def get_equivalent_atoms(mol_file1, mol_file2):
"""Get a dictionary of equivalent atom pairs based on bonds
mol_file1 -- path to a .mol file
mol_file2 -- path to a second .mol file
Will return an empty dictionary if no mapping is found """
# Get coordinates and number atoms from a mol file
coords_and_bonds1 = Iab.coords_to_lists(mol_file1)
# Construct graph where nodes are atom numbers and edges are bonds
G1 = Iab.construct_graph(coords_and_bonds1)
# Get coordinates and number atoms for molecule 2
coords_and_bonds2 = Iab.coords_to_lists(mol_file2)
# Construct graph where nodes are atom numbers and edges are bonds
# for molecule 2
G2 = Iab.construct_graph(coords_and_bonds2)
# Find the combination of atoms that exclude the hydroxyl protons
# and return the mapping dictionary
return [Iab.get_redox_graph_mapping(G1, G2), coords_and_bonds1, \
coords_and_bonds2, G1, G2]
def get_max_delta_and_bonds(mapping_and_coords, name):
"""Return top three bond length changes and their atom number bonds
**Updated to also return highest non carbonyl to hydroxyl oxygen bond
length change**"""
#mapping_dictionary
md = mapping_and_coords[0][0]
#First molecule coordinates
coords0 = mapping_and_coords[1][0]
#Second molecule coordinates
coords1 = mapping_and_coords[2][0]
#First molecule bonds
#This is the only bond set needed because they should be matched up
bonds = mapping_and_coords[1][1]
coord_dict0, coord_dict1 = {}, {}
G1, G2 = mapping_and_coords[3], mapping_and_coords[4]
for atom, x, y, z in coords0:
coord_dict0[atom[1]] = (x, y, z)
for atom, x, y, z in coords1:
coord_dict1[atom[1]] = (x, y, z)
atom_dict = Find_Protons.build_atom_dict(coords0)
atoms_used_list = []
bond_lengths_list = []
for bond in nx.edges(G1):
atom_1 = coord_dict0.get(bond[0])
atom_2 = coord_dict0.get(bond[1])
atom_3 = coord_dict1.get(md.get(bond[0]))
atom_4 = coord_dict1.get(md.get(bond[1]))
print(bond)
print(atom_1)
print(atom_2)
print('.... .... .... ....')
print(atom_3)
print(atom_4)
# Length change calculation outlined
length0 = Iab.atom_distance(*(atom_1 + atom_2))
length1 = Iab.atom_distance(*(atom_3 + atom_4))
print((abs(length0-length1)))
#Produce a list of bond lengths and bond identites
bond_lengths_list.append((abs(length0-length1), bond))
bond_lengths_list = sorted(bond_lengths_list, key = lambda tup: tup[0], reverse=True)
#Variables assigned for readability
third_to_max = []
bond3 = []
second_to_max = []
bond2 = []
max_delta_bond_length = []
bond1 = []
#Try//except statements here for creating a list of failing files
#Exclude this for normal use
fourth_to_max = bond_lengths_list[3][0]
bond4 = bond_lengths_list[3][1]
third_to_max = bond_lengths_list[2][0]
bond3 = bond_lengths_list[2][1]
second_to_max = bond_lengths_list[1][0]
bond2 = bond_lengths_list[1][1]
max_delta_bond_length = bond_lengths_list[0][0]
bond1 = bond_lengths_list[0][1]
#This is where I find atom pairs my program is unable to match
#Get the highest bond not directly involved with the reduction mechanism
highest_non = None
Redox_involved_oxygen = mapping_and_coords[0][1]
print(Redox_involved_oxygen)
for bond in [bond1, bond2, bond3]:
if Redox_involved_oxygen[-1] == True:
a = bond[0] not in Redox_involved_oxygen
b = bond[1] not in Redox_involved_oxygen
else:
a = md.get(bond[0]) not in Redox_involved_oxygen
b = md.get(bond[1]) not in Redox_involved_oxygen
if a and b:
if bond == bond1:
non_bond = bond1
highest_non = max_delta_bond_length
elif bond == bond2:
non_bond = bond2
highest_non = second_to_max
elif bond == bond3:
non_bond = bond3
highest_non = third_to_max
break
else:
continue
print(bond_lengths_list)
print(highest_non)
template_string = "{}, {}-{},"
first = template_string.format(max_delta_bond_length, atom_dict.get(bond1[0]), atom_dict.get(bond1[1]))
second = template_string.format(second_to_max, atom_dict.get(bond2[0]), atom_dict.get(bond2[1]))
third = template_string.format(third_to_max, atom_dict.get(bond3[0]), atom_dict.get(bond3[1]))
fourth = template_string.format(fourth_to_max, atom_dict.get(bond4[0]), atom_dict.get(bond4[1]))
fifth = template_string.format(highest_non, atom_dict.get(non_bond[0]), atom_dict.get(non_bond[1]))
return first + second + third + fourth + fifth