score_util.py

import networkx as nx
from rdkit.Chem import AllChem as Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import MolFromSmiles
from rdkit.Chem import rdmolops
from rdkit import rdBase

import sascorer

rdBase.DisableLog('rdApp.error')


# from https://github.com/gablg1/ORGAN/blob/master/organ/mol_metrics.py#L83
def verify_sequence(smile):
    mol = Chem.MolFromSmiles(smile)
    return smile != '' and mol is not None and mol.GetNumAtoms() > 1

# from grammar VAE
# logP_values = np.loadtxt('logP_values.txt')
# SA_scores = np.loadtxt('SA_scores.txt')
# cycle_scores = np.loadtxt('cycle_scores.txt')
logP_mean = 2.457    # np.mean(logP_values)
logP_std = 1.434     # np.std(logP_values)
SA_mean = -3.053     # np.mean(SA_scores)
SA_std = 0.834       # np.std(SA_scores)
cycle_mean = -0.048  # np.mean(cycle_scores)
cycle_std = 0.287    # np.std(cycle_scores)


def calc_score(smiles):
    if verify_sequence(smiles):
        try:
            molecule = MolFromSmiles(smiles)
            if Descriptors.MolWt(molecule) > 500:
                return -1e10
            current_log_P_value = Descriptors.MolLogP(molecule)
            current_SA_score = -sascorer.calculateScore(molecule)
            cycle_list = nx.cycle_basis(nx.Graph(rdmolops.GetAdjacencyMatrix(molecule)))
            if len(cycle_list) == 0:
                cycle_length = 0
            else:
                cycle_length = max([len(j) for j in cycle_list])
            if cycle_length <= 6:
                cycle_length = 0
            else:
                cycle_length = cycle_length - 6
            current_cycle_score = -cycle_length

            current_SA_score_normalized = (current_SA_score - SA_mean) / SA_std
            current_log_P_value_normalized = (current_log_P_value - logP_mean) / logP_std
            current_cycle_score_normalized = (current_cycle_score - cycle_mean) / cycle_std

            score = (current_SA_score_normalized
                     + current_log_P_value_normalized
                     + current_cycle_score_normalized)
            return score
        except Exception:
            return -1e10
    else:
        return -1e10