From 6ee7c17f1d41430e7bbc2ef48518549e78eb76cb Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 16:31:23 +1100
Subject: [PATCH 01/30] add tests

---
 .../MDAnalysisTests/guesser/test_base.py      | 52 ++++++++++++++++++-
 1 file changed, 51 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index b429826647..af10f9f6ad 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -27,10 +27,11 @@
 from MDAnalysis.core.topology import Topology
 from MDAnalysis.core.topologyattrs import Masses, Atomnames, Atomtypes
 import MDAnalysis.tests.datafiles as datafiles
+from MDAnalysis.exceptions import NoDataError
 from numpy.testing import assert_allclose, assert_equal
 
 
-class TesttBaseGuesser():
+class TestBaseGuesser():
 
     def test_get_guesser(self):
         class TestGuesser1(GuesserBase):
@@ -100,3 +101,52 @@ def test_partial_guess_attr_with_unknown_no_value_label(self):
         top = Topology(4, 1, 1, attrs=[names, types, ])
         u = mda.Universe(top, to_guess=['types'])
         assert_equal(u.atoms.types, ['', '', '', ''])
+
+    def test_guess_topology_objects_existing(self):
+        u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+        assert list(u.bonds[0].indices) == [0, 1]
+
+        # delete some bonds
+        u.delete_bonds(u.atoms.bonds[:100])
+        assert len(u.atoms.bonds) == 1822
+        assert list(u.bonds[0].indices) == [94, 99]
+
+        all_indices = [tuple(x.indices) for x in u.bonds]
+        assert (0, 1) not in all_indices
+        
+        # guess old bonds back
+        u.guess_TopologyAttrs("default", to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+        # check TopologyGroup contains new (old) bonds
+        assert list(u.bonds[0].indices) == [0, 1]
+
+    def test_guess_topology_objects_force(self):
+        u = mda.Universe(datafiles.CONECT, force_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+
+        with pytest.raises(NoDataError):
+            u.atoms.angles
+
+
+    def test_guess_topology_objects_out_of_order_init(self):
+        u = mda.Universe(
+            datafiles.PDB_small,
+            to_guess=["dihedrals", "angles", "bonds"],
+            guess_bonds=False
+        )
+        assert len(u.atoms.angles) == 6123
+        assert len(u.atoms.dihedrals) == 8921
+    
+    def test_guess_topology_objects_out_of_order_guess(self):
+        u = mda.Universe(datafiles.PDB_small)
+        with pytest.raises(NoDataError):
+            u.atoms.angles
+
+        u.guess_TopologyAttrs(
+            "default",
+            to_guess=["dihedrals", "angles", "bonds"]
+        )
+        assert len(u.atoms.angles) == 6123
+        assert len(u.atoms.dihedrals) == 8921
+

From ada696759d07f3e603d67eef9c3a545d47350500 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 16:33:22 +1100
Subject: [PATCH 02/30] special case connections

---
 package/MDAnalysis/guesser/base.py | 43 ++++++++++++++++++------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index aab0723aaa..f307a661b3 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -36,9 +36,9 @@
 .. autofunction:: get_guesser
 
 """
-from .. import _GUESSERS
+from .. import _GUESSERS, _TOPOLOGY_ATTRS
+from ..core.topologyattrs import _Connection
 import numpy as np
-from .. import _TOPOLOGY_ATTRS
 import logging
 from typing import Dict
 import copy
@@ -136,6 +136,11 @@ def guess_attr(self, attr_to_guess, force_guess=False):
         NDArray of guessed values
 
         """
+        try:
+            guesser_method = self._guesser_methods[attr_to_guess]
+        except KeyError:
+            raise ValueError(f'{type(self).__name__} cannot guess the following '
+                             f'attribute: {attr_to_guess}')
 
         # check if the topology already has the attribute to partially guess it
         if hasattr(self._universe.atoms, attr_to_guess) and not force_guess:
@@ -143,23 +148,27 @@ def guess_attr(self, attr_to_guess, force_guess=False):
                 getattr(self._universe.atoms, attr_to_guess, None))
 
             top_attr = _TOPOLOGY_ATTRS[attr_to_guess]
-
-            empty_values = top_attr.are_values_missing(attr_values)
-
-            if True in empty_values:
-                # pass to the guesser_method boolean mask to only guess the
-                # empty values
-                attr_values[empty_values] = self._guesser_methods[attr_to_guess](
-                    indices_to_guess=empty_values)
-                return attr_values
-
+            if issubclass(top_attr, _Connection):
+                return guesser_method()
+            
             else:
-                logger.info(
-                    f'There is no empty {attr_to_guess} values. Guesser did '
-                    f'not guess any new values for {attr_to_guess} attribute')
-                return None
+                empty_values = top_attr.are_values_missing(attr_values)
+
+                if True in empty_values:
+                    # pass to the guesser_method boolean mask to only guess the
+                    # empty values
+                    attr_values[empty_values] = guesser_method(
+                        indices_to_guess=empty_values
+                    )
+                    return attr_values
+
+                else:
+                    logger.info(
+                        f'There is no empty {attr_to_guess} values. Guesser did '
+                        f'not guess any new values for {attr_to_guess} attribute')
+                    return None
         else:
-            return np.array(self._guesser_methods[attr_to_guess]())
+            return np.array(guesser_method())
 
 
 def get_guesser(context, u=None, **kwargs):

From 5ce43e035215d9c22dd5da62ecad7d90950c25fe Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 16:34:00 +1100
Subject: [PATCH 03/30] pep8 tests

---
 testsuite/MDAnalysisTests/guesser/test_base.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index af10f9f6ad..d5e093739b 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -114,7 +114,7 @@ def test_guess_topology_objects_existing(self):
 
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (0, 1) not in all_indices
-        
+
         # guess old bonds back
         u.guess_TopologyAttrs("default", to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922
@@ -128,7 +128,6 @@ def test_guess_topology_objects_force(self):
         with pytest.raises(NoDataError):
             u.atoms.angles
 
-
     def test_guess_topology_objects_out_of_order_init(self):
         u = mda.Universe(
             datafiles.PDB_small,
@@ -137,7 +136,7 @@ def test_guess_topology_objects_out_of_order_init(self):
         )
         assert len(u.atoms.angles) == 6123
         assert len(u.atoms.dihedrals) == 8921
-    
+
     def test_guess_topology_objects_out_of_order_guess(self):
         u = mda.Universe(datafiles.PDB_small)
         with pytest.raises(NoDataError):
@@ -149,4 +148,3 @@ def test_guess_topology_objects_out_of_order_guess(self):
         )
         assert len(u.atoms.angles) == 6123
         assert len(u.atoms.dihedrals) == 8921
-

From 7db0f6aae1c694c9efbe427748ba56d945ddd755 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 16:40:16 +1100
Subject: [PATCH 04/30] add failing force_guess bond test

