From 3e87eec5f6ef8abe226efedc56c9491ab56b5b73 Mon Sep 17 00:00:00 2001
From: Estefania Barreto-Ojeda <estefania.barretooje@ucalgary.ca>
Date: Mon, 5 Jul 2021 22:47:44 -0600
Subject: [PATCH] Added explicit imports.  (#44)

* Explicit imports added. Folder reorganization.
---
 membrane_curvature/__init__.py                |  3 +-
 membrane_curvature/core.py                    |  7 ++-
 membrane_curvature/curvature.py               | 54 +++++++++++++++++++
 .../{lib/mods.py => surface.py}               | 50 -----------------
 ...membcurv.py => test_membrane_curvature.py} |  3 +-
 5 files changed, 61 insertions(+), 56 deletions(-)
 create mode 100644 membrane_curvature/curvature.py
 rename membrane_curvature/{lib/mods.py => surface.py} (77%)
 rename membrane_curvature/tests/{test_mdakit_membcurv.py => test_membrane_curvature.py} (98%)

diff --git a/membrane_curvature/__init__.py b/membrane_curvature/__init__.py
index 38923a2..c803aeb 100644
--- a/membrane_curvature/__init__.py
+++ b/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
diff --git a/membrane_curvature/core.py b/membrane_curvature/core.py
index da0a66f..8883003 100644
--- a/membrane_curvature/core.py
+++ b/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
 
 
diff --git a/membrane_curvature/curvature.py b/membrane_curvature/curvature.py
new file mode 100644
index 0000000..6ff8e26
--- /dev/null
+++ b/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
diff --git a/membrane_curvature/lib/mods.py b/membrane_curvature/surface.py
similarity index 77%
rename from membrane_curvature/lib/mods.py
rename to membrane_curvature/surface.py
index b6751c0..17c3b76 100644
--- a/membrane_curvature/lib/mods.py
+++ b/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
diff --git a/membrane_curvature/tests/test_mdakit_membcurv.py b/membrane_curvature/tests/test_membrane_curvature.py
similarity index 98%
rename from membrane_curvature/tests/test_mdakit_membcurv.py
rename to membrane_curvature/tests/test_membrane_curvature.py
index 563f8c0..0a5efb8 100644
--- a/membrane_curvature/tests/test_mdakit_membcurv.py
+++ b/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