From 14412daeef35e9a01d8827567bfdd34c88de303f Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 10 Mar 2020 14:20:22 -0700
Subject: Add epsilon index representation
---
ml_exp/compound.py | 15 +++++++++++++--
ml_exp/representations.py | 34 ++++++++++++++++++++++++++++++++++
2 files changed, 47 insertions(+), 2 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 6c8525195..eae280d38 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -23,7 +23,7 @@ SOFTWARE.
import numpy as np
from ml_exp.data import NUCLEAR_CHARGE
from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
- get_helping_data, adjacency_matrix, bag_of_bonds
+ get_helping_data, adjacency_matrix, epsilon_index, bag_of_bonds
class Compound:
@@ -47,6 +47,7 @@ class Compound:
self.cm = None
self.ljm = None
self.am = None
+ self.ei = None
self.bob = None
self.bo_atoms = None
self.bok_cx = None
@@ -133,10 +134,20 @@ class Compound:
use_forces=use_forces,
size=size)
+ def gen_ei(self,
+ size=23):
+ """
+ Generates the Epsilon Index for the compound.
+ size: compound size.
+ """
+ self.ei = epsilon_index(self.am,
+ bonds_i,
+ size=size)
+
def gen_bob(self,
size=23):
"""
- Generate the Bag of Stuff for the compound.
+ Generate the Bag of Bonds for the compound.
size: compound size.
"""
self.bob = bag_of_bonds(self.cm,
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 4a685d388..ff5741816 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -254,6 +254,40 @@ the current compound.')
return np.pad(am, ((0, size - n), (0, size - n)), 'constant')
+def epsilon_index(am,
+ bonds_i,
+ size=23):
+ """
+ Calculates the Epsilon index of G, presented by Estrada.
+ am: adjacency matrix.
+ bonds_i: list of bond indexes (tuple of indexes).
+ size: compund size.
+ """
+ if am is None:
+ raise ValueError('The adjacency matrix hasn\'t been initialized for\
+the current compound.')
+
+ n = len(bonds_i)
+ if size < n:
+ print('Error. Compound size (n) is greater han (size). Using (n)\
+ instead of (size).')
+ size = n
+
+ deltas = np.zeros(n, dtype=np.float64)
+
+ for i in range(n):
+ deltas[i] = np.sum(am[i, :])
+
+ ei = 0.0
+ for i in range(n - 1):
+ for j in range(i +1, n):
+ if (bonds_i[i][0] in bonds_i[j]) or (bonds_i[i][0] in bonds_i[j]):
+ val = deltas[i]*deltas[j]
+ ei += 1.0/val**0.5
+
+ return ei
+
+
def check_bond(bags,
bond):
"""
--
cgit v1.2.3-70-g09d2