Merge pull request #101 from BranniganLab/100-requested-changes-to-at…

…tribute-names

changed leaflet to leaflet_id

python/Site.py

@@ -22,7 +22,7 @@ class Site:
     name : str
         The name of this Site. e.g. "Binding site 1," "Left anterior cleft," or \
         something else descriptive.
-    leaflet : int
+    leaflet_id : int
         If 1, outer leaflet. If 2, inner leaflet.
     temperature : float
         The temperature of your system in K.
@@ -55,7 +55,7 @@ class Site:
         The binding affinity of the lipid for the Site, in kcal/mol.
     """
 
-    def __init__(self, name, leaflet, temperature):
+    def __init__(self, name, leaflet_id, temperature):
         """
         Create a Site object.
 
@@ -64,14 +64,14 @@ def __init__(self, name, leaflet, temperature):
         name : str
             The name of this Site. e.g. "Binding site 1," \
             "Left anterior cleft," or something else descriptive.
-        leaflet : int
+        leaflet_id : int
             If 1, outer leaflet. If 2, inner leaflet.
         temperature : float
             The temperature of your system in K.
         """
         self.name = name
-        assert leaflet in [1, 2], "leaflet must be 1 or 2 (1 for outer leaflet or 2 for inner leaflet)"
-        self.leaflet = leaflet
+        assert leaflet_id in [1, 2], "leaflet_id must be 1 or 2 (1 for outer leaflet or 2 for inner leaflet)"
+        self.leaflet_id = leaflet_id
         self.temperature = temperature
         self._bin_coords = None
         self._site_counts_histogram = None

python/Symmetric_Site.py

@@ -259,7 +259,7 @@ def _make_symmetric_sites(self, base_site, Ntheta):
         site_list = [base_site]
         for site_number in range(1, self.symmetry):
             site_name = base_site.name + '_' + str(site_number + 1)
-            new_site = Site(site_name, base_site.leaflet, base_site.temperature)
+            new_site = Site(site_name, base_site.leaflet_id, base_site.temperature)
             new_site.bin_coords = self._rotate_bin_coords(base_site.bin_coords, Ntheta, site_number)
             site_list.append(new_site)
         return site_list