add more unitcell tests

Author: kain88-de

testsuite/MDAnalysisTests/formats/test_libdcd.py

@@ -476,7 +476,7 @@ def setUp(self):
                                              dtype=np.float32)
 
 
-class TestDCDWriteRandom():
+class _TestDCDWriteRandom(object):
     # should only be supported for Charmm24 format writing (for now)
 
     def setUp(self):
@@ -489,15 +489,19 @@ def setUp(self):
         self.expected_remarks = '''* DIMS ADK SEQUENCE FOR PORE PROGRAM                                            * WRITTEN BY LIZ DENNING (6.2008)                                               *  DATE:     6/ 6/ 8     17:23:56      CREATED BY USER: denniej0                '''
 
         np.random.seed(1178083)
-        self.random_unitcells = np.random.random((self.expected_frames, 6)).astype(np.float64)
+        if self.charmm:
+            self.random_unitcells = np.random.random((self.expected_frames, 6)).astype(np.float64)
+        else:
+            self.random_unitcells = np.random.uniform(high=80,size=(self.expected_frames, 6)).astype(np.float64)
+
         with DCDFile(self.readfile) as f_in, DCDFile(self.testfile, 'w') as f_out:
             for index, frame in enumerate(f_in):
                 box=frame.unitcell.astype(np.float64)
                 f_out.write(xyz=frame.x,
                             box=self.random_unitcells[index],
                             step=f_in.istart,
                             natoms=frame.x.shape[0],
-                            charmm=1, # DCD should be CHARMM
+                            charmm=self.charmm, # DCD should be CHARMM
                             time_step=f_in.delta,
                             ts_between_saves=f_in.nsavc,
                             remarks=f_in.remarks)
@@ -521,17 +525,25 @@ def test_written_unit_cell_random(self):
             while curr_frame < test.n_frames:
                 written_unitcell = test.read()[1]
                 ref_unitcell = self.random_unitcells[curr_frame]
-                ref_unitcell[1] = math.degrees(math.acos(ref_unitcell[1]))
-                ref_unitcell[3] = math.degrees(math.acos(ref_unitcell[3]))
-                ref_unitcell[4] = math.degrees(math.acos(ref_unitcell[4]))
+                if self.charmm:
+                    ref_unitcell[1] = math.degrees(math.acos(ref_unitcell[1]))
+                    ref_unitcell[3] = math.degrees(math.acos(ref_unitcell[3]))
+                    ref_unitcell[4] = math.degrees(math.acos(ref_unitcell[4]))
 
-                _ts_order = [0, 2, 5, 4, 3, 1]
-                ref_unitcell = np.take(ref_unitcell, _ts_order)
+                    _ts_order = [0, 2, 5, 4, 3, 1]
+                    ref_unitcell = np.take(ref_unitcell, _ts_order)
                 curr_frame += 1
                 assert_allclose(written_unitcell, ref_unitcell,
                                 rtol=1e-05)
 
 
+class TestRandomUnitCellCHARMM(_TestDCDWriteRandom):
+    charmm = 1
+
+class TestRandomUnitCellNAMD(_TestDCDWriteRandom):
+    charmm = 0
+
+
 class TestDCDByteArithmetic(object):
 
     def setUp(self):