Merge branch 'develop' into fix-bond-deletion

package/CHANGELOG

@@ -26,6 +26,8 @@ Fixes
  * Fixes bug where multiple identical connection topologies could be
    added to a _Connection TopologyAttr, and that deleting connections
    by index would only delete one of them (Issue #4762, PR #4763)
+ * Changes error to warning on Universe creation if guessing fails
+   due to missing information (Issue #4750, PR #4754)
  * 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)
@@ -115,6 +117,10 @@ Changes
    numpy.testing.assert_allclose #4438)
 
 Deprecations
+ * MDAnalysis.topology.guessers is deprecated in favour of the new
+   Guessers API and will be removed in version 3.0 (PR #4752)
+ * MDAnalysis.topology.tables is deprecated in favour of
+   MDAnalysis.guesser.tables and will be removed in version 3.0 (PR #4752)
  * Element guessing in the ITPParser is deprecated and will be removed in version 3.0
    (Issue #4698)
  * Unknown masses are set to 0.0 for current version, this will be depracated

package/MDAnalysis/core/universe.py

@@ -410,7 +410,8 @@ def __init__(self, topology=None, *coordinates, all_coordinates=False,
             force_guess = list(force_guess) + ['bonds', 'angles', 'dihedrals']
 
         self.guess_TopologyAttrs(
-            context, to_guess, force_guess, vdwradii=vdwradii, **kwargs)
+            context, to_guess, force_guess, error_if_missing=False
+        )
 
 
     def copy(self):
@@ -1498,7 +1499,9 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True,
         return cls(mol, **kwargs)
 
     def guess_TopologyAttrs(
-            self, context=None, to_guess=None, force_guess=None, **kwargs):
+        self, context=None, to_guess=None, force_guess=None,
+        error_if_missing=True, **kwargs
+    ):
         """
         Guess and add attributes through a specific context-aware guesser.
 
@@ -1523,6 +1526,13 @@ def guess_TopologyAttrs(
             TopologyAttr does not already exist in the Universe, this has no
             effect. If the TopologyAttr does already exist, all values will
             be overwritten by guessed values.
+        error_if_missing: bool
+            If `True`, raise an error if the guesser cannot guess the attribute
+            due to missing TopologyAttrs used as the inputs for guessing.
+            If `False`, a warning will be raised instead.
+            Errors will always be raised if an attribute is in the
+            ``force_guess`` list, even if this parameter is set to False.
+
         **kwargs: extra arguments to be passed to the guesser class
 
         Examples
@@ -1537,7 +1547,11 @@ def guess_TopologyAttrs(
         if not context:
             context = self._context
 
-        guesser = get_guesser(context, self.universe, **kwargs)
+        # update iteratively to avoid multiple kwargs clashing
+        guesser_kwargs = {}
+        guesser_kwargs.update(self._kwargs)
+        guesser_kwargs.update(kwargs)
+        guesser = get_guesser(context, self.universe, **guesser_kwargs)
         self._context = guesser
 
         if to_guess is None:
@@ -1577,7 +1591,14 @@ def guess_TopologyAttrs(
             for attr in total_guess:
                 if guesser.is_guessable(attr):
                     fg =  attr in force_guess
-                    values = guesser.guess_attr(attr, fg)
+                    try:
+                        values = guesser.guess_attr(attr, fg)
+                    except ValueError 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:

package/MDAnalysis/guesser/default_guesser.py

@@ -293,7 +293,7 @@ def guess_types(self, atom_types=None, indices_to_guess=None):
                 atom_types = self._universe.atoms.names
             except AttributeError:
                 raise ValueError(
-                    "there is no reference attributes in this universe"
+                    "there is no reference attributes in this universe "
                     "to guess types from")
 
         if indices_to_guess is not None: