to_positions.anchor.parent.add_bond(
                     (from_positions.anchor, to_positions.anchor)
                 )
-                from_positions.anchor.parent.remove(from_positions)
-                to_positions.anchor.parent.remove(to_positions)
+                from_positions.anchor.parent.remove(
+                    from_positions, reset_labels=reset_labels
+                )
+                to_positions.anchor.parent.remove(
+                    to_positions, reset_labels=reset_labels
+                )
 
 
 class CoordinateTransform(object):

mbuild/tests/test_compound.py

@@ -915,9 +915,10 @@ def test_remove(self, ethane):
         ethane6 = mb.clone(ethane)
         ethane6.flatten()
         hydrogens = ethane6.particles_by_name("H")
-        ethane6.remove(hydrogens, reset_labels=False)
-
+        ethane6.remove(hydrogens)
         assert list(ethane6.labels.keys()) == [
+            "methyl1",
+            "methyl2",
             "C",
             "C[0]",
             "H",
@@ -934,7 +935,7 @@ def test_remove(self, ethane):
         ethane7 = mb.clone(ethane)
         ethane7.flatten()
         hydrogens = ethane7.particles_by_name("H")
-        ethane7.remove(hydrogens)
+        ethane7.remove(hydrogens, reset_labels=True)
 
         assert list(ethane7.labels.keys()) == [
             "C",