From 0875100926939b088492ea0a736277c4ea354d1c Mon Sep 17 00:00:00 2001
From: Pranav Khade <Pranavkhade@users.noreply.github.com>
Date: Mon, 17 Jul 2023 12:31:49 -0700
Subject: [PATCH 1/2] Update geometry.py

.vertices is replaced by .simplices (https://docs.scipy.org/doc/scipy-1.11.0/release/1.11.0-notes.html#expired-deprecations)
---
 packman/geometry/geometry.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packman/geometry/geometry.py b/packman/geometry/geometry.py
index e1f6774..7be4264 100644
--- a/packman/geometry/geometry.py
+++ b/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
\ No newline at end of file
+        return AlphaShape

From 9ad0fb6e8c79e49f6d9c372b9c0683b0b7088e7a Mon Sep 17 00:00:00 2001
From: Pranav Khade <pranav.m.khade@gmail.com>
Date: Mon, 17 Jul 2023 12:55:44 -0700
Subject: [PATCH 2/2] warning fixes

---
 packman/__init__.py       | 2 +-
 packman/molecule/model.py | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/packman/__init__.py b/packman/__init__.py
index b86f282..15f7dc0 100644
--- a/packman/__init__.py
+++ b/packman/__init__.py
@@ -15,4 +15,4 @@
 
 
 #VERSION CHANGE HERE CHANGES IT IN docs AND setup.py
-__version__='1.4.7'
\ No newline at end of file
+__version__='1.4.8'
\ No newline at end of file
diff --git a/packman/molecule/model.py b/packman/molecule/model.py
index e2a5b6f..b2390c4 100644
--- a/packman/molecule/model.py
+++ b/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):