Change syntax to remove ghost ports (#995)

* Change syntax to remove ghost ports

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* also remove label from when removing port

* add unit test

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: daico007

mbuild/compound.py

@@ -833,17 +833,24 @@ def _check_if_empty(child):
                 removed_part.parent.children.remove(removed_part)
             self._remove_references(removed_part)
 
-        # Remove ghost ports
-        all_ports_list = list(self.all_ports())
-        for port in all_ports_list:
-            if port.anchor not in [i for i in self.particles()]:
-                port.parent.children.remove(port)
-
         # Check and reorder rigid id
         for _ in particles_to_remove:
             if self.contains_rigid:
                 self.root._reorder_rigid_ids()
 
+        # Remove ghsot ports
+        self._prune_ghost_ports()
+
+    def _prune_ghost_ports(self):
+        """Worker for remove(). Remove all ports whose anchor has been deleted."""
+        all_ports_list = list(self.all_ports())
+        particles = list(self.particles())
+        for port in all_ports_list:
+            if port.anchor not in particles:
+                self._remove(port)
+                port.parent.children.remove(port)
+                self._remove_references(port)
+
     def _remove(self, removed_part):
         """Worker for remove(). Fixes rigid IDs and removes bonds."""
         if removed_part.rigid_id is not None:

mbuild/tests/test_compound.py

@@ -1278,6 +1278,20 @@ def test_add_bond_remove_ports(self, hydrogen):
         assert len(hydrogen.all_ports()) == 0
         assert len(h_clone.all_ports()) == 0
 
+    def test_pruning_ghost_ports(self, ethane):
+        eth1 = ethane
+        h1 = eth1.particles_by_name("H")
+        eth1.remove(h1)
+        assert len(eth1.all_ports()) == 6
+        for port in eth1.all_ports():
+            assert port.anchor in list(eth1.particles())
+
+        eth2 = mb.load("CC", smiles=True)
+        h2 = eth2[-1]
+        eth2.remove(h2)
+        assert len(eth2.all_ports()) == len(eth2.available_ports()) == 1
+        assert eth2.all_ports()[0] is eth2.available_ports()[0]
+
     def test_remove_bond_add_ports(self, hydrogen):
         h_clone = mb.clone(hydrogen)
         h2 = Compound(subcompounds=(hydrogen, h_clone))