From 2db295947a75ab0347ba0e11b98564da9d228c6a Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 09:08:22 -0700
Subject: Temp fix for adj mat

---
 ml_exp/representations.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 5e684314b..5e99627df 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -242,12 +242,14 @@ size. Arrays are not of the right shape.')
 def adjacency_matrix(fnm,
                      bonds,
                      forces,
+                     use_forces=False,
                      size=22):
     """
     Calculates the adjacency matrix given the bond list.
     fnm: first neighbour matrix.
     bonds: list of bonds (tuple of indexes).
     forces: list of forces.
+    use_forces: if the use of forces instead of k_cx should be used.
     size: compund size.
     """
     n = len(bonds)
@@ -264,7 +266,7 @@ def adjacency_matrix(fnm,
             # Ignore the diagonal.
             if i != j:
                 if (bond_i[0] in bond_j) or (bond_i[1] in bond_j):
-                    if forces:
+                    if use_forces:
                         am[i, j] = np.dot(forces[i], forces[j])
                     else:
                         am[i, j] = fnm[bond_i[0], bond_i[1]]
-- 
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