---
 testsuite/MDAnalysisTests/guesser/test_base.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index d5e093739b..8087302e61 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -148,3 +148,16 @@ def test_guess_topology_objects_out_of_order_guess(self):
         )
         assert len(u.atoms.angles) == 6123
         assert len(u.atoms.dihedrals) == 8921
+
+    def test_force_guess_overwrites_existing_bonds(self):
+        u = mda.Universe(datafiles.PDB_conect)
+        assert len(u.atoms.bonds) == 8
+
+        # PDB_conect only has Cs. This low radius should find no bonds
+        cvdw = {"C": 0.1}
+        u.guess_TopologyAttrs("default", to_guess=["bonds"], vdwradii=cvdw)
+        assert len(u.atoms.bonds) == 8
+
+        # Now force guess bonds
+        u.guess_TopologyAttrs("default", force_guess=["bonds"], vdwradii=cvdw)
+        assert len(u.atoms.bonds) == 0

From f22a9a6b799e87c0acfaa160ca5d2f0869373597 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:10:27 +1100
Subject: [PATCH 05/30] add force guessing removal

---
 package/MDAnalysis/core/topologyattrs.py      |  1 -
 package/MDAnalysis/core/universe.py           | 57 ++++++++++++-------
 package/MDAnalysis/guesser/base.py            | 49 +++++++++-------
 .../MDAnalysisTests/guesser/test_base.py      | 17 +++---
 4 files changed, 78 insertions(+), 46 deletions(-)

diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py
index 5e2621dc63..1cbc83c2ed 100644
--- a/package/MDAnalysis/core/topologyattrs.py
+++ b/package/MDAnalysis/core/topologyattrs.py
@@ -3117,7 +3117,6 @@ def _add_bonds(self, values, types=None, guessed=True, order=None):
             guessed = itertools.cycle((guessed,))
         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 existing:
diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index c0ac6bcf6f..1ffa426256 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -84,7 +84,10 @@
                      Atom, Residue, Segment,
                      AtomGroup, ResidueGroup, SegmentGroup)
 from .topology import Topology
-from .topologyattrs import AtomAttr, ResidueAttr, SegmentAttr, BFACTOR_WARNING
+from .topologyattrs import (
+    AtomAttr, ResidueAttr, SegmentAttr,
+    BFACTOR_WARNING, _Connection
+)
 from .topologyobjects import TopologyObject
 from ..guesser.base import get_guesser
 
@@ -1132,7 +1135,6 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
             self.add_TopologyAttr(object_type, [])
             attr = getattr(self._topology, object_type)
 
-
         attr._add_bonds(indices, types=types, guessed=guessed, order=order)
 
     def add_bonds(self, values, types=None, guessed=False, order=None):
@@ -1183,6 +1185,14 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
         """
         self._add_topology_objects('bonds', values, types=types,
                                  guessed=guessed, order=order)
+        self._invalidate_bond_related_caches()
+        
+    def _invalidate_bond_related_caches(self):
+        """
+        Invalidate caches related to bonds and fragments.
+
+        .. versionadded: 2.8.0
+        """
         # Invalidate bond-related caches
         self._cache.pop('fragments', None)
         self._cache['_valid'].pop('fragments', None)
@@ -1259,7 +1269,7 @@ def _delete_topology_objects(self, object_type, values):
         Parameters
         ----------
         object_type : {'bonds', 'angles', 'dihedrals', 'impropers'}
-            The type of TopologyObject to add.
+            The type of TopologyObject to delete.
         values : iterable of tuples, AtomGroups, or TopologyObjects; or TopologyGroup
             An iterable of: tuples of atom indices, or AtomGroups,
             or TopologyObjects.
@@ -1282,7 +1292,6 @@ def _delete_topology_objects(self, object_type, values):
             attr = getattr(self._topology, object_type)
         except AttributeError:
             raise ValueError('There are no {} to delete'.format(object_type))
-
         attr._delete_bonds(indices)
 
     def delete_bonds(self, values):
@@ -1323,10 +1332,7 @@ def delete_bonds(self, values):
         .. versionadded:: 1.0.0
         """
         self._delete_topology_objects('bonds', values)
-        # Invalidate bond-related caches
-        self._cache.pop('fragments', None)
-        self._cache['_valid'].pop('fragments', None)
-        self._cache['_valid'].pop('fragindices', None)
+        self._invalidate_bond_related_caches()
 
     def delete_angles(self, values):
         """Delete Angles from this Universe.
@@ -1552,7 +1558,10 @@ def guess_TopologyAttrs(
         # in the same order that the user provided
         total_guess = list(dict.fromkeys(total_guess))
 
-        objects = ['bonds', 'angles', 'dihedrals', 'impropers']
+        objects = set(
+            topattr.attrname for topattr in _TOPOLOGY_ATTRS.values()
+            if issubclass(topattr, _Connection)
+        )
 
         # Checking if the universe is empty to avoid errors
         # from guesser methods
@@ -1579,16 +1588,26 @@ def guess_TopologyAttrs(
                     fg =  attr in force_guess
                     values = guesser.guess_attr(attr, fg)
 
-                    if values is not None:
-                        if attr in objects:
-                            self._add_topology_objects(
-                                attr, values, guessed=True)
-                        else:
-                            guessed_attr = _TOPOLOGY_ATTRS[attr](values, True)
-                            self.add_TopologyAttr(guessed_attr)
-                        logger.info(
-                            f'attribute {attr} has been guessed'
-                            ' successfully.')
+                    # None indicates no additional guessing was done
+                    if values is None:
+                        continue
+                    if attr in objects:
+                        # delete existing connections if they exist
+                        if fg and hasattr(self.atoms, attr):
+                            group = getattr(self.atoms, attr)
+                            self.delete_bonds(group)
+                            self._delete_topology_objects(attr, group)
+                        # this method appends to existing bonds
+                        self._add_topology_objects(
+                            attr, values, guessed=True)
+                        if attr == "bonds":
+                            self._invalidate_bond_related_caches()
+                    else:
+                        guessed_attr = _TOPOLOGY_ATTRS[attr](values, True)
+                        self.add_TopologyAttr(guessed_attr)
+                    logger.info(
+                        f'attribute {attr} has been guessed'
+                        ' successfully.')
 
                 else:
                     raise ValueError(f'{context} guesser can not guess the'
diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index f307a661b3..2bd9cb8423 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -136,37 +136,48 @@ def guess_attr(self, attr_to_guess, force_guess=False):
         NDArray of guessed values
 
         """
+        try:
+            top_attr = _TOPOLOGY_ATTRS[attr_to_guess]
+        except KeyError:
+            raise KeyError(
+                f"{attr_to_guess} is not a recognized MDAnalysis "
+                "topology attribute"
+            )
         try:
             guesser_method = self._guesser_methods[attr_to_guess]
         except KeyError:
             raise ValueError(f'{type(self).__name__} cannot guess the following '
                              f'attribute: {attr_to_guess}')
+    
+        # make attribute to guess plural
+        attr_to_guess = top_attr.attrname
+        
+        # Connection attributes should be just returned as they are always
+        # appended to the Universe. ``force_guess`` handling should happen
+        # at Universe level.
+        if issubclass(top_attr, _Connection):
+            return guesser_method()
 
