Emit warnings for empty Ag and user grid in DensityAnalysis

package/CHANGELOG

@@ -21,6 +21,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+  * UserWarning displayed when empty atomgroup is given 
+    to DensityAnalysis (Issue #3055)
   * atommethods (_get_prev/next_residues_by_resid) returns empty residue group 
     when given empty residue group (Issue #3089)
   * MOL2 files without bonds can now be read and written (Issue #3057)

package/MDAnalysis/analysis/density.py

@@ -369,6 +369,7 @@ class DensityAnalysis(AnalysisBase):
     .. versionchanged:: 2.0.0
        :func:`_set_user_grid` is now a method of :class:`DensityAnalysis`.
     """
+
     def __init__(self, atomgroup, delta=1.0,
                  metadata=None, padding=2.0,
                  gridcenter=None,
@@ -394,8 +395,18 @@ def _prepare(self):
                 logger.warning(msg)
             # Generate a copy of smin/smax from coords to later check if the
             # defined box might be too small for the selection
-            smin = np.min(coord, axis=0)
-            smax = np.max(coord, axis=0)
+            try:
+                smin = np.min(coord, axis=0)
+                smax = np.max(coord, axis=0)
+            except ValueError as err:
+                msg = ("No atoms in AtomGroup at input time frame. "
+                       "Grid for density could not be automatically"
+                       " generated. A user defined grid was found"
+                       " and is being used as the density grid")
+                warnings.warn(msg)
+                logger.warning(msg)
+                smin = self._gridcenter
+                smax = self._gridcenter
             # Overwrite smin/smax with user defined values
             smin, smax = self._set_user_grid(self._gridcenter, self._xdim,
                                              self._ydim, self._zdim, smin,
@@ -408,8 +419,16 @@ def _prepare(self):
             # ideal solution would use images: implement 'looking across the
             # periodic boundaries' but that gets complicated when the box
             # rotates due to RMS fitting.
-            smin = np.min(coord, axis=0) - self._padding
-            smax = np.max(coord, axis=0) + self._padding
+            try:
+                smin = np.min(coord, axis=0) - self._padding
+                smax = np.max(coord, axis=0) + self._padding
+            except ValueError as err:
+                errmsg = ("No atoms in AtomGroup at input time frame. "
+                          "Grid for density could not be automatically"
+                          " generated. If this is expected, a user"
+                          " defined grid will need to be "
+                          "provided instead.")
+                raise ValueError(errmsg) from err
         BINS = fixedwidth_bins(self._delta, smin, smax)
         arange = np.transpose(np.vstack((BINS['min'], BINS['max'])))
         bins = BINS['Nbins']
@@ -487,8 +506,8 @@ def _set_user_grid(gridcenter, xdim, ydim, zdim, smin, smax):
             raise ValueError("xdim, ydim, and zdim must be numbers") from err
 
         # Set min/max by shifting by half the edge length of each dimension
-        umin = gridcenter - xyzdim/2
-        umax = gridcenter + xyzdim/2
+        umin = gridcenter - xyzdim / 2
+        umax = gridcenter + xyzdim / 2
 
         # Here we test if coords of selection fall outside of the defined grid
         # if this happens, we warn users they may want to resize their grids
@@ -657,7 +676,7 @@ def __init__(self, *args, **kwargs):
 
         parameters = kwargs.pop('parameters', {})
         if (len(args) > 0 and isinstance(args[0], str) or
-            isinstance(kwargs.get('grid', None), str)):
+                isinstance(kwargs.get('grid', None), str)):
             # try to be smart: when reading from a file then it is likely that
             # this is a density
             parameters.setdefault('isDensity', True)
@@ -695,7 +714,8 @@ def _check_set_unit(self, u):
         # all this unit crap should be a class...
         try:
             for unit_type, value in u.items():
-                if value is None:  # check here, too iffy to use dictionary[None]=None
+                # check here, too iffy to use dictionary[None]=None
+                if value is None:
                     self.units[unit_type] = None
                     continue
                 try:
@@ -763,7 +783,8 @@ def convert_length(self, unit='Angstrom'):
         """
         if unit == self.units['length']:
             return
-        cvnfact = units.get_conversion_factor('length', self.units['length'], unit)
+        cvnfact = units.get_conversion_factor(
+            'length', self.units['length'], unit)
         self.edges = [x * cvnfact for x in self.edges]
         self.units['length'] = unit
         self._update()  # needed to recalculate midpoints and origin
@@ -814,8 +835,8 @@ def convert_density(self, unit='Angstrom'):
         if unit == self.units['density']:
             return
         try:
-            self.grid *= units.get_conversion_factor('density',
-                                                     self.units['density'], unit)
+            self.grid *= units.get_conversion_factor(
+                'density', self.units['density'], unit)
         except KeyError:
             errmsg = (f"The name of the unit ({unit} supplied) must be one "
                       f"of:\n{units.conversion_factor['density'].keys()}")
@@ -827,4 +848,4 @@ def __repr__(self):
             grid_type = 'density'
         else:
             grid_type = 'histogram'
-        return '<Density ' + grid_type + ' with ' + str(self.grid.shape) + ' bins>'
+        return f"<Density {grid_type} with {self.grid.shape} bins>"

testsuite/MDAnalysisTests/analysis/test_density.py

@@ -120,7 +120,8 @@ class DensityParameters(object):
     topology = TPR
     trajectory = XTC
     delta = 2.0
-    selections = {'static': "name OW",
+    selections = {'none': "resname None",
+                  'static': "name OW",
                   'dynamic': "name OW and around 4 (protein and resid 1-10)",
                   'solute': "protein and not name H*",
                   }
@@ -254,6 +255,25 @@ def test_ValueError_userdefn_xdim_type(self, universe):
                 delta=self.delta, xdim="MDAnalysis", ydim=10.0, zdim=10.0,
                 gridcenter=self.gridcenters['static_defined']).run(step=5)
 
+    def test_warn_noatomgroup(self, universe):
+        regex = ("No atoms in AtomGroup at input time frame. "
+                 "Grid for density could not be automatically"
+                 " generated. A user defined grid was found"
+                 " and is being used as the density grid")
+        with pytest.warns(UserWarning, match=regex):
+            D = density.DensityAnalysis(
+                universe.select_atoms(self.selections['none']),
+                delta=self.delta, xdim=1.0, ydim=2.0, zdim=2.0, padding=0.0,
+                gridcenter=self.gridcenters['static_defined']).run(step=5)
+
+    def test_ValueError_noatomgroup(self,universe):        
+        with pytest.raises(ValueError, match="No atoms in AtomGroup at input time frame. "
+                                             "Grid for density could not be automatically"
+                                             " generated. If this is expected, a user"
+                                             " defined grid will need to be "
+                                             "provided instead."):
+            D = density.DensityAnalysis(
+                universe.select_atoms(self.selections['none'])).run(step=5)
 
 class TestGridImport(object):