graph_decoder/visualize_utils.py

import os
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
from rdkit.Geometry import Point3D
from rdkit import RDLogger
import numpy as np
import rdkit.Chem

class MolecularVisualization:
    def __init__(self, atom_decoder):
        self.atom_decoder = atom_decoder

    def mol_from_graphs(self, node_list, adjacency_matrix):
        """
        Convert graphs to rdkit molecules
        node_list: the nodes of a batch of nodes (bs x n)
        adjacency_matrix: the adjacency_matrix of the molecule (bs x n x n)
        """
        # dictionary to map integer value to the char of atom
        atom_decoder = self.atom_decoder

        # create empty editable mol object
        mol = Chem.RWMol()

        # add atoms to mol and keep track of index
        node_to_idx = {}
        for i in range(len(node_list)):
            if node_list[i] == -1:
                continue
            a = Chem.Atom(atom_decoder[int(node_list[i])])
            molIdx = mol.AddAtom(a)
            node_to_idx[i] = molIdx

        for ix, row in enumerate(adjacency_matrix):
            for iy, bond in enumerate(row):
                # only traverse half the symmetric matrix
                if iy <= ix:
                    continue
                if bond == 1:
                    bond_type = Chem.rdchem.BondType.SINGLE
                elif bond == 2:
                    bond_type = Chem.rdchem.BondType.DOUBLE
                elif bond == 3:
                    bond_type = Chem.rdchem.BondType.TRIPLE
                elif bond == 4:
                    bond_type = Chem.rdchem.BondType.AROMATIC
                else:
                    continue
                mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type)

        try:
            mol = mol.GetMol()
        except rdkit.Chem.KekulizeException:
            print("Can't kekulize molecule")
            mol = None
        return mol

    def visualize_chain(self, nodes_list, adjacency_matrix):
        RDLogger.DisableLog('rdApp.*')
        # convert graphs to the rdkit molecules
        mols = [self.mol_from_graphs(nodes_list[i], adjacency_matrix[i]) for i in range(nodes_list.shape[0])]

        # find the coordinates of atoms in the final molecule
        final_molecule = mols[-1]
        AllChem.Compute2DCoords(final_molecule)

        coords = []
        for i, atom in enumerate(final_molecule.GetAtoms()):
            positions = final_molecule.GetConformer().GetAtomPosition(i)
            coords.append((positions.x, positions.y, positions.z))

        # align all the molecules
        for i, mol in enumerate(mols):
            AllChem.Compute2DCoords(mol)
            conf = mol.GetConformer()
            for j, atom in enumerate(mol.GetAtoms()):
                x, y, z = coords[j]
                conf.SetAtomPosition(j, Point3D(x, y, z))

        # create list of molecule images
        mol_images = []
        for frame, mol in enumerate(mols):
            img = Draw.MolToImage(mol, size=(300, 300), legend=f"Frame {frame}")
            mol_images.append(img)

        return mol_images