added test avg_mean with wrap True and False

membrane_curvature/base.py

@@ -75,9 +75,11 @@ class MembraneCurvature(AnalysisBase):
 
     Notes
     -----
-    Use `wrap=True` when `mda.Universe` contains the raw trajectory, and
-    `wrap=False` for processed trajectories. For more details on when to use
-    `wrap=True`, check the `Usage
+    Use `wrap=True` to translates the atoms of your `mda.Universe` back 
+    in the unit cell. Use `wrap=False` for processed trajectories where 
+    rotational/translational fit is performed.
+    
+    For more details on when to use `wrap=True`, check the `Usage
     <https://membrane-curvature.readthedocs.io/en/latest/source/pages/Usage.html>`_
     page.
 
@@ -127,6 +129,7 @@ def __init__(self, universe, select='all',
         self.n_y_bins = n_y_bins
         self.x_range = x_range if x_range else (0, universe.dimensions[0])
         self.y_range = y_range if y_range else (0, universe.dimensions[1])
+        print(universe.dimensions)
 
         # Raise if selection doesn't exist
         if len(self.ag) == 0:
@@ -145,10 +148,13 @@ def __init__(self, universe, select='all',
         # Apply wrapping coordinates
         if self.wrap:
             self.ag.wrap()
+        # Warning
         else:
             msg = (" `wrap == False` may result in inaccurate calculation "
                    "of membrane curvature. Surfaces will be derived from "
-                   "a reduced number of atoms.")
+                   "a reduced number of atoms. \n " 
+                   " Ignore this warning if your trajectory has "
+                   " rotational/translational fit rotations! ")
             warnings.warn(msg)
             logger.warn(msg)
 

membrane_curvature/data/test_po4_small.gro

@@ -9,4 +9,4 @@ Test file 9 lipids in grid
  2708POPC   PO4    7   0.000   2.000  12.000
  2713POPC   PO4    8   1.000   2.000  12.000
  2999POPC   PO4    9   2.000   2.000  12.000
-  3.00000  3.00000  3.00000   
+  3.00000  3.00000  30.00000   

membrane_curvature/tests/test_membrane_curvature.py

@@ -2,7 +2,7 @@
 Unit and regression test for the membrane_curvature package.
 """
 
-from numpy.lib.stride_tricks import DummyArray
+
 import pytest
 from membrane_curvature.surface import normalized_grid, derive_surface, get_z_surface
 from membrane_curvature.curvature import mean_curvature, gaussian_curvature
@@ -212,7 +212,7 @@ def test_get_z_surface(x_bin, y_bin, x_range, y_range, expected_surface):
 class TestMembraneCurvature(object):
     @pytest.fixture()
     def universe(self):
-        return mda.Universe(GRO_PO4_SMALL, XTC_PO4_SMALL)
+        return mda.Universe(GRO_PO4_SMALL)
 
     @pytest.fixture()
     def universe_dummy(self):
@@ -299,6 +299,32 @@ def test_analysis_get_z_surface(self, universe, x_bin, y_bin, expected_surface):
         avg_surface = mc.results.average_z_surface
         assert_almost_equal(avg_surface, expected_surface)
 
+    # test using wrap=True
+    def test_analysis_mean_wrap(self, universe):
+        expected_mean = np.array([[7.50000000e+00,  1.33985392e-01,  2.77315457e-04],
+                                  [-2.77315457e-04, -3.53944270e-01, -7.50000000e+00],
+                                  [-2.77315457e-04, -5.01100068e-01, -7.50000000e+00]])
+        mc = MembraneCurvature(universe,
+                               select='name PO4',
+                               n_x_bins=3,
+                               n_y_bins=3).run()
+        avg_mean = mc.results.average_mean
+        assert_almost_equal(avg_mean, expected_mean)
+
+    # test using wrap=False
+    def test_analysis_mean_no_wrap(self, universe):
+        expected_mean = np.array([[7.50000000e+00,  1.33985392e-01,  2.77315457e-04],
+                                  [-2.77315457e-04, -3.53944270e-01, -7.50000000e+00],
+                                  [-2.77315457e-04, -5.01100068e-01, -7.50000000e+00]])
+        mc = MembraneCurvature(universe,
+                               select='name PO4',
+                               n_x_bins=3,
+                               n_y_bins=3,
+                               wrap='False').run()
+        avg_mean = mc.results.average_mean
+        assert_almost_equal(avg_mean, expected_mean)
+
+
     # Expected values update after applying coordinates wrap
     @pytest.mark.parametrize('x_bin, y_bin, expected_surface', [
         (3, 3,