Update visuals.py

Added comments.

visuals.py

@@ -6,9 +6,22 @@
 
 def plot_coords(coords, array=True, bare_plot=False):
     '''
-    Takes a list of coordinates and coverts to correct format for matplotlib
-    '''
+    Plots a list of coordinates in 3D.
+
+    Parameters:
+        coords (list or ndarray): A list of coordinates. If `array` is `True`,
+                                  `coords` should be an ndarray with shape (3, N).
+                                  If `array` is `False`, `coords` should be a list of
+                                  tuples containing the X, Y, Z, alpha, beta, diam,
+                                  ect. values for each coordinate.
+        array (bool): Determines if `coords` is an ndarray or a list. Default is `True`.
+        bare_plot (bool): Determines if the plot should be bare or not. Default is `False`.
+                          If `True`, axis markers are turned off.
 
+    Returns:
+        None
+    '''
+    # Create the plot and configure it appropriately.
     ax = plt.figure()
     if bare_plot:
         # Turns off the axis markers.
@@ -18,29 +31,40 @@ def plot_coords(coords, array=True, bare_plot=False):
         ax = ax.gca(projection='3d')
 
     if array:
-        print(coords.shape)
+        # Loop over each coordinate and plot it.
         for i in range(coords.shape[1]-1):
-            # print('%f %f %f' %(coords[0,i], coords[1,i], coords[2,i]))
             ax.plot(coords[0,i:i+2], coords[1,i:i+2], coords[2,i:i+2], color='blue')
     else:
-        # Converts a list of coordinates into
-        # lists of X and Y values, respectively.
+        # Unpack the coordinates into separate arrays.
         X, Y, Z, alpha, beta, diam, _, _, _, _ = zip(*coords)
         X = np.array(X)
         Y = np.array(Y)
         Z = np.array(Z)
         diam = np.array(diam)
 
+        # Loop over each coordinate and plot it.
         for i in range(len(X)-1):
-            # print(Z[i:i+2])
-            # print('break')
             ax.plot(X[i:i+2], Y[i:i+2], Z[i:i+2], linewidth=0.5*diam[i], color='blue')
 
+    # Show the plot.
     plt.show()
 
 def print_coords(coords):
+    """
+    Prints the coordinates provided, with gaps for any `NaN` values.
+
+    Parameters:
+        coords (list): A list of coordinates to be printed. Each coordinate should be a tuple of (x, y, z, alpha, beta, diam, label).
+
+    Returns:
+        None
+    """
+
+    # Iterate through each coordinate in the list.
     for (x, y, z, _, _, _, _) in coords:
         if isnan(x):
+            # If there is a `NaN` value for the x-coordinate, print a gap.
             print('<gap>')
         else:
-            print('({:.2f}, {:.2f}, {:.2f})'.format(x, y, z))
+            # Otherwise, print the x, y, and z-coordinates rounded to 2 decimal places.
+            print('({:.2f}, {:.2f}, {:.2f})'.format(x, y, z))