         # check if the topology already has the attribute to partially guess it
         if hasattr(self._universe.atoms, attr_to_guess) and not force_guess:
             attr_values = np.array(
                 getattr(self._universe.atoms, attr_to_guess, None))
 
-            top_attr = _TOPOLOGY_ATTRS[attr_to_guess]
-            if issubclass(top_attr, _Connection):
-                return guesser_method()
-            
+            empty_values = top_attr.are_values_missing(attr_values)
+
+            if True in empty_values:
+                # pass to the guesser_method boolean mask to only guess the
+                # empty values
+                attr_values[empty_values] = guesser_method(
+                    indices_to_guess=empty_values
+                )
+                return attr_values
+
             else:
-                empty_values = top_attr.are_values_missing(attr_values)
-
-                if True in empty_values:
-                    # pass to the guesser_method boolean mask to only guess the
-                    # empty values
-                    attr_values[empty_values] = guesser_method(
-                        indices_to_guess=empty_values
-                    )
-                    return attr_values
-
-                else:
-                    logger.info(
-                        f'There is no empty {attr_to_guess} values. Guesser did '
-                        f'not guess any new values for {attr_to_guess} attribute')
-                    return None
+                logger.info(
+                    f'There is no empty {attr_to_guess} values. Guesser did '
+                    f'not guess any new values for {attr_to_guess} attribute')
+                return None
         else:
             return np.array(guesser_method())
 
diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 8087302e61..3e3c9bef51 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -30,6 +30,8 @@
 from MDAnalysis.exceptions import NoDataError
 from numpy.testing import assert_allclose, assert_equal
 
+from MDAnalysis import _TOPOLOGY_ATTRS, _GUESSERS
+
 
 class TestBaseGuesser():
 
@@ -150,14 +152,15 @@ def test_guess_topology_objects_out_of_order_guess(self):
         assert len(u.atoms.dihedrals) == 8921
 
     def test_force_guess_overwrites_existing_bonds(self):
-        u = mda.Universe(datafiles.PDB_conect)
-        assert len(u.atoms.bonds) == 8
+        u = mda.Universe(datafiles.CONECT)
+        assert len(u.atoms.bonds) == 72
 
-        # PDB_conect only has Cs. This low radius should find no bonds
-        cvdw = {"C": 0.1}
-        u.guess_TopologyAttrs("default", to_guess=["bonds"], vdwradii=cvdw)
-        assert len(u.atoms.bonds) == 8
+        # This low radius should find no bonds
+        vdw = dict.fromkeys(set(u.atoms.types), 0.1)
+        u.guess_TopologyAttrs("default", to_guess=["bonds"], vdwradii=vdw)
+        assert len(u.atoms.bonds) == 72
 
         # Now force guess bonds
-        u.guess_TopologyAttrs("default", force_guess=["bonds"], vdwradii=cvdw)
+        u.guess_TopologyAttrs("default", force_guess=["bonds"], vdwradii=vdw)
         assert len(u.atoms.bonds) == 0
+        assert False

From e21059c67c2c3e70d01e58d03454c64c17fd9b61 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:26:50 +1100
Subject: [PATCH 06/30] fix pep8

---
 package/MDAnalysis/core/universe.py | 2 +-
 package/MDAnalysis/guesser/base.py  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 1ffa426256..ed2c34354d 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1186,7 +1186,7 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
         self._add_topology_objects('bonds', values, types=types,
                                  guessed=guessed, order=order)
         self._invalidate_bond_related_caches()
-        
+
     def _invalidate_bond_related_caches(self):
         """
         Invalidate caches related to bonds and fragments.
diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index 2bd9cb8423..7360df7b43 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -146,12 +146,12 @@ def guess_attr(self, attr_to_guess, force_guess=False):
         try:
             guesser_method = self._guesser_methods[attr_to_guess]
         except KeyError:
-            raise ValueError(f'{type(self).__name__} cannot guess the following '
+            raise ValueError(f'{type(self).__name__} cannot guess this '
                              f'attribute: {attr_to_guess}')
-    
+
         # make attribute to guess plural
         attr_to_guess = top_attr.attrname
-        
+
         # Connection attributes should be just returned as they are always
         # appended to the Universe. ``force_guess`` handling should happen
         # at Universe level.

From aed3d3108c6613651ee55e830c5264648dac9c47 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:30:56 +1100
Subject: [PATCH 07/30] cleanup

---
 package/MDAnalysis/core/universe.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index ed2c34354d..338f894874 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1135,6 +1135,7 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
             self.add_TopologyAttr(object_type, [])
             attr = getattr(self._topology, object_type)
 
+
         attr._add_bonds(indices, types=types, guessed=guessed, order=order)
 
     def add_bonds(self, values, types=None, guessed=False, order=None):
@@ -1292,6 +1293,7 @@ def _delete_topology_objects(self, object_type, values):
             attr = getattr(self._topology, object_type)
         except AttributeError:
             raise ValueError('There are no {} to delete'.format(object_type))
+
         attr._delete_bonds(indices)
 
     def delete_bonds(self, values):
@@ -1595,7 +1597,6 @@ def guess_TopologyAttrs(
                         # delete existing connections if they exist
                         if fg and hasattr(self.atoms, attr):
                             group = getattr(self.atoms, attr)
-                            self.delete_bonds(group)
                             self._delete_topology_objects(attr, group)
                         # this method appends to existing bonds
                         self._add_topology_objects(

From e88af7ab25bce3aa2aa3b818a65e7acc8446cfbe Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:50:21 +1100
Subject: [PATCH 08/30] add more tests

---
 .../MDAnalysisTests/guesser/test_base.py      | 44 ++++++++++++++++++-
 1 file changed, 43 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 3e3c9bef51..6a9698391f 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -104,7 +104,26 @@ def test_partial_guess_attr_with_unknown_no_value_label(self):
         u = mda.Universe(top, to_guess=['types'])
         assert_equal(u.atoms.types, ['', '', '', ''])
 
