Merge pull request #46 from Pranavkhade/41-deprecationwarning-delauna…

…y-attribute-vertices-is-deprecated-in-favor-of-simplices

Update geometry.py

packman/__init__.py

@@ -15,4 +15,4 @@
 
 
 #VERSION CHANGE HERE CHANGES IT IN docs AND setup.py
-__version__='1.4.7'
+__version__='1.4.8'

packman/geometry/geometry.py

@@ -97,7 +97,7 @@ def calculate_alphafitness(alpha, circumradius):
     AlphaShape   = []
     ProteinGraph = Graph()
 
-    for a, b, c, d in DelaunayTesssellations.vertices:
+    for a, b, c, d in DelaunayTesssellations.simplices:
         Tetrahydron = [atoms[a],atoms[b],atoms[c],atoms[d]]
         Centre, Radius = Circumsphere(Tetrahydron)
         #Alpha Test
@@ -109,4 +109,4 @@ def calculate_alphafitness(alpha, circumradius):
     if(get_graph):
         return AlphaShape, ProteinGraph
     else:
-        return AlphaShape
+        return AlphaShape

packman/molecule/model.py

@@ -90,10 +90,10 @@ def __init__(self,id,AllAtoms,AllResidues,AllChains,AllHetAtoms,AllHetMols):
         self.__properties = {}
 
     def __getitem__(self,ChainID):
-        try:
-            return self.__AllChains[ChainID]
-        except KeyError:
-            logging.warning('Please provide a valid chain ID.')
+        #try:
+        return self.__AllChains[ChainID]
+        #except KeyError:
+        #    logging.warning('Please provide a valid chain ID.')
 
     #Get Functions
     def get_id(self):