Added explicit imports. (#44)

* Explicit imports added. Folder reorganization.

membrane_curvature/__init__.py

@@ -4,7 +4,8 @@
 """
 
 # Add imports here
-from .core import *
+from membrane_curvature.surface import normalized_grid, derive_surface, get_z_surface
+from membrane_curvature.curvature import mean_curvature, gaussian_curvature
 
 # Handle versioneer
 from ._version import get_versions

membrane_curvature/core.py

@@ -5,7 +5,8 @@
 Handles the primary functions
 """
 
-from .lib.mods import derive_surface, gaussian_curvature, mean_curvature
+from membrane_curvature.surface import normalized_grid, derive_surface, get_z_surface
+from membrane_curvature.curvature import mean_curvature, gaussian_curvature
 import time
 import MDAnalysis as mda
 import math
@@ -16,7 +17,7 @@
 
 def main():
 
-    start_time = time.time()
+
 
     # 1. Populate universe with coordinates and trajectory
     u = mda.Universe(topology, trajectory)
@@ -38,8 +39,6 @@ def main():
     K = gaussian_curvature(z_coords)
     H = mean_curvature(z_coords)
 
-    timer(time.time(), start_time)
-
     return
 
 

membrane_curvature/curvature.py

@@ -0,0 +1,54 @@
+import numpy as np
+
+
+def gaussian_curvature(Z):
+    """
+    Calculate gaussian curvature from Z cloud points.
+
+
+    Parameters
+    ----------
+    Z : Numpy array, cloud of points.
+
+
+    Returns
+    -------
+    K : 2d-array
+        Returns 2-dimensional array object with values of mean curvature.
+
+    """
+
+    Zy, Zx = np.gradient(Z)
+    Zxy, Zxx = np.gradient(Zx)
+    Zyy, _ = np.gradient(Zy)
+
+    K = (Zxx * Zyy - (Zxy ** 2)) / (1 + (Zx ** 2) + (Zy ** 2)) ** 2
+
+    return K
+
+
+def mean_curvature(Z):
+    """
+    Calculates mean curvature from Z cloud points.
+
+
+    Parameters
+    ----------
+    Z : Numpy array, cloud of points.
+
+
+    Returns
+    -------
+    H : 2d-array
+        Returns 2-dimensional array object with values of gaussian curvature.
+
+    """
+
+    Zy, Zx = np.gradient(Z)
+    Zxy, Zxx = np.gradient(Zx)
+    Zyy, _ = np.gradient(Zy)
+
+    H = (Zx**2 + 1) * Zyy - 2 * Zx * Zy * Zxy + (Zy**2 + 1) * Zxx
+    H = -H / (2 * (Zx**2 + Zy**2 + 1)**(1.5))
+
+    return H

membrane_curvature/lib/mods.py → membrane_curvature/surface.py

@@ -107,54 +107,4 @@ def normalized_grid(grid_z_coordinates, grid_norm_unit):
     return z_normalized
 
 
-def gaussian_curvature(Z):
-    """
-    Calculate gaussian curvature from Z cloud points.
-
-
-    Parameters
-    ----------
-    Z : Numpy array, cloud of points.
-
-
-    Returns
-    -------
-    K : 2d-array
-        Returns 2-dimensional array object with values of mean curvature.
-
-    """
-
-    Zy, Zx = np.gradient(Z)
-    Zxy, Zxx = np.gradient(Zx)
-    Zyy, _ = np.gradient(Zy)
-
-    K = (Zxx * Zyy - (Zxy ** 2)) / (1 + (Zx ** 2) + (Zy ** 2)) ** 2
-
-    return K
-
-
-def mean_curvature(Z):
-    """
-    Calculates mean curvature from Z cloud points.
-
-
-    Parameters
-    ----------
-    Z : Numpy array, cloud of points.
-
-
-    Returns
-    -------
-    H : 2d-array
-        Returns 2-dimensional array object with values of gaussian curvature.
-
-    """
-
-    Zy, Zx = np.gradient(Z)
-    Zxy, Zxx = np.gradient(Zx)
-    Zyy, _ = np.gradient(Zy)
-
-    H = (Zx**2 + 1) * Zyy - 2 * Zx * Zy * Zxy + (Zy**2 + 1) * Zxx
-    H = -H / (2 * (Zx**2 + Zy**2 + 1)**(1.5))
 
-    return H

membrane_curvature/tests/test_mdakit_membcurv.py → membrane_curvature/tests/test_membrane_curvature.py

@@ -3,7 +3,8 @@
 """
 
 import pytest
-from ..lib.mods import mean_curvature, gaussian_curvature, normalized_grid, derive_surface, get_z_surface
+from membrane_curvature.surface import normalized_grid, derive_surface, get_z_surface
+from membrane_curvature.curvature import mean_curvature, gaussian_curvature
 import numpy as np
 from numpy.testing import assert_almost_equal
 import MDAnalysis as mda