Allow bonds etc to be additively guessed when present (#4761)

Allow bonds to be additively guessed (fixes #4759)

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Author: lilyminium

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)
  * Fixes bug where deleting connections by index would only delete
    one of multiple, if multiple are present (Issue #4762, PR #4763)
  * Changes error to warning on Universe creation if guessing fails

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:

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
 
@@ -454,7 +457,10 @@ def __init__(self, topology=None, *coordinates, all_coordinates=False,
                 "the previous Context values.",
                 DeprecationWarning
             )
-            force_guess = list(force_guess) + ['bonds', 'angles', 'dihedrals']
+            # 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(
             context, to_guess, force_guess, error_if_missing=False
@@ -1180,7 +1186,6 @@ 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):
@@ -1231,6 +1236,16 @@ 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.
+        
+        This should be called whenever the Universe's bonds are modified.
+
+        .. versionadded: 2.8.0
+        """
         # Invalidate bond-related caches
         self._cache.pop('fragments', None)
         self._cache['_valid'].pop('fragments', None)
@@ -1307,7 +1322,7 @@ 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.
@@ -1330,7 +1345,6 @@ 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):
@@ -1371,10 +1385,7 @@ 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.
@@ -1613,7 +1624,12 @@ def guess_TopologyAttrs(
         # in the same order that the user provided
         total_guess = list(dict.fromkeys(total_guess))
 
-        objects = ['bonds', 'angles', 'dihedrals', 'impropers']
+        # 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)
+        )
 
         # Checking if the universe is empty to avoid errors
         # from guesser methods
@@ -1640,23 +1656,32 @@ 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:
                             warnings.warn(str(e))
                             continue
 
-                    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_topology_objects(attr, group)
+                        # this method appends any new bonds in values 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'

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
@@ -136,21 +136,41 @@ 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"
+            )
+        # 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}')
+
+        # 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]
-
             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)
+                attr_values[empty_values] = guesser_method(
+                    indices_to_guess=empty_values
+                )
                 return attr_values
 
             else:
@@ -159,7 +179,7 @@ def guess_attr(self, attr_to_guess, force_guess=False):
                     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):

testsuite/MDAnalysisTests/guesser/test_base.py

@@ -27,8 +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
 
+from MDAnalysis import _TOPOLOGY_ATTRS, _GUESSERS
+
 
 class TestBaseGuesser():
 
@@ -101,6 +104,141 @@ 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_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
+        # first bond has changed
+        assert list(u.bonds[0].indices) == [1545, 1552]
+        # count number of (1545, 1552) bonds
+        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
+
+        # test guessing new bonds doesn't remove old ones
+        u.guess_TopologyAttrs("default", to_guess=["bonds"])
+        assert len(u.atoms.bonds) == 1922
+        old_bonds = ag.bonds.atomgroup_intersection(ag, strict=True)
+        assert len(old_bonds) == 1
+        # test guessing new bonds doesn't duplicate old ones
+        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"])
+        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_force_guess_overwrites_existing_bonds(self):
+        u = mda.Universe(datafiles.CONECT)
+        assert len(u.atoms.bonds) == 72
+
+        # 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=vdw)
+        assert len(u.atoms.bonds) == 0
+
+    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")
+
+    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(