Merge pull request #1842 from palnabarun/1685-load-new-memory-reader

Adds a check to MDAnalysis.coordinates.memory.MemoryReader to check f…

package/CHANGELOG

@@ -13,14 +13,15 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/18 richardjgowers
+??/??/18 richardjgowers, palnabarun
 
   * 0.18.1
 
 Enhancements
 
 Fixes
   * Fixed order of indices in Angle/Dihedral/Improper repr
+  * coordinates.memory.MemoryReader now takes np.ndarray only (Issue #1685)
 
 Changes
 

package/MDAnalysis/coordinates/memory.py

@@ -234,7 +234,8 @@ def __init__(self, coordinate_array, order='fac',
         Parameters
         ----------
         coordinate_array : numpy.ndarray
-            The underlying array of coordinates
+            The underlying array of coordinates. The MemoryReader now
+            necessarily requires a np.ndarray
         order : {"afc", "acf", "caf", "fac", "fca", "cfa"} (optional)
             the order/shape of the return data array, corresponding
             to (a)tom, (f)rame, (c)oordinates all six combinations
@@ -252,19 +253,35 @@ def __init__(self, coordinate_array, order='fac',
             The name of the file from which this instance is created. Set to ``None``
             when created from an array
 
+        Raises
+        ------
+        TypeError if the coordinate array passed is not a np.ndarray
+
         Note
         ----
         At the moment, only a fixed `dimension` is supported, i.e., the same
         unit cell for all frames in `coordinate_array`. See issue `#1041`_.
 
         .. _`#1041`: https://github.com/MDAnalysis/mdanalysis/issues/1041
 
+        .. versionchanged:: 0.18.1
+            The input to the MemoryReader now must be a np.ndarray
+
         """
 
         super(MemoryReader, self).__init__()
         self.filename = filename
         self.stored_order = order
-        self.set_array(np.asarray(coordinate_array), order)
+
+        # See Issue #1685. The block below checks if the coordinate array passed is of shape (N, 3) and if it is, the coordiante array is reshaped to (1, N, 3)
+        try:
+            if len(coordinate_array.shape) == 2 and coordinate_array.shape[1] == 3:
+                    coordinate_array = coordinate_array[np.newaxis, :, :]
+        except AttributeError as e:
+            raise TypeError("The input has to be a numpy.ndarray that corresponds to the layout specified by the 'order' keyword."
+                )
+
+        self.set_array(coordinate_array, order)
         self.n_frames = \
             self.coordinate_array.shape[self.stored_order.find('f')]
         self.n_atoms = \
@@ -323,7 +340,7 @@ def copy(self):
         for auxname, auxread in self._auxs.items():
             new.add_auxiliary(auxname, auxread.copy())
 
-        return new        
+        return new
 
     def set_array(self, coordinate_array, order='fac'):
         """

testsuite/MDAnalysisTests/core/test_universe.py

@@ -183,6 +183,22 @@ def test_load_new_VE(self):
         with pytest.raises(TypeError):
             u.load_new('thisfile', format = 'soup')
 
+    def test_load_new_memory_reader_success(self):
+        u = mda.Universe(GRO)
+        prot = u.select_atoms('protein')
+        u2 = mda.Merge(prot)
+        assert u2.load_new( [ prot.positions ], format=mda.coordinates.memory.MemoryReader) is u2
+
+    def test_load_new_memory_reader_fails(self):
+        def load():
+            u = mda.Universe(GRO)
+            prot = u.select_atoms('protein')
+            u2 = mda.Merge(prot)
+            u2.load_new( [[ prot.positions ]], format=mda.coordinates.memory.MemoryReader)
+
+        with pytest.raises(TypeError):
+            load()
+
     def test_universe_kwargs(self):
         u = mda.Universe(PSF, PDB_small, fake_kwarg=True)
         assert_equal(len(u.atoms), 3341, "Loading universe failed somehow")