Molecule utilities

get_modification_nodes	Calculates the modification sites between two molecules when one molecule is a substructure of the other molecule
get_modification_edges	Calculates the modification edges between two molecules when one molecule is a substructure of the other molecule
get_edit_distance	Calculates the edit distance between mol1 and mol2.
get_edit_distance_detailed	Calculates the edit distance between mol1 and mol2.
get_transition	Calculates the transition between mol1 and mol2.
get_modification_graph	Calculates the substructure difference between main_struct and sub_struct when there is exactly one modification edge,
attach_mols	Attaches the attachment structure to main molecule at the attach_location_main and attach_location_attachment with bond_type.
generate_possible_stuctures	Generates all possible structures after attaching the difference between sub_struct and main_struct to main_struct.

GNPS Utils - Molecule Utils

This file contains utility functions around molecules and molecules modification based on RDKit library.

modifinder.utilities.mol_utils.attach_mols(main_mol, attachment_mol, attach_location_main, attach_location_attachment, bond_type)

Attaches the attachment structure to main molecule at the attach_location_main and attach_location_attachment with bond_type.

Input:

main_mol:

rdkit molecule of the main molecule

attachment_mol:

rdkit molecule of the attachment molecule

attach_location_main:

the index of the atom in the main molecule where the attachment should be done

attach_location_attachment:

the index of the atom in the attachment molecule where the attachment should be done

bond_type:

the type of the bond between the main molecule and the attachment molecule

Output:

new_mol:

the new molecule after attachment

modifinder.utilities.mol_utils.generate_possible_stuctures(main_struct, sub_struct)

Generates all possible structures after attaching the difference between sub_struct and main_struct to main_struct.

Input:

main_struct:

main molecule

sub_struct:

substructure molecule

Output:

list of possible_structures:

all possible structures after attachment with the index of the atom

Example

import modifinder.utilities.mol_utils as mf_mu
import modifinder.utilities.visualizer as mf_vis
from matplotlib import pyplot as plt
from rdkit import Chem
from rdkit.Chem import Draw
modification = Chem.MolFromSmiles("C1=C(NC(=O)N=C1)N")
mol1 = Chem.MolFromSmiles("CC1=C(NC(=O)N=C1)N")
res = mf_mu.generate_possible_stuctures(mol1, modification)
img = mf_vis.draw_modifications(modification, mol1)
plt.imshow(img)
plt.axis("off")
plt.show()
res_mols = [x[1] for x in res]
res_index = ["attach modification at location: " + str(x[0]) for x in res]
img = Draw.MolsToGridImage(res_mols, molsPerRow=2, subImgSize=(200, 200), legends=res_index, returnPNG=False)
img.save("molgrid.png")
display(img)

modifinder.utilities.mol_utils.get_edit_distance(mol1, mol2)

Calculates the edit distance between mol1 and mol2.

Input:

mol1:

first molecule

mol2:

second molecule

Output:

edit_distance:

edit distance between mol1 and mol2

modifinder.utilities.mol_utils.get_edit_distance_detailed(mol1, mol2, mcs=None)

Calculates the edit distance between mol1 and mol2.

Input:

mol1:

first molecule

mol2:

second molecule

mcs:

the maximum common substructure between mol1 and mol2

Output:

removed edges:

the removed modification edges

added edges:

the added modification edges

modifinder.utilities.mol_utils.get_modification_edges(mol1, mol2, only_outward_edges=False)

Calculates the modification edges between two molecules when one molecule is a substructure of the other molecule

Input:

mol1:

first molecule

mol2:

second molecule

only_outward_edges:

bool, if True, only the modification edges that go from atoms in the substructure to atoms outside the substructure are returned

Output:

list of the the modification edges in the parent molecule as tuples of atom indices

modifinder.utilities.mol_utils.get_modification_graph(main_struct, sub_struct)

Calculates the substructure difference between main_struct and sub_struct when there is exactly one modification edge,

if there are multiple modification edges, one of the modifications is returned randomly.

Input:

main_struct:

main molecule

sub_struct:

substructure molecule

Output:

all_modifications:

a list of the modifications structures, each modification is a tuple of: 1. the modified subgraph molecule (as an rdkit editable molecule) 2. a dictionary that maps the wildcard atom indices in subgraph to its true index in the main molecule 3. the SMARTS representation of the modification

modifinder.utilities.mol_utils.get_modification_nodes(mol1, mol2, in_mol1=True)

Calculates the modification sites between two molecules when one molecule is a substructure of the other molecule

Input:

mol1:

first molecule

mol2:

second molecule

in_mol1:

bool, if True, the modification sites are given in the mol1, if False, the modification sites are given in the mol2

Output:

list of modification sites

Example

import modifinder.utilities.mol_utils as mf_mu
import modifinder.utilities.visualizer as mf_vis
from matplotlib import pyplot as plt
from rdkit import Chem
def mol_with_atom_index(mol):
    for atom in mol.GetAtoms():
        atom.SetAtomMapNum(atom.GetIdx())
    return mol
mol1 = mol_with_atom_index(Chem.MolFromSmiles("O=C1C2=C(N=CN2)N(C)C(N1C)=O"))
mol2 = mol_with_atom_index(Chem.MolFromInchi("InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3"))
edit_in_mol1 = mf_mu.get_modification_nodes(mol1, mol2, True)
edit_in_mol2 = mf_mu.get_modification_nodes(mol1, mol2, False)
fig, ax = plt.subplots(1, 2, figsize=(10, 5))
ax[0].imshow(mf_vis.draw_molecule(mol1, highlightAtoms=edit_in_mol1))
ax[1].imshow(mf_vis.draw_molecule(mol2, highlightAtoms=edit_in_mol2))
for i in range(2):
    ax[i].axis("off")
plt.show()
print("edit_in_mol1", edit_in_mol1)
print("edit_in_mol2", edit_in_mol2)

>>> edit_in_mol1 6
>>> edit_in_mol2 9

modifinder.utilities.mol_utils.get_transition(input1, input2)

Calculates the transition between mol1 and mol2.

Input:

input1:

first molecule

input2:

second molecule

Output:

result:

a dictionary with the following keys:

merged_mol: the merged molecule

common_bonds: the common bonds between mol1 and mol2

common_atoms: the common atoms between mol1 and mol2

removed_atoms: the removed atoms from mol1

added_atoms: the added atoms from mol2

modified_added_edges_inside: the added edges inside the common substructure

modified_added_edges_bridge: the added edges between the common substructure and the added atoms

modified_removed_edges_inside: the removed edges inside the common substructure

modified_removed_edges_bridge: the removed edges between the common substructure and the removed

added_edges: the added edges that are not modification edges

removed_edges: the removed edges that are not modification edges