From 652c520bc4384ab591d26942812390799bd5a5e2 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Sat, 1 Feb 2020 13:07:49 -0700
Subject: Fix zero padding
---
ml_exp/bob.py | 16 ++++++++++++----
1 file changed, 12 insertions(+), 4 deletions(-)
diff --git a/ml_exp/bob.py b/ml_exp/bob.py
index 5f45019a0..e3d54c5fa 100644
--- a/ml_exp/bob.py
+++ b/ml_exp/bob.py
@@ -43,6 +43,7 @@ def check_bond(bags,
def bob(c_matrix,
atoms,
+ max_n=25,
max_bond_len=325):
"""
Creates the bag of bond using the coulomb matrix data.
@@ -54,10 +55,15 @@ def bob(c_matrix,
bond_n = (n * n - n) / 2 + n
n_r = range(n)
+ if max_n < n:
+ print(''.join(['Error. Molecule matrix dimension (mol_n) is ',
+ 'greater than max_len. Using mol_n.']))
+ max_n = n
+
if max_bond_len < bond_n:
print(''.join(['Error. Molecule bond lenght (bond_n) is ',
'greater than max_bond_len. Using bond_n.']))
- max_bond_len = None
+ max_bond_len = bond_n
# List where each bag data is stored.
bags = []
@@ -90,11 +96,13 @@ def bob(c_matrix,
# Create the final vector for the bob.
bob = array(zeros(max_bond_len), dtype=float)
c_i = 0
- for bond in bonds:
+ for i, bond in enumerate(bonds):
checker = check_bond(bags, bond)
if checker[0]:
- for num in bags[checker[1]][1:]:
- bob[c_i] = num
+ for j, num in enumerate(bags[checker[1]][1:]):
+ # 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.
+ bob[i*max_n + j] = num
c_i += 1
# This is set to false because this was a debugging measure.
elif False:
--
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