diff options
| -rw-r--r-- | ml_exp/compound.py | 15 | ||||
| -rw-r--r-- | 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): """ |