From fe4e5afebaf7320ba5bed7f159c84bc5d1e5faec Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Sat, 29 Feb 2020 06:23:02 -0700
Subject: Rename bos to bob

---
 ml_exp/compound.py        |  9 +++------
 ml_exp/representations.py | 15 +++++++--------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 1598fa482..4dbd8c95c 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -116,18 +116,15 @@ class Compound:
                                    forces,
                                    size=size)
 
-    def gen_bos(self,
-                size=23,
-                stuff='bonds'):
+    def gen_bob(self,
+                size=23):
         """
         Generate the Bag of Stuff for the compound.
         size: compound size.
-        stuff: elements of the bag, by default the known bag of bonds.
         """
         self.bos = bag_of_stuff(self.cm,
                                 self.atoms,
-                                size=size,
-                                stuff=stuff)
+                                size=size)
 
     def read_xyz(self,
                  filename):
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index ea079595e..d4e79c7d9 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -308,10 +308,9 @@ def check_bond(bags,
     return False, None
 
 
-def bag_of_stuff(cm,
+def bag_of_bonds(cm,
                  atoms,
-                 size=23,
-                 stuff='bonds'):
+                 size=23):
     """
     Creates the Bag of Bonds using the Coulomb Matrix.
     cm: coulomb matrix.
@@ -366,19 +365,19 @@ generated as the vector of eigenvalues, try (re-)generating the CM.')
                 bonds.append(''.join(sorted([a_i, a_j])))
     bonds = atom_list + bonds
 
-    # Create the final vector for the bos.
-    bos = np.zeros(bond_size, dtype=float)
+    # Create the final vector for the bob.
+    bob = np.zeros(bond_size, dtype=float)
     c_i = 0
     for i, bond in enumerate(bonds):
         checker = check_bond(bags, bond)
         if checker[0]:
             for j, num in enumerate(sorted(bags[checker[1]][1:])[::-1]):
-                # Use c_i as the index for bos if the zero padding should
+                # Use c_i as the index for bob if the zero padding should
                 # be at the end of the vector instead of between each bond.
-                bos[i*size + j] = num
+                bob[i*size + j] = num
                 c_i += 1
         else:
             print(f'Error. Bond {bond} from bond list coudn\'t be found',
                   'in the bags list. This could be a case where the atom',
                   'is only present oncce in the molecule.')
-    return bos
+    return bob
-- 
cgit v1.2.3-70-g09d2