-    def test_guess_topology_objects_existing(self):
+    def test_guess_topology_objects_existing_read(self):
+        u = mda.Universe(datafiles.CONECT)
+        assert len(u.atoms.bonds) == 72
+        assert list(u.bonds[0].indices) == [623, 630]
+
+        # delete some bonds
+        u.delete_bonds(u.atoms.bonds[:10])
+        assert len(u.atoms.bonds) == 62
+        assert list(u.bonds[0].indices) == [623, 630]
+
+        all_indices = [tuple(x.indices) for x in u.bonds]
+        assert (0, 1) not in all_indices
+
+        # guess old bonds back
+        u.guess_TopologyAttrs("default", to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 72
+        # check TopologyGroup contains new (old) bonds
+        assert list(u.bonds[0].indices) == [623, 630]
+
+    def test_guess_topology_objects_existing_in_universe(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922
         assert list(u.bonds[0].indices) == [0, 1]
@@ -164,3 +183,26 @@ def test_force_guess_overwrites_existing_bonds(self):
         u.guess_TopologyAttrs("default", force_guess=["bonds"], vdwradii=vdw)
         assert len(u.atoms.bonds) == 0
         assert False
+
+    def test_guessing_angles_respects_bond_kwargs(self):
+        u = mda.Universe(datafiles.PDB)
+        assert not hasattr(u.atoms, "angles")
+
+        # This low radius should find no angles
+        vdw = dict.fromkeys(set(u.atoms.types), 0.01)
+
+        u.guess_TopologyAttrs("default", to_guess=["angles"], vdwradii=vdw)
+        assert len(u.atoms.angles) == 0
+
+        # set higher radii for lots of angles!
+        vdw = dict.fromkeys(set(u.atoms.types), 1)
+        u.guess_TopologyAttrs("default", force_guess=["angles"], vdwradii=vdw)
+        assert len(u.atoms.angles) == 89466
+
+    def test_guessing_dihedrals_respects_bond_kwargs(self):
+        u = mda.Universe(datafiles.CONECT)
+        assert len(u.atoms.bonds) == 72
+
+        u.guess_TopologyAttrs("default", to_guess=["dihedrals"])
+        assert len(u.atoms.dihedrals) == 3548
+        assert not hasattr(u.atoms, "angles")

From 11a14c10b22a69a15462e8bef034e1c032be0920 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:52:12 +1100
Subject: [PATCH 09/30] update changelog

---
 package/CHANGELOG | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index 52e8eb077b..7be6db672e 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -23,6 +23,9 @@ The rules for this file:
  * 2.8.0
 
 Fixes
+ * Allows bond/angle/dihedral connectivity to be guessed additively with
+   `to_guess`, and as a replacement of existing values with `force_guess`.
+   Also updates cached bond attributes when updating bonds. (Issue #4759, PR #4761)
  * Adds guessed attributes documentation back to each parser page
    and updates overall guesser docs (Issue #4696)
  * Fix Bohrium (Bh) atomic mass in tables.py (PR #3753)

From 219ee09906fdf48fc9cb5b7334ae6daa62e60479 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 16:31:23 +1100
Subject: [PATCH 10/30] add tests

---
 .../MDAnalysisTests/guesser/test_base.py      | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index d9c7ffc3e2..882d034378 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -230,3 +230,51 @@ def test_universe_creation_from_specific_array():
         [0., 200., 150.], [100., 200., 150.], [200., 200., 150.]
     ])
     mda.Universe(a, n_atoms=9)
+    def test_guess_topology_objects_existing(self):
+        u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+        assert list(u.bonds[0].indices) == [0, 1]
+
+        # delete some bonds
+        u.delete_bonds(u.atoms.bonds[:100])
+        assert len(u.atoms.bonds) == 1822
+        assert list(u.bonds[0].indices) == [94, 99]
+
+        all_indices = [tuple(x.indices) for x in u.bonds]
+        assert (0, 1) not in all_indices
+        
+        # guess old bonds back
+        u.guess_TopologyAttrs("default", to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+        # check TopologyGroup contains new (old) bonds
+        assert list(u.bonds[0].indices) == [0, 1]
+
+    def test_guess_topology_objects_force(self):
+        u = mda.Universe(datafiles.CONECT, force_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+
+        with pytest.raises(NoDataError):
+            u.atoms.angles
+
+
+    def test_guess_topology_objects_out_of_order_init(self):
+        u = mda.Universe(
+            datafiles.PDB_small,
+            to_guess=["dihedrals", "angles", "bonds"],
+            guess_bonds=False
+        )
+        assert len(u.atoms.angles) == 6123
+        assert len(u.atoms.dihedrals) == 8921
+    
+    def test_guess_topology_objects_out_of_order_guess(self):
+        u = mda.Universe(datafiles.PDB_small)
+        with pytest.raises(NoDataError):
+            u.atoms.angles
+
+        u.guess_TopologyAttrs(
+            "default",
+            to_guess=["dihedrals", "angles", "bonds"]
+        )
+        assert len(u.atoms.angles) == 6123
+        assert len(u.atoms.dihedrals) == 8921
+

From 1e6d9ab93edefc894eb779a0c4f56f8f949bc055 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:10:27 +1100
Subject: [PATCH 11/30] add force guessing removal

---
 package/MDAnalysis/core/universe.py           |  8 ++--
 package/MDAnalysis/guesser/base.py            |  9 ++++
 .../MDAnalysisTests/guesser/test_base.py      | 48 +++++++++----------
 3 files changed, 38 insertions(+), 27 deletions(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 7b635788bf..00b5e2e2f3 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1183,7 +1183,6 @@ def _add_topology_objects(self, object_type, values, types=None, guessed=False,
             self.add_TopologyAttr(object_type, [])
             attr = getattr(self._topology, object_type)
 
-
         attr._add_bonds(indices, types=types, guessed=guessed, order=order)
 
     def add_bonds(self, values, types=None, guessed=False, order=None):
@@ -1235,7 +1234,7 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
         self._add_topology_objects('bonds', values, types=types,
                                  guessed=guessed, order=order)
         self._invalidate_bond_related_caches()
-
+    
     def _invalidate_bond_related_caches(self):
         """
         Invalidate caches related to bonds and fragments.
@@ -1341,7 +1340,6 @@ def _delete_topology_objects(self, object_type, values):
             attr = getattr(self._topology, object_type)
         except AttributeError:
             raise ValueError('There are no {} to delete'.format(object_type))
-
         attr._delete_bonds(indices)
 
     def delete_bonds(self, values):
@@ -1665,6 +1663,10 @@ def guess_TopologyAttrs(
                         # delete existing connections if they exist
                         if fg and hasattr(self.atoms, attr):
                             group = getattr(self.atoms, attr)
+<<<<<<< HEAD
+=======
+                            self.delete_bonds(group)
+>>>>>>> ed1ba84de (add force guessing removal)
                             self._delete_topology_objects(attr, group)
                         # this method appends to existing bonds
                         self._add_topology_objects(
diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index 7360df7b43..5ba4d731bf 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -148,6 +148,15 @@ def guess_attr(self, attr_to_guess, force_guess=False):
         except KeyError:
             raise ValueError(f'{type(self).__name__} cannot guess this '
                              f'attribute: {attr_to_guess}')
+    
+        # make attribute to guess plural
+        attr_to_guess = top_attr.attrname
+        
+        # Connection attributes should be just returned as they are always
+        # appended to the Universe. ``force_guess`` handling should happen
+        # at Universe level.
+        if issubclass(top_attr, _Connection):
+            return guesser_method()
 
