src/get_studies_datasets.py

import os
import sys

sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
import protac_degradation_predictor as pdp

from collections import defaultdict
import warnings
import logging
from typing import Literal

from sklearn.preprocessing import OrdinalEncoder
from tqdm import tqdm
import pandas as pd
import numpy as np
import pytorch_lightning as pl
from rdkit import DataStructs


root = logging.getLogger()
root.setLevel(logging.DEBUG)

handler = logging.StreamHandler(sys.stdout)
handler.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
handler.setFormatter(formatter)
root.addHandler(handler)


def get_random_split_indices(active_df: pd.DataFrame, test_split: float) -> pd.Index:
    """ Get the indices of the test set using a random split.
    
    Args:
        active_df (pd.DataFrame): The DataFrame containing the active PROTACs.
        test_split (float): The percentage of the active PROTACs to use as the test set.
    
    Returns:
        pd.Index: The indices of the test set.
    """
    test_df = active_df.sample(frac=test_split, random_state=42)
    return test_df.index


def get_e3_ligase_split_indices(active_df: pd.DataFrame) -> pd.Index:
    """ Get the indices of the test set using the E3 ligase split.
    
    Args:
        active_df (pd.DataFrame): The DataFrame containing the active PROTACs.
    
    Returns:
        pd.Index: The indices of the test set.
    """
    encoder = OrdinalEncoder()
    active_df['E3 Group'] = encoder.fit_transform(active_df[['E3 Ligase']]).astype(int)
    test_df = active_df[(active_df['E3 Ligase'] != 'VHL') & (active_df['E3 Ligase'] != 'CRBN')]
    return test_df.index


def get_smiles2fp_and_avg_tanimoto(protac_df: pd.DataFrame) -> tuple:
    """ Get the SMILES to fingerprint dictionary and the average Tanimoto similarity.
    
    Args:
        protac_df (pd.DataFrame): The DataFrame containing the PROTACs.
    
    Returns:
        tuple: The SMILES to fingerprint dictionary and the average Tanimoto similarity.
    """
    unique_smiles = protac_df['Smiles'].unique().tolist()

    smiles2fp = {}
    for smiles in tqdm(unique_smiles, desc='Precomputing fingerprints'):
        smiles2fp[smiles] = pdp.get_fingerprint(smiles)

    # # Get the pair-wise tanimoto similarity between the PROTAC fingerprints
    # tanimoto_matrix = defaultdict(list)
    # for i, smiles1 in enumerate(tqdm(protac_df['Smiles'].unique(), desc='Computing Tanimoto similarity')):
    #     fp1 = smiles2fp[smiles1]
    #     # TODO: Use BulkTanimotoSimilarity for better performance
    #     for j, smiles2 in enumerate(protac_df['Smiles'].unique()[i:]):
    #         fp2 = smiles2fp[smiles2]
    #         tanimoto_dist = 1 - DataStructs.TanimotoSimilarity(fp1, fp2)
    #         tanimoto_matrix[smiles1].append(tanimoto_dist)
    # avg_tanimoto = {k: np.mean(v) for k, v in tanimoto_matrix.items()}
    # protac_df['Avg Tanimoto'] = protac_df['Smiles'].map(avg_tanimoto)


    tanimoto_matrix = defaultdict(list)
    fps = list(smiles2fp.values())

    # Compute all-against-all Tanimoto similarity using BulkTanimotoSimilarity
    for i, (smiles1, fp1) in enumerate(tqdm(zip(unique_smiles, fps), desc='Computing Tanimoto similarity', total=len(fps))):
        similarities = DataStructs.BulkTanimotoSimilarity(fp1, fps[i:])  # Only compute for i to end, avoiding duplicates
        for j, similarity in enumerate(similarities):
            distance = 1 - similarity
            tanimoto_matrix[smiles1].append(distance)  # Store as distance
            if i != i + j:
                tanimoto_matrix[unique_smiles[i + j]].append(distance)  # Symmetric filling

    # Calculate average Tanimoto distance for each unique SMILES
    avg_tanimoto = {k: np.mean(v) for k, v in tanimoto_matrix.items()}
    protac_df['Avg Tanimoto'] = protac_df['Smiles'].map(avg_tanimoto)

    smiles2fp = {s: np.array(fp) for s, fp in smiles2fp.items()}

    return smiles2fp, protac_df


def get_tanimoto_split_indices(
        active_df: pd.DataFrame,
        active_col: str,
        test_split: float,
        n_bins_tanimoto: int = 200,
) -> pd.Index:
    """ Get the indices of the test set using the Tanimoto-based split.
    
    Args:
        active_df (pd.DataFrame): The DataFrame containing the active PROTACs.
        n_bins_tanimoto (int): The number of bins to use for the Tanimoto similarity.