Change error to warning on Universe creation

package/CHANGELOG

@@ -23,6 +23,8 @@ The rules for this file:
  * 2.8.0
 
 Fixes
+ * 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)

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:

package/doc/sphinx/source/documentation_pages/guesser_modules.rst

@@ -17,7 +17,8 @@ Default behavior
 
 By default, MDAnalysis will guess the "mass" and "type" (atom type) attributes for all particles in the Universe
 using the :class:`~MDAnalysis.guesser.default_guesser.DefaultGuesser` at the time of Universe creation,
-if they are not read from the input file.
+if they are not read from the input file. If the required information is not present in the input file,
+a warning will be raised.
 Please see the :class:`~MDAnalysis.guesser.default_guesser.DefaultGuesser` for more information.
 
 

testsuite/MDAnalysisTests/guesser/test_base.py

@@ -30,7 +30,7 @@
 from numpy.testing import assert_allclose, assert_equal
 
 
-class TesttBaseGuesser():
+class TestBaseGuesser():
 
     def test_get_guesser(self):
         class TestGuesser1(GuesserBase):
@@ -100,3 +100,20 @@ 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, ['', '', '', ''])
+
+
+@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)

testsuite/MDAnalysisTests/guesser/test_default_guesser.py

@@ -117,9 +117,11 @@ def test_partial_guess_elements(self, default_guesser):
 
     def test_guess_elements_from_no_data(self):
         top = Topology(5)
-        msg = "there is no reference attributes in this universe"
-        "to guess types from"
-        with pytest.raises(ValueError, match=(msg)):
+        msg = (
+            "there is no reference attributes in this "
+            "universe to guess types from"
+        )
+        with pytest.warns(UserWarning, match=msg):
             mda.Universe(top, to_guess=['types'])
 
     @pytest.mark.parametrize('name, element', (
@@ -236,6 +238,19 @@ def test_guess_bonds_water():
                          (3, 5)))
 
 
+@pytest.mark.parametrize(
+    "fudge_factor, n_bonds",
+    [(0, 0), (0.55, 4), (200, 6)]
+)
+def test_guess_bonds_water_fudge_factor_passed(fudge_factor, n_bonds):
+    u = mda.Universe(
+            datafiles.two_water_gro,
+            fudge_factor=fudge_factor,
+            to_guess=("types", "bonds")
+        )
+    assert len(u.atoms.bonds) == n_bonds
+
+
 def test_guess_bonds_adk():
     u = mda.Universe(datafiles.PSF, datafiles.DCD)
     u.guess_TopologyAttrs(force_guess=['types'])