         # make attribute to guess plural
         attr_to_guess = top_attr.attrname
diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 882d034378..16637eebdc 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -207,29 +207,6 @@ def test_guessing_dihedrals_respects_bond_kwargs(self):
         assert len(u.atoms.dihedrals) == 3548
         assert not hasattr(u.atoms, "angles")
 
-def test_Universe_guess_bonds_deprecated():
-    with pytest.warns(
-        DeprecationWarning,
-        match='`guess_bonds` keyword is deprecated'
-    ):
-        u = mda.Universe(datafiles.PDB_full, guess_bonds=True)
-
-
-@pytest.mark.parametrize(
-    "universe_input",
-    [datafiles.DCD, datafiles.XTC, np.random.rand(3, 3), datafiles.PDB]
-)
-def test_universe_creation_from_coordinates(universe_input):
-    mda.Universe(universe_input)
-
-
-def test_universe_creation_from_specific_array():
-    a = np.array([
-        [0., 0., 150.], [0., 0., 150.], [200., 0., 150.],
-        [0., 0., 150.], [100., 100., 150.], [200., 100., 150.],
-        [0., 200., 150.], [100., 200., 150.], [200., 200., 150.]
-    ])
-    mda.Universe(a, n_atoms=9)
     def test_guess_topology_objects_existing(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922
@@ -256,7 +233,6 @@ def test_guess_topology_objects_force(self):
         with pytest.raises(NoDataError):
             u.atoms.angles
 
-
     def test_guess_topology_objects_out_of_order_init(self):
         u = mda.Universe(
             datafiles.PDB_small,
@@ -278,3 +254,27 @@ def test_guess_topology_objects_out_of_order_guess(self):
         assert len(u.atoms.angles) == 6123
         assert len(u.atoms.dihedrals) == 8921
 
+
+def test_Universe_guess_bonds_deprecated():
+    with pytest.warns(
+        DeprecationWarning,
+        match='`guess_bonds` keyword is deprecated'
+    ):
+        u = mda.Universe(datafiles.PDB_full, guess_bonds=True)
+
+
+@pytest.mark.parametrize(
+    "universe_input",
+    [datafiles.DCD, datafiles.XTC, np.random.rand(3, 3), datafiles.PDB]
+)
+def test_universe_creation_from_coordinates(universe_input):
+    mda.Universe(universe_input)
+
+
+def test_universe_creation_from_specific_array():
+    a = np.array([
+        [0., 0., 150.], [0., 0., 150.], [200., 0., 150.],
+        [0., 0., 150.], [100., 100., 150.], [200., 100., 150.],
+        [0., 200., 150.], [100., 200., 150.], [200., 200., 150.]
+    ])
+    mda.Universe(a, n_atoms=9)
\ No newline at end of file

From 2918ae7da2b5b2c4d070480ac8cc301420e44602 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Fri, 25 Oct 2024 18:50:21 +1100
Subject: [PATCH 12/30] add more tests

---
 .../MDAnalysisTests/guesser/test_base.py      | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 16637eebdc..4995baa36e 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -109,6 +109,7 @@ def test_guess_topology_objects_existing_read(self):
         assert len(u.atoms.bonds) == 72
         assert list(u.bonds[0].indices) == [623, 630]
 
+<<<<<<< HEAD
         # delete some bonds
         u.delete_bonds(u.atoms.bonds[:10])
         assert len(u.atoms.bonds) == 62
@@ -123,6 +124,27 @@ def test_guess_topology_objects_existing_read(self):
         # check TopologyGroup contains new (old) bonds
         assert list(u.bonds[0].indices) == [623, 630]
 
+=======
+    def test_guess_topology_objects_existing_read(self):
+        u = mda.Universe(datafiles.CONECT)
+        assert len(u.atoms.bonds) == 72
+        assert list(u.bonds[0].indices) == [623, 630]
+
+        # delete some bonds
+        u.delete_bonds(u.atoms.bonds[:10])
+        assert len(u.atoms.bonds) == 62
+        assert list(u.bonds[0].indices) == [623, 630]
+
+        all_indices = [tuple(x.indices) for x in u.bonds]
+        assert (0, 1) not in all_indices
+
+        # guess old bonds back
+        u.guess_TopologyAttrs("default", to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 72
+        # check TopologyGroup contains new (old) bonds
+        assert list(u.bonds[0].indices) == [623, 630]
+
+>>>>>>> 7236e9112 (add more tests)
     def test_guess_topology_objects_existing_in_universe(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922

From 3e170077f2919986e0d591a2d2d6f59d5ba0addc Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 01:19:41 +1100
Subject: [PATCH 13/30] update tests after deletion fix

---
 testsuite/MDAnalysisTests/guesser/test_base.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 4995baa36e..0c9415e824 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -133,16 +133,16 @@ def test_guess_topology_objects_existing_read(self):
         # delete some bonds
         u.delete_bonds(u.atoms.bonds[:10])
         assert len(u.atoms.bonds) == 62
-        assert list(u.bonds[0].indices) == [623, 630]
+        assert list(u.bonds[0].indices) == [1545, 1552] # first bond has changed
 
         all_indices = [tuple(x.indices) for x in u.bonds]
-        assert (0, 1) not in all_indices
+        assert (623, 630) not in all_indices
 
-        # guess old bonds back
+        # test guessing new bonds doesn't remove old ones
         u.guess_TopologyAttrs("default", to_guess=["bonds"])
-        assert len(u.atoms.bonds) == 72
-        # check TopologyGroup contains new (old) bonds
-        assert list(u.bonds[0].indices) == [623, 630]
+        assert len(u.atoms.bonds) == 1922
+        all_indices = [tuple(x.indices) for x in u.bonds]
+        assert (1545, 1552) in all_indices
 
 >>>>>>> 7236e9112 (add more tests)
     def test_guess_topology_objects_existing_in_universe(self):
@@ -204,7 +204,6 @@ def test_force_guess_overwrites_existing_bonds(self):
         # Now force guess bonds
         u.guess_TopologyAttrs("default", force_guess=["bonds"], vdwradii=vdw)
         assert len(u.atoms.bonds) == 0
-        assert False
 
     def test_guessing_angles_respects_bond_kwargs(self):
         u = mda.Universe(datafiles.PDB)

From 892bc42ef22c27eb9698a47624c29d04f89a499f Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 01:23:49 +1100
Subject: [PATCH 14/30] fix problematic merge

---
 .../MDAnalysisTests/guesser/test_base.py      | 22 -------------------
 1 file changed, 22 deletions(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 0c9415e824..e3c9553089 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -109,27 +109,6 @@ def test_guess_topology_objects_existing_read(self):
         assert len(u.atoms.bonds) == 72
         assert list(u.bonds[0].indices) == [623, 630]
 
-<<<<<<< HEAD
-        # delete some bonds
-        u.delete_bonds(u.atoms.bonds[:10])
-        assert len(u.atoms.bonds) == 62
-        assert list(u.bonds[0].indices) == [623, 630]
-
-        all_indices = [tuple(x.indices) for x in u.bonds]
-        assert (0, 1) not in all_indices
-
-        # guess old bonds back
-        u.guess_TopologyAttrs("default", to_guess=["bonds"])
-        assert len(u.atoms.bonds) == 72
-        # check TopologyGroup contains new (old) bonds
-        assert list(u.bonds[0].indices) == [623, 630]
-
-=======
-    def test_guess_topology_objects_existing_read(self):
-        u = mda.Universe(datafiles.CONECT)
-        assert len(u.atoms.bonds) == 72
-        assert list(u.bonds[0].indices) == [623, 630]
-
         # delete some bonds
         u.delete_bonds(u.atoms.bonds[:10])
         assert len(u.atoms.bonds) == 62
@@ -144,7 +123,6 @@ def test_guess_topology_objects_existing_read(self):
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (1545, 1552) in all_indices
 
->>>>>>> 7236e9112 (add more tests)
     def test_guess_topology_objects_existing_in_universe(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922

From 451d6a82fbd2217367369cb02dc14c60ddfc43c7 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 01:24:45 +1100
Subject: [PATCH 15/30] fix other merge problem

---
 package/MDAnalysis/core/universe.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 00b5e2e2f3..16ffc1dc42 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1663,10 +1663,6 @@ def guess_TopologyAttrs(
                         # delete existing connections if they exist
                         if fg and hasattr(self.atoms, attr):
                             group = getattr(self.atoms, attr)
-<<<<<<< HEAD
-=======
-                            self.delete_bonds(group)
->>>>>>> ed1ba84de (add force guessing removal)
                             self._delete_topology_objects(attr, group)
                         # this method appends to existing bonds
                         self._add_topology_objects(

From f044fa1d3787c7eb634ab5a6e6de778be294ef5f Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 01:26:34 +1100
Subject: [PATCH 16/30] how did this rebase go so wrong

---
 .../MDAnalysisTests/guesser/test_base.py      | 47 -------------------
 1 file changed, 47 deletions(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index e3c9553089..6e43c41e70 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -206,53 +206,6 @@ def test_guessing_dihedrals_respects_bond_kwargs(self):
         assert len(u.atoms.dihedrals) == 3548
         assert not hasattr(u.atoms, "angles")
 
-    def test_guess_topology_objects_existing(self):
-        u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
-        assert len(u.atoms.bonds) == 1922
-        assert list(u.bonds[0].indices) == [0, 1]
-
-        # delete some bonds
-        u.delete_bonds(u.atoms.bonds[:100])
-        assert len(u.atoms.bonds) == 1822
-        assert list(u.bonds[0].indices) == [94, 99]
-
-        all_indices = [tuple(x.indices) for x in u.bonds]
-        assert (0, 1) not in all_indices
-        
-        # guess old bonds back
-        u.guess_TopologyAttrs("default", to_guess=["bonds"])
-        assert len(u.atoms.bonds) == 1922
-        # check TopologyGroup contains new (old) bonds
-        assert list(u.bonds[0].indices) == [0, 1]
-
-    def test_guess_topology_objects_force(self):
-        u = mda.Universe(datafiles.CONECT, force_guess=["bonds"])
-        assert len(u.atoms.bonds) == 1922
-
-        with pytest.raises(NoDataError):
-            u.atoms.angles
-
-    def test_guess_topology_objects_out_of_order_init(self):
-        u = mda.Universe(
-            datafiles.PDB_small,
-            to_guess=["dihedrals", "angles", "bonds"],
-            guess_bonds=False
-        )
-        assert len(u.atoms.angles) == 6123
-        assert len(u.atoms.dihedrals) == 8921
-    
-    def test_guess_topology_objects_out_of_order_guess(self):
-        u = mda.Universe(datafiles.PDB_small)
-        with pytest.raises(NoDataError):
-            u.atoms.angles
-
-        u.guess_TopologyAttrs(
-            "default",
-            to_guess=["dihedrals", "angles", "bonds"]
-        )
-        assert len(u.atoms.angles) == 6123
-        assert len(u.atoms.dihedrals) == 8921
-
 
 def test_Universe_guess_bonds_deprecated():
     with pytest.warns(

From e17c57ef19a5b6868e644fa4840702fce1fe3e42 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 01:28:08 +1100
Subject: [PATCH 17/30] repep8

---
 package/MDAnalysis/core/universe.py            | 2 +-
 package/MDAnalysis/guesser/base.py             | 4 ++--
 testsuite/MDAnalysisTests/guesser/test_base.py | 5 +++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 16ffc1dc42..69b5fe0ef9 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1234,7 +1234,7 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
         self._add_topology_objects('bonds', values, types=types,
                                  guessed=guessed, order=order)
         self._invalidate_bond_related_caches()
-    
+
     def _invalidate_bond_related_caches(self):
         """
         Invalidate caches related to bonds and fragments.
diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index 5ba4d731bf..bb526914e3 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -148,10 +148,10 @@ def guess_attr(self, attr_to_guess, force_guess=False):
         except KeyError:
             raise ValueError(f'{type(self).__name__} cannot guess this '
                              f'attribute: {attr_to_guess}')
-    
+
         # make attribute to guess plural
         attr_to_guess = top_attr.attrname
-        
+
         # Connection attributes should be just returned as they are always
         # appended to the Universe. ``force_guess`` handling should happen
         # at Universe level.
diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 6e43c41e70..3c425ae319 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -112,7 +112,8 @@ def test_guess_topology_objects_existing_read(self):
         # delete some bonds
         u.delete_bonds(u.atoms.bonds[:10])
         assert len(u.atoms.bonds) == 62
-        assert list(u.bonds[0].indices) == [1545, 1552] # first bond has changed
+        # first bond has changed
+        assert list(u.bonds[0].indices) == [1545, 1552]
 
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (623, 630) not in all_indices
@@ -229,4 +230,4 @@ def test_universe_creation_from_specific_array():
         [0., 0., 150.], [100., 100., 150.], [200., 100., 150.],
         [0., 200., 150.], [100., 200., 150.], [200., 200., 150.]
     ])
-    mda.Universe(a, n_atoms=9)
\ No newline at end of file
+    mda.Universe(a, n_atoms=9)

From 1fc4514bfb8b6bd74ae0bbb3075b2a9097171d9e Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 01:33:49 +1100
Subject: [PATCH 18/30] more merge fixes

---
 package/MDAnalysis/guesser/base.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index bb526914e3..7360df7b43 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -152,15 +152,6 @@ def guess_attr(self, attr_to_guess, force_guess=False):
         # make attribute to guess plural
         attr_to_guess = top_attr.attrname
 
-        # Connection attributes should be just returned as they are always
-        # appended to the Universe. ``force_guess`` handling should happen
-        # at Universe level.
-        if issubclass(top_attr, _Connection):
-            return guesser_method()
-
-        # make attribute to guess plural
-        attr_to_guess = top_attr.attrname
-
         # Connection attributes should be just returned as they are always
         # appended to the Universe. ``force_guess`` handling should happen
         # at Universe level.

