density_from_PDB: deprecated, test, and bugfix

- density_from_PDB is terrible code (I wrote it) and not used: deprecated and to be
  removed for 2.0.0
- added test so that it is covered
- fixed bug that was uncovered by test (us ag.tempfactors)
- added test for Bfactors2RMSF

package/CHANGELOG

@@ -129,8 +129,9 @@ Deprecations
   * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)
   * analysis.density.density_from_Universe() (remove in 2.0)
   * analysis.density.notwithin_coordinates_factory() (remove in 2.0)
+  * analysis.density.density_from_PDB and BfactorDensityCreator (remove in 2.0)
+
 
-
 09/05/19 IAlibay, richardjgowers
 
   * 0.20.1

package/MDAnalysis/analysis/density.py

@@ -1268,6 +1268,7 @@ def Bfactor2RMSF(B):
     return np.sqrt(3. * B / 8.) / np.pi
 
 
+@deprecate(release="1.0.0", remove="2.0.0")
 def density_from_PDB(pdb, **kwargs):
     """Create a density from a single frame PDB.
 
@@ -1313,10 +1314,15 @@ def density_from_PDB(pdb, **kwargs):
     --------
     :func:`Bfactor2RMSF` and :class:`BfactorDensityCreator`
 
+
+    .. deprecated: 1.0.0
+       This function is not well tested or optimized and will be removed
+       in 2.0.0.
     """
     return BfactorDensityCreator(pdb, **kwargs).Density()
 
 
+@deprecate(release="1.0.0", remove="2.0.0")
 class BfactorDensityCreator(object):
     """Create a density grid from a pdb file using MDAnalysis.
 
@@ -1337,6 +1343,10 @@ class BfactorDensityCreator(object):
     .. * Using a temporary Creator class with the
     ..   :meth:`BfactorDensityCreator.Density` helper method is clumsy.
 
+
+    .. deprecated: 1.0.0
+       This function is not well tested or optimized and will be removed
+       in 2.0.0.
     """
 
     @deprecate(release="1.0.0", remove="2.0.0")
@@ -1405,11 +1415,11 @@ def __init__(self, pdb, delta=1.0, select='resname HOH and name O',
         if sigma is None:
             # histogram individually, and smear out at the same time
             # with the appropriate B-factor
-            if np.any(group.bfactors == 0.0):
+            if np.any(group.tempfactors == 0.0):
                 wmsg = "Some B-factors are Zero (will be skipped)."
                 logger.warning(wmsg)
                 warnings.warn(wmsg, category=MissingDataWarning)
-            rmsf = Bfactor2RMSF(group.bfactors)
+            rmsf = Bfactor2RMSF(group.tempfactors)
             grid *= 0.0  # reset grid
             self.g = self._smear_rmsf(coord, grid, self.edges, rmsf)
         else:
@@ -1450,7 +1460,7 @@ def _smear_sigma(self, grid, sigma):
         for iwat in range(len(pos[0])):  # super-ugly loop
             p = tuple([wp[iwat] for wp in pos])
             g += grid[p] * np.fromfunction(self._gaussian, grid.shape, dtype=np.int, p=p, sigma=sigma)
-            print("Smearing out atom position {0:4d}/{1:5d} with RMSF {2:4.2f} A\r".format(iwat + 1, len(pos[0]), sigma),)
+            # print("Smearing out atom position {0:4d}/{1:5d} with RMSF {2:4.2f} A\r".format(iwat + 1, len(pos[0]), sigma),)
         return g
 
     def _smear_rmsf(self, coordinates, grid, edges, rmsf):
@@ -1463,7 +1473,7 @@ def _smear_rmsf(self, coordinates, grid, edges, rmsf):
                 continue
             g += np.fromfunction(self._gaussian_cartesian, grid.shape, dtype=np.int,
                                     c=coord, sigma=rmsf[iwat])
-            print("Smearing out atom position {0:4d}/{1:5d} with RMSF {2:4.2f} A\r".format(iwat + 1, N, rmsf[iwat]),)
+            # print("Smearing out atom position {0:4d}/{1:5d} with RMSF {2:4.2f} A\r".format(iwat + 1, N, rmsf[iwat]),)
         return g
 
     def _gaussian(self, i, j, k, p, sigma):

testsuite/MDAnalysisTests/analysis/test_density.py

@@ -36,7 +36,7 @@
 import MDAnalysis as mda
 from MDAnalysis.analysis import density
 
-from MDAnalysisTests.datafiles import TPR, XTC, GRO
+from MDAnalysisTests.datafiles import TPR, XTC, GRO, PDB_full
 
 
 class TestDensity(object):
@@ -425,3 +425,15 @@ def test_Bfactor2RMSF(B):
     values = density.Bfactor2RMSF(B)
     ref = np.sqrt(3. * B / 8.) / np.pi  # original equation
     assert_almost_equal(values, ref)
+
+@pytest.mark.parametrize('sigma,ref_shape,ref_gridsum',
+                         [(None, (21, 26, 29), 108.710149),
+                          (1.5,  (21, 26, 29), 160.050167)])
+def test_density_from_PDB(sigma, ref_shape, ref_gridsum):
+    # simple test that the code runs: use B-factors from PDB or fixed sigma
+    D = density.density_from_PDB(PDB_full, delta=2.0, sigma=sigma)
+
+    assert isinstance(D, density.Density)
+    assert_equal(D.grid.shape, ref_shape)
+    assert_almost_equal(D.grid.sum(), ref_gridsum, decimal=6)
+