From c245130b09450c3b37ec150a0e58d0d42ac2d754 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Mon, 27 Jan 2020 00:16:44 -0700
Subject: Add bag of bonds

---
 ml_exp/__main__.py |  12 +++++-
 ml_exp/bob.py      | 105 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 116 insertions(+), 1 deletion(-)
 create mode 100644 ml_exp/bob.py

diff --git a/ml_exp/__main__.py b/ml_exp/__main__.py
index 6d62333e2..9b4a18cc3 100644
--- a/ml_exp/__main__.py
+++ b/ml_exp/__main__.py
@@ -23,7 +23,9 @@ SOFTWARE.
 # from ml_exp.do_ml import do_ml
 # from ml_exp.misc import plot_benchmarks
 from ml_exp.read_qm7_data import read_qm7_data
-from ml_exp.adj_matrix import fneig_matrix, adj_matrix
+# from ml_exp.adj_matrix import fneig_matrix, adj_matrix
+from ml_exp.c_matrix import c_matrix
+from ml_exp.bob import bob
 
 if __name__ == '__main__':
     """
@@ -39,6 +41,7 @@ if __name__ == '__main__':
           show_msgs=True)
     """
     # plot_benchmarks()
+    """
     xyz, nc, pbe0, delta, atoms = read_qm7_data(return_atoms=True)
     for i in range(1):
         fnm, bonds, forces = fneig_matrix(atoms[i], xyz[i], nc[i], True)
@@ -50,3 +53,10 @@ if __name__ == '__main__':
         print(f'{i} adjacency matrix\n{am}')
         print('-'*30)
     print('OK!')
+    """
+    xyz, nc, pbe0, delta, atoms = read_qm7_data(return_atoms=True)
+    for i in range(1):
+        cm = c_matrix(xyz[i], nc[i], as_eig=False)
+        bob = bob(cm, atoms[i])
+        print(f'{i} coulomb matrix\n{cm}')
+        print(f'{i} bag of bonds\n{bob}')
diff --git a/ml_exp/bob.py b/ml_exp/bob.py
new file mode 100644
index 000000000..0d31face0
--- /dev/null
+++ b/ml_exp/bob.py
@@ -0,0 +1,105 @@
+"""MIT License
+
+Copyright (c) 2019 David Luevano Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+from numpy import array, zeros
+
+
+def check_bond(bags,
+               bond):
+    """
+    Checks if a bond is in a bag.
+    bags: list of bags, containing a bag per entry, which in turn
+    contains a list of bond-values.
+    bond: bond to check.
+    """
+    if bags == []:
+        return False, None
+
+    for i, bag in enumerate(bags):
+        if bag[0] == bond:
+            return True, i
+
+    return False, None
+
+
+def bob(c_matrix,
+        atoms,
+        max_bond_len=325):
+    """
+    Creates the bag of bond using the coulomb matrix data.
+    c_matrix: coulomb matrix.
+    atoms: list of atoms.
+    max_len: maximum amount of bonds in molecule.
+    """
+    n = len(atoms)
+    bond_n = (n*n-n)/2+n
+    n_r = range(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
+
+    # List where each bag data is stored.
+    bags = []
+    for i in n_r:
+        for j in n_r:
+            # Work only in the upper triangle of the coulomb matrix.
+            if j >= i:
+                # Get the string of the current bond.
+                if i == j:
+                    current_bond = atoms[i]
+                else:
+                    current_bond = ''.join(sorted([atoms[i], atoms[j]]))
+
+                # Check if that bond is already in a bag.
+                checker = check_bond(bags, current_bond)
+                # Either create a new bag or add values to an existing one.
+                if not checker[0]:
+                    bags.append([current_bond, c_matrix[i, j]])
+                else:
+                    bags[checker[1]].append(c_matrix[i, j])
+
+    # Create the actual bond list ordered.
+    atom_list = sorted(list(set(atoms)))
+    bonds = []
+    for i, a_i in enumerate(atom_list):
+        for a_j in atom_list[i:]:
+            bonds.append(''.join(sorted([a_i, a_j])))
+    bonds = atom_list + bonds
+
+    # Create the final vector for the bob.
+    bob = array(zeros(max_bond_len), dtype=float)
+    c_i = 0
+    for bond in bonds:
+        checker = check_bond(bags, bond)
+        if checker[0]:
+            for num in bags[checker[1]][1:]:
+                bob[c_i] = num
+                c_i += 1
+        # This is set to false because this was a debugging measure.
+        elif False:
+            print(''.join([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 once',
+                           ' in the molecule.']))
+    return bob
-- 
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