From 7305e60340eff2a38ed3dde4f6754c44df6370df Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 02:02:09 +1100
Subject: [PATCH 19/30] change guessing bonds with force to additive

---
 package/MDAnalysis/core/universe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 69b5fe0ef9..101f2d37db 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -457,7 +457,7 @@ def __init__(self, topology=None, *coordinates, all_coordinates=False,
                 "the previous Context values.",
                 DeprecationWarning
             )
-            force_guess = list(force_guess) + ['bonds', 'angles', 'dihedrals']
+            to_guess = list(to_guess) + ['bonds', 'angles', 'dihedrals']
 
         self.guess_TopologyAttrs(
             context, to_guess, force_guess, error_if_missing=False

From 970371fd4c2e1d49b312736bd45750a913fdf15d Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 02:38:05 +1100
Subject: [PATCH 20/30] change valueerror to nodataerror

---
 package/MDAnalysis/core/universe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 101f2d37db..a9046be103 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1649,7 +1649,7 @@ def guess_TopologyAttrs(
                     fg =  attr in force_guess
                     try:
                         values = guesser.guess_attr(attr, fg)
-                    except ValueError as e:
+                    except NoDataError as e:
                         if error_if_missing or fg:
                             raise e
                         else:

From 909ec37dc28bf65b65990802f5967ae3a8d01825 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Sun, 27 Oct 2024 12:41:41 +1100
Subject: [PATCH 21/30] add tests for errors

---
 package/MDAnalysis/guesser/base.py            |  6 ++---
 .../MDAnalysisTests/guesser/test_base.py      | 22 +++++++++++++++++++
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py
index 7360df7b43..0fd7a7e18e 100644
--- a/package/MDAnalysis/guesser/base.py
+++ b/package/MDAnalysis/guesser/base.py
@@ -143,15 +143,15 @@ def guess_attr(self, attr_to_guess, force_guess=False):
                 f"{attr_to_guess} is not a recognized MDAnalysis "
                 "topology attribute"
             )
+        # make attribute to guess plural
+        attr_to_guess = top_attr.attrname
+
         try:
             guesser_method = self._guesser_methods[attr_to_guess]
         except KeyError:
             raise ValueError(f'{type(self).__name__} cannot guess this '
                              f'attribute: {attr_to_guess}')
 
-        # make attribute to guess plural
-        attr_to_guess = top_attr.attrname
-
         # Connection attributes should be just returned as they are always
         # appended to the Universe. ``force_guess`` handling should happen
         # at Universe level.
diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 3c425ae319..8c80bed4b6 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -207,6 +207,28 @@ def test_guessing_dihedrals_respects_bond_kwargs(self):
         assert len(u.atoms.dihedrals) == 3548
         assert not hasattr(u.atoms, "angles")
 
+    def test_guess_invalid_attribute(self):
+        default_guesser = get_guesser("default")
+        err = "not a recognized MDAnalysis topology attribute"
+        with pytest.raises(KeyError, match=err):
+            default_guesser.guess_attr('not_an_attribute')
+
+    def test_guess_unsupported_attribute(self):
+        default_guesser = get_guesser("default")
+        err = "cannot guess this attribute"
+        with pytest.raises(ValueError, match=err):
+            default_guesser.guess_attr('tempfactors')
+    
+    def test_guess_singular(self):
+        default_guesser = get_guesser("default")
+        u = mda.Universe(datafiles.PDB, to_guess=[])
+        assert not hasattr(u.atoms, "masses")
+
+        default_guesser._universe = u
+        masses = default_guesser.guess_attr('mass')
+
+
+
 
 def test_Universe_guess_bonds_deprecated():
     with pytest.warns(

From c190ca8c41bedff979fbd6bc97d986a4d5252ff9 Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Tue, 29 Oct 2024 06:28:23 +1100
Subject: [PATCH 22/30] Update package/MDAnalysis/core/universe.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/universe.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index a9046be103..467a2f8e7f 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -457,6 +457,9 @@ def __init__(self, topology=None, *coordinates, all_coordinates=False,
                 "the previous Context values.",
                 DeprecationWarning
             )
+            # Original behaviour is to add additionally guessed bond info
+            # this is achieved by adding to the `to_guess` list (unliked `force_guess`
+            # which replaces existing bonds).
             to_guess = list(to_guess) + ['bonds', 'angles', 'dihedrals']
 
         self.guess_TopologyAttrs(

From f03a39425c07cc8151f399013ecbe5f789a03a39 Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Tue, 29 Oct 2024 06:28:39 +1100
Subject: [PATCH 23/30] Update package/MDAnalysis/core/universe.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/universe.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 467a2f8e7f..090078fd35 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1241,6 +1241,8 @@ def add_bonds(self, values, types=None, guessed=False, order=None):
     def _invalidate_bond_related_caches(self):
         """
         Invalidate caches related to bonds and fragments.
+        
+        This should be called whenever the Universe's bonds are modified.
 
         .. versionadded: 2.8.0
         """

From 80c68a6ec5873cdbfe57df07b2cf5dc118abb4b7 Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Tue, 29 Oct 2024 06:28:52 +1100
Subject: [PATCH 24/30] Update package/MDAnalysis/core/universe.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/universe.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 090078fd35..2b8b3aa605 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1624,6 +1624,8 @@ def guess_TopologyAttrs(
         # in the same order that the user provided
         total_guess = list(dict.fromkeys(total_guess))
 
+        # Set of all Connectivity related attribute names
+        # used to special case attribute replacement after calling the guesser
         objects = set(
             topattr.attrname for topattr in _TOPOLOGY_ATTRS.values()
             if issubclass(topattr, _Connection)

From 5ab97d4beac994f4c0a6004150a80da356eadb4f Mon Sep 17 00:00:00 2001
From: Lily Wang <31115101+lilyminium@users.noreply.github.com>
Date: Tue, 29 Oct 2024 06:34:05 +1100
Subject: [PATCH 25/30] Update package/MDAnalysis/core/universe.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
---
 package/MDAnalysis/core/universe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 2b8b3aa605..a2bc60c25f 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -1671,7 +1671,7 @@ def guess_TopologyAttrs(
                         if fg and hasattr(self.atoms, attr):
                             group = getattr(self.atoms, attr)
                             self._delete_topology_objects(attr, group)
-                        # this method appends to existing bonds
+                        # this method appends any new bonds in values to existing bonds
                         self._add_topology_objects(
                             attr, values, guessed=True)
                         if attr == "bonds":

From 38077d6e9a545688388a542af7575ad2351e5503 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Tue, 29 Oct 2024 06:44:43 +1100
Subject: [PATCH 26/30] add new test

