app.py

from huggingface_hub import from_pretrained_keras
import gradio as gr
from rdkit import Chem, RDLogger
from rdkit.Chem.Draw import IPythonConsole, MolsToGridImage
import numpy as np
import tensorflow as tf
from tensorflow import keras
import pandas as pd

# Config 
class Featurizer:
    def __init__(self, allowable_sets):
        self.dim = 0
        self.features_mapping = {}
        for k, s in allowable_sets.items():
            s = sorted(list(s))
            self.features_mapping[k] = dict(zip(s, range(self.dim, len(s) + self.dim)))
            self.dim += len(s)

    def encode(self, inputs):
        output = np.zeros((self.dim,))
        for name_feature, feature_mapping in self.features_mapping.items():
            feature = getattr(self, name_feature)(inputs)
            if feature not in feature_mapping:
                continue
            output[feature_mapping[feature]] = 1.0
        return output


class AtomFeaturizer(Featurizer):
    def __init__(self, allowable_sets):
        super().__init__(allowable_sets)

    def symbol(self, atom):
        return atom.GetSymbol()

    def n_valence(self, atom):
        return atom.GetTotalValence()

    def n_hydrogens(self, atom):
        return atom.GetTotalNumHs()

    def hybridization(self, atom):
        return atom.GetHybridization().name.lower()


class BondFeaturizer(Featurizer):
    def __init__(self, allowable_sets):
        super().__init__(allowable_sets)
        self.dim += 1

    def encode(self, bond):
        output = np.zeros((self.dim,))
        if bond is None:
            output[-1] = 1.0
            return output
        output = super().encode(bond)
        return output

    def bond_type(self, bond):
        return bond.GetBondType().name.lower()

    def conjugated(self, bond):
        return bond.GetIsConjugated()


atom_featurizer = AtomFeaturizer(
    allowable_sets={
        "symbol": {"B", "Br", "C", "Ca", "Cl", "F", "H", "I", "N", "Na", "O", "P", "S"},
        "n_valence": {0, 1, 2, 3, 4, 5, 6},
        "n_hydrogens": {0, 1, 2, 3, 4},
        "hybridization": {"s", "sp", "sp2", "sp3"},
    }
)

bond_featurizer = BondFeaturizer(
    allowable_sets={
        "bond_type": {"single", "double", "triple", "aromatic"},
        "conjugated": {True, False},
    }
)

def molecule_from_smiles(smiles):
    # MolFromSmiles(m, sanitize=True) should be equivalent to
    # MolFromSmiles(m, sanitize=False) -> SanitizeMol(m) -> AssignStereochemistry(m, ...)
    molecule = Chem.MolFromSmiles(smiles, sanitize=False)

    # If sanitization is unsuccessful, catch the error, and try again without
    # the sanitization step that caused the error
    flag = Chem.SanitizeMol(molecule, catchErrors=True)
    if flag != Chem.SanitizeFlags.SANITIZE_NONE:
        Chem.SanitizeMol(molecule, sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL ^ flag)

    Chem.AssignStereochemistry(molecule, cleanIt=True, force=True)
    return molecule


def graph_from_molecule(molecule):
    # Initialize graph
    atom_features = []
    bond_features = []
    pair_indices = []

    for atom in molecule.GetAtoms():
        atom_features.append(atom_featurizer.encode(atom))

        # Add self-loops
        pair_indices.append([atom.GetIdx(), atom.GetIdx()])
        bond_features.append(bond_featurizer.encode(None))

        for neighbor in atom.GetNeighbors():
            bond = molecule.GetBondBetweenAtoms(atom.GetIdx(), neighbor.GetIdx())
            pair_indices.append([atom.GetIdx(), neighbor.GetIdx()])
            bond_features.append(bond_featurizer.encode(bond))

    return np.array(atom_features), np.array(bond_features), np.array(pair_indices)


def graphs_from_smiles(smiles_list):
    # Initialize graphs
    atom_features_list = []
    bond_features_list = []
    pair_indices_list = []

    for smiles in smiles_list:
        molecule = molecule_from_smiles(smiles)
        atom_features, bond_features, pair_indices = graph_from_molecule(molecule)

        atom_features_list.append(atom_features)
        bond_features_list.append(bond_features)
        pair_indices_list.append(pair_indices)

    # Convert lists to ragged tensors for tf.data.Dataset later on
    return (
        tf.ragged.constant(atom_features_list, dtype=tf.float32),
        tf.ragged.constant(bond_features_list, dtype=tf.float32),
        tf.ragged.constant(pair_indices_list, dtype=tf.int64),
    )
    
    
def MPNNDataset(X, y, batch_size=32, shuffle=False):
    dataset = tf.data.Dataset.from_tensor_slices((X, (y)))
    if shuffle:
        dataset = dataset.shuffle(1024)
    return dataset.batch(batch_size).map(prepare_batch, -1).prefetch(-1)
   
       
model = from_pretrained_keras("keras-io/MPNN-for-molecular-property-prediction")


def predict(smiles, label):
    molecules = [molecule_from_smiles(smiles)]
    input = graphs_from_smiles([smiles])
    label = pd.Series([label])
    test_dataset = MPNNDataset(input, label)
    y_pred = tf.squeeze(model.predict(test_dataset), axis=1)
    legends = [f"y_true/y_pred = {label[i]}/{y_pred[i]:.2f}" for i in range(len(label))]
    MolsToGridImage(molecules, molsPerRow=1, legends=legends, returnPNG=False, subImgSize=(550, 550)).save("img.png")
    return 'img.png'

inputs = [
         gr.Textbox(label='Smiles of molecular'),
         gr.Textbox(label='Molecular permeability')
]

examples = [
            ["CO/N=C(C(=O)N[C@H]1[C@H]2SCC(=C(N2C1=O)C(O)=O)C)/c3csc(N)n3", 0],
            ["[C@H]37[C@H]2[C@@]([C@](C(COC(C1=CC(=CC=C1)[S](O)(=O)=O)=O)=O)(O)[C@@H](C2)C)(C[C@@H]([C@@H]3[C@@]4(C(=CC5=C(C4)C=N[N]5C6=CC=CC=C6)C(=C7)C)C)O)C", 1],
            ["CNCCCC2(C)C(=O)N(c1ccccc1)c3ccccc23", 1],
            ["O.N[C@@H](C(=O)NC1C2CCC(=C(N2C1=O)C(O)=O)Cl)c3ccccc3", 0],
            ["[C@@]4([C@@]3([C@H]([C@H]2[C@@H]([C@@]1(C(=CC(=O)CC1)CC2)C)[C@H](C3)O)CC4)C)(C(COC(C)=O)=O)OC(CC)=O", 1],
            ["[C@]34([C@H](C2[C@@](F)([C@@]1(C(=CC(=O)C=C1)[C@@H](F)C2)C)[C@@H](O)C3)C[C@H]5OC(O[C@@]45C(=O)COC(=O)C6CC6)(C)C)C", 1]
            
]
gr.Interface(
    fn=predict,
    title="Predict blood-brain barrier permeability of molecular",
    description = "Message-passing neural network (MPNN) for molecular property prediction",
    inputs=inputs,
    examples=examples,
    outputs="image",
    article = "Author: <a href=\"https://huggingface.co/vumichien\">Vu Minh Chien</a>. Based on the keras example from <a href=\"https://keras.io/examples/graph/mpnn-molecular-graphs/\">Alexander Kensert</a>",
).launch(debug=True, enable_queue=True)