From fa68282771689ceeedf30abdaabb979e9b2cdf3f Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sat, 26 Oct 2024 13:19:11 +1100
Subject: [PATCH] remove "adding" fixes -- keep only "deletion" fixes

---
 package/MDAnalysis/core/topologyattrs.py      | 20 +++++++++++++------
 .../MDAnalysisTests/topology/test_pdb.py      |  4 ++--
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py
index 57e5cc84f5..e5cf003b5b 100644
--- a/package/MDAnalysis/core/topologyattrs.py
+++ b/package/MDAnalysis/core/topologyattrs.py
@@ -3042,12 +3042,19 @@ class _Connection(AtomAttr, metaclass=_ConnectionTopologyAttrMeta):
 
     @_check_connection_values
     def __init__(self, values, types=None, guessed=False, order=None):
-        self.values = []
-        self.types = []
-        self._guessed = []
-        self.order = []
+        self.values = values
+        if types is None:
+            types = [None] * len(values)
+        self.types = types
+        if guessed in (True, False):
+            # if single value passed, multiply this across
+            # all bonds
+            guessed = [guessed] * len(values)
+        self._guessed = guessed
+        if order is None:
+            order = [None] * len(values)
+        self.order = order
         self._cache = dict()
-        self._add_bonds(values, types, guessed, order)
 
     def copy(self):
         """Return a deepcopy of this attribute"""
@@ -3111,8 +3118,9 @@ def _add_bonds(self, values, types=None, guessed=True, order=None):
         if order is None:
             order = itertools.cycle((None,))
 
+        existing = set(self.values)
         for v, t, g, o in zip(values, types, guessed, order):
-            if v not in self.values:
+            if v not in existing:
                 self.values.append(v)
                 self.types.append(t)
                 self._guessed.append(g)
diff --git a/testsuite/MDAnalysisTests/topology/test_pdb.py b/testsuite/MDAnalysisTests/topology/test_pdb.py
index 93115a92d3..c176d50be1 100644
--- a/testsuite/MDAnalysisTests/topology/test_pdb.py
+++ b/testsuite/MDAnalysisTests/topology/test_pdb.py
@@ -146,7 +146,7 @@ def parse():
         struc = parse()
 
     assert hasattr(struc, 'bonds')
-    assert len(struc.bonds.values) == 2
+    assert len(struc.bonds.values) == 4
 
 
 def test_single_conect():
@@ -158,7 +158,7 @@ def parse():
     with pytest.warns(UserWarning):
         struc = parse()
     assert hasattr(struc, 'bonds')
-    assert len(struc.bonds.values) == 1
+    assert len(struc.bonds.values) == 2
 
 
 def test_new_chainid_new_res():