From c911e871d0644829122b260572a5fe06823c2142 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Thu, 26 Mar 2020 19:49:49 -0700
Subject: Rewrite bob

---
 ml_exp/compound.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

(limited to 'ml_exp/compound.py')

diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index a85daefa4..6ace7738a 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -176,14 +176,18 @@ class Compound:
                                 size=size)
 
     def gen_bob(self,
-                size=23):
+                sort=False,
+                acount={'C':7, 'H':16, 'N':3, 'O':3, 'S':1}):
         """
         Generate the Bag of Bonds for the compound.
-        size: compound size.
+        sort: if the representation should be sorted bag-wise.
+        acount: atom count for the compound.
+        NOTE: 'cm' shouldn't be sorted by row-norm since 'atoms' isn't (sorted).
         """
         self.bob = bag_of_bonds(self.cm,
                                 self.atoms,
-                                size=size)
+                                sort=sort,
+                                acount=acount)
 
     def read_xyz(self,
                  filename,
-- 
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