utils.py

from drugex.logs import logger

import numpy as np
import pandas as pd
import logging
import os
import copy

from rdkit import Chem
from rdkit.Chem import RDConfig
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdDepictor, rdMolDraw2D
opts = Draw.DrawingOptions()
Draw.SetComicMode(opts)

def initLogger(filename, dir_name='data/logs/'):
    """
    Initializes a logging directory if necessary and places all DrugEx outputs in the specified file.
    
    Args:
        filename: name of the log file for DrugEx outputs
        dir_name: directory where the log file will be placed
    """
    
    filename = os.path.join(dir_name, filename)
    
    if not os.path.exists(dir_name):
        os.makedirs(dir_name)
        
    if os.path.exists(filename):
        os.remove(filename)
    
    formatter = logging.Formatter('%(asctime)s | %(levelname)s | %(message)s', 
                              '%m-%d-%Y %H:%M:%S')
    fh = logging.FileHandler(filename)
    fh.setFormatter(formatter)
    
    logger.addHandler(fh)

# different grid visualizations
standard_grid = Chem.Draw.MolsToGridImage
def interactive_grid(mols, *args, molsPerRow=5, **kwargs):
    """
    install mols2grid with pip to use
    """
    
    import mols2grid
    
    return mols2grid.display(mols, *args, n_cols=molsPerRow, **kwargs)

# show molecules as grid
make_grid = interactive_grid # change this to 'standard_grid' if you do not have the mols2grid package
def smilesToGrid(smiles, *args, molsPerRow=5, **kwargs):
    mols = []
    for smile in smiles:
        try:
            m = Chem.MolFromSmiles(smile)
            if m:
                AllChem.Compute2DCoords(m)
                mols.append(m)
            else:
                raise Exception(f'Molecule empty for SMILES: {smile}')
        except Exception as exp:
            pass
        
    return make_grid(mols, *args, molsPerRow=molsPerRow, **kwargs)