Move bob to representations

2 files changed, 94 insertions, 117 deletions

diff --git a/ml_exp/bob.py b/ml_exp/bob.py
deleted file mode 100644
index 86efecdb4..000000000
--- a/ml_exp/bob.py
+++ /dev/null
@@ -1,117 +0,0 @@
-"""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
-from collections import Counter
-
-
-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_n=25,
-        max_bond_len=325):
-    """
-    Creates the bag of bond using the coulomb matrix data.
-    c_matrix: coulomb matrix.
-    atoms: list of atoms.
-    max_n: maximum amount of atoms.
-    max_bond_len: maximum amount of bonds in molecule.
-    """
-    n = len(atoms)
-    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 = bond_n
-
-    # 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_counter = Counter(atoms)
-    atom_list = sorted(list(set(atoms)))
-    bonds = []
-    for i, a_i in enumerate(atom_list):
-        if atom_counter[a_i] > 1:
-            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 i, bond in enumerate(bonds):
-        checker = check_bond(bags, bond)
-        if checker[0]:
-            for j, num in enumerate(sorted(bags[checker[1]][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.
-        else:
-            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
diff --git a/ml_exp/representations.py b/ml_exp/representations.py
index 11c30dfd2..3119a4a88 100644
--- a/ml_exp/representations.py
+++ b/ml_exp/representations.py
@@ -21,6 +21,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import numpy as np
+from collections import Counter
 
 
 def coulomb_matrix(coords,
@@ -287,3 +288,96 @@ def adjacency_matrix(fnm,
                         am[i, j] = fnm[bond_i[0], bond_i[1]]
 
     return am
+
+
+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_n=25,
+        max_bond_len=325):
+    """
+    Creates the bag of bond using the coulomb matrix data.
+    c_matrix: coulomb matrix.
+    atoms: list of atoms.
+    max_n: maximum amount of atoms.
+    max_bond_len: maximum amount of bonds in molecule.
+    """
+    n = len(atoms)
+    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 = bond_n
+
+    # 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_counter = Counter(atoms)
+    atom_list = sorted(list(set(atoms)))
+    bonds = []
+    for i, a_i in enumerate(atom_list):
+        if atom_counter[a_i] > 1:
+            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 i, bond in enumerate(bonds):
+        checker = check_bond(bags, bond)
+        if checker[0]:
+            for j, num in enumerate(sorted(bags[checker[1]][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.
+        else:
+            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