---
 testsuite/MDAnalysisTests/guesser/test_base.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 8c80bed4b6..e3e7e340a5 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -114,6 +114,10 @@ def test_guess_topology_objects_existing_read(self):
         assert len(u.atoms.bonds) == 62
         # first bond has changed
         assert list(u.bonds[0].indices) == [1545, 1552]
+        # count number of (1545, 1552) bonds
+        bond_values = u._topology.bonds.values
+        n_bonds = sum(1 for bond in bond_values if bond == (1545, 1552))
+        assert n_bonds == 2
 
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (623, 630) not in all_indices
@@ -124,6 +128,11 @@ def test_guess_topology_objects_existing_read(self):
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (1545, 1552) in all_indices
 
+        # test guessing new bonds doesn't duplicate old ones
+        bond_values = u._topology.bonds.values
+        n_bonds = sum(1 for bond in bond_values if bond == (1545, 1552))
+        assert n_bonds == 2
+
     def test_guess_topology_objects_existing_in_universe(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922

From ab6418e23d874b3c6e3aa43b87ebb5d2c83ab26c Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Tue, 29 Oct 2024 06:57:16 +1100
Subject: [PATCH 27/30] add guessing check

---
 package/MDAnalysis/core/topologyattrs.py       |  1 +
 testsuite/MDAnalysisTests/guesser/test_base.py | 12 ++++++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py
index ef5897268c..d4310e472e 100644
--- a/package/MDAnalysis/core/topologyattrs.py
+++ b/package/MDAnalysis/core/topologyattrs.py
@@ -3129,6 +3129,7 @@ def _add_bonds(self, values, types=None, guessed=True, order=None):
             del self._cache['bd']
         except KeyError:
             pass
+        print(self._guessed[69], self._guessed[100])
 
     @_check_connection_values
     def _delete_bonds(self, values):
diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index e3e7e340a5..a56003500c 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -116,8 +116,10 @@ def test_guess_topology_objects_existing_read(self):
         assert list(u.bonds[0].indices) == [1545, 1552]
         # count number of (1545, 1552) bonds
         bond_values = u._topology.bonds.values
-        n_bonds = sum(1 for bond in bond_values if bond == (1545, 1552))
-        assert n_bonds == 2
+        bond_indices = [i for i, x in enumerate(bond_values) if x == (1545, 1552)]
+        for i in bond_indices:
+            assert u._topology.bonds._guessed[i] == False
+        assert len(bond_indices) == 2
 
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (623, 630) not in all_indices
@@ -130,8 +132,10 @@ def test_guess_topology_objects_existing_read(self):
 
         # test guessing new bonds doesn't duplicate old ones
         bond_values = u._topology.bonds.values
-        n_bonds = sum(1 for bond in bond_values if bond == (1545, 1552))
-        assert n_bonds == 2
+        bond_indices = [i for i, x in enumerate(bond_values) if x == (1545, 1552)]
+        for i in bond_indices:
+            assert u._topology.bonds._guessed[i] == False
+        assert len(bond_indices) == 2
 
     def test_guess_topology_objects_existing_in_universe(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])

From 26f91b5777a36660ce24679cb95e046744a238bf Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Tue, 29 Oct 2024 06:59:50 +1100
Subject: [PATCH 28/30] oopsie

---
 package/MDAnalysis/core/topologyattrs.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py
index d4310e472e..ef5897268c 100644
--- a/package/MDAnalysis/core/topologyattrs.py
+++ b/package/MDAnalysis/core/topologyattrs.py
@@ -3129,7 +3129,6 @@ def _add_bonds(self, values, types=None, guessed=True, order=None):
             del self._cache['bd']
         except KeyError:
             pass
-        print(self._guessed[69], self._guessed[100])
 
     @_check_connection_values
     def _delete_bonds(self, values):

From 36b62e659c4416c912d12dfd8c0c4acd22de75c2 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Wed, 30 Oct 2024 00:58:51 +1100
Subject: [PATCH 29/30] update test

---
 .../MDAnalysisTests/guesser/test_base.py      | 25 +++++++++----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index a56003500c..7edb18ef28 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -115,11 +115,10 @@ def test_guess_topology_objects_existing_read(self):
         # first bond has changed
         assert list(u.bonds[0].indices) == [1545, 1552]
         # count number of (1545, 1552) bonds
-        bond_values = u._topology.bonds.values
-        bond_indices = [i for i, x in enumerate(bond_values) if x == (1545, 1552)]
-        for i in bond_indices:
-            assert u._topology.bonds._guessed[i] == False
-        assert len(bond_indices) == 2
+        ag = u.atoms[[1545, 1552]]
+        bonds = ag.bonds.atomgroup_intersection(ag, strict=True)
+        assert len(bonds) == 1
+        assert not bonds[0].is_guessed
 
         all_indices = [tuple(x.indices) for x in u.bonds]
         assert (623, 630) not in all_indices
@@ -127,15 +126,15 @@ def test_guess_topology_objects_existing_read(self):
         # test guessing new bonds doesn't remove old ones
         u.guess_TopologyAttrs("default", to_guess=["bonds"])
         assert len(u.atoms.bonds) == 1922
-        all_indices = [tuple(x.indices) for x in u.bonds]
-        assert (1545, 1552) in all_indices
-
+        old_bonds = ag.bonds.atomgroup_intersection(ag, strict=True)
+        assert len(old_bonds) == 1
         # test guessing new bonds doesn't duplicate old ones
-        bond_values = u._topology.bonds.values
-        bond_indices = [i for i, x in enumerate(bond_values) if x == (1545, 1552)]
-        for i in bond_indices:
-            assert u._topology.bonds._guessed[i] == False
-        assert len(bond_indices) == 2
+        assert not old_bonds[0].is_guessed
+
+        new_ag = u.atoms[[623, 630]]
+        new_bonds = new_ag.bonds.atomgroup_intersection(new_ag, strict=True)
+        assert len(new_bonds) == 1
+        assert new_bonds[0].is_guessed
 
     def test_guess_topology_objects_existing_in_universe(self):
         u = mda.Universe(datafiles.CONECT, to_guess=["bonds"])

From 839e7f383e6a40a58c0d9d3c3f0a504d4632cb27 Mon Sep 17 00:00:00 2001
From: Irfan Alibay <IAlibay@users.noreply.github.com>
Date: Mon, 11 Nov 2024 08:38:22 +0000
Subject: [PATCH 30/30] Update testsuite/MDAnalysisTests/guesser/test_base.py

---
 testsuite/MDAnalysisTests/guesser/test_base.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/testsuite/MDAnalysisTests/guesser/test_base.py b/testsuite/MDAnalysisTests/guesser/test_base.py
index 7edb18ef28..c44fdc3c59 100644
--- a/testsuite/MDAnalysisTests/guesser/test_base.py
+++ b/testsuite/MDAnalysisTests/guesser/test_base.py
@@ -240,8 +240,6 @@ def test_guess_singular(self):
         masses = default_guesser.guess_attr('mass')
 
 
-
-
 def test_Universe_guess_bonds_deprecated():
     with pytest.warns(
         DeprecationWarning,