utils.py

import rdkit
from rdkit import Chem
from rdkit.Chem import rdmolfiles, rdmolops
import numpy as np
import openbabel as ob


def obsmitosmile(smi):
    conv = ob.OBConversion()
    conv.SetInAndOutFormats("smi", "can")
    conv.SetOptions("K", conv.OUTOPTIONS)
    mol = ob.OBMol()
    conv.ReadString(mol, smi)
    smile = conv.WriteString(mol)
    smile = smile.replace('\t\n', '')
    return smile

def smiles2adjoin(smiles,explicit_hydrogens=True,canonical_atom_order=False):

    mol = Chem.MolFromSmiles(smiles)
    if mol is None:
        print('error')
        mol = Chem.MolFromSmiles(obsmitosmile(smiles))
        assert mol is not None, smiles + ' is not valid '

    if explicit_hydrogens:
        mol = Chem.AddHs(mol)
    else:
        mol = Chem.RemoveHs(mol)

    if canonical_atom_order:
        new_order = rdmolfiles.CanonicalRankAtoms(mol)
        mol = rdmolops.RenumberAtoms(mol, new_order)
    num_atoms = mol.GetNumAtoms()
    atoms_list = []
    for i in range(num_atoms):
        atom = mol.GetAtomWithIdx(i)
        atoms_list.append(atom.GetSymbol())

    adjoin_matrix = np.eye(num_atoms)
    # Add edges
    num_bonds = mol.GetNumBonds()
    for i in range(num_bonds):
        bond = mol.GetBondWithIdx(i)
        u = bond.GetBeginAtomIdx()
        v = bond.GetEndAtomIdx()
        adjoin_matrix[u,v] = 1.0
        adjoin_matrix[v,u] = 1.0
    return atoms_list,adjoin_matrix