From 3943ddc4480ae6d9bb9fc15f0042832e6bef93f1 Mon Sep 17 00:00:00 2001
From: Vedant Rathore <vedantr1998@gmail.com>
Date: Wed, 1 Feb 2017 02:33:43 +0530
Subject: [PATCH] Added exception and unittest for dist_mat_to_vec of
 analysis/psa.py (Part of #597)

---
 package/MDAnalysis/analysis/psa.py            | 36 +++++--------------
 .../MDAnalysisTests/analysis/test_psa.py      | 17 ++++++++-
 2 files changed, 24 insertions(+), 29 deletions(-)

diff --git a/package/MDAnalysis/analysis/psa.py b/package/MDAnalysis/analysis/psa.py
index 6db5120b4b3..baf6756b701 100644
--- a/package/MDAnalysis/analysis/psa.py
+++ b/package/MDAnalysis/analysis/psa.py
@@ -573,10 +573,14 @@ def dist_mat_to_vec(N, i, j):
     :Returns:
       int, index (of the matrix element) in the corresponding distance vector
     """
-    try:
-        validate_dist_mat_to_vec_inputs(N, i, j)
-    except Exception as E:
-        raise E
+
+    if not (isinstance(N, int) or isinstance(i, int) or isinstance(j, int)):
+        raise ValueError("N, i, j all must be of type int")
+
+    if i < 0 or j < 0 or N < 2:
+        error_str = "Matrix indices are invalid; i and j must be greater than 0 and N must be greater the 2"
+        raise ValueError(error_str)
+
     if i > N or j > N:
         err_str = "Matrix indices are out of range; i and j must be less than"  \
                 + " N = {0:d}".format(N)
@@ -595,30 +599,6 @@ def dist_mat_to_vec(N, i, j):
         raise ValueError(err_str)
 
 
-def validate_dist_mat_to_vec_inputs(N, i, j):
-    """
-    Validate the inputs of the function dist_mat_to_vec else raise an exception
-    :param N: int
-    :param i: int
-    :param j: int
-    :return: null
-    """
-
-    # Validating if the inputs are integer
-    try:
-        NValue = int(N)
-        iValue = int(i)
-        jValue = int(j)
-    except ValueError:
-        raise ValueError
-
-    # Check if the inputs are not out of bounds
-    if N-1 > i > 0 and N >= 2 and i < j < N:
-        pass
-    else:
-        raise ValueError
-
-
 class Path(object):
     """Pre-process a :class:`MDAnalysis.Universe` object: (1) fit the
     trajectory to a reference structure, (2) convert fitted time series to a
diff --git a/testsuite/MDAnalysisTests/analysis/test_psa.py b/testsuite/MDAnalysisTests/analysis/test_psa.py
index 64443a797ba..9c6e03d3a2f 100644
--- a/testsuite/MDAnalysisTests/analysis/test_psa.py
+++ b/testsuite/MDAnalysisTests/analysis/test_psa.py
@@ -140,12 +140,27 @@ def test_dist_mat_to_vec_func_out_of_bounds(self):
         with self.assertRaises(ValueError):
             PSA.dist_mat_to_vec(5, 6, 7)
 
+        # Check if i is negative
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, -1, 2)
+
+        # Check if i is negative
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(5, 1, -2)
+
+        # Check if N is less than 2
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(1, 0, 0)
+
     def test_dist_mat_to_vec_func_i_equals_j(self):
-        """Test that ValueError is raised when i == j"""
+        """Test that ValueError is raised when i == j or i,j == N"""
 
         with self.assertRaises(ValueError):
             PSA.dist_mat_to_vec(5, 4, 4)
 
+        with self.assertRaises(ValueError):
+            PSA.dist_mat_to_vec(4, 6, 4)
+
     def test_dist_mat_to_vec_func_bad_integers(self):
         """Test that ValueError is raised when i or j are
         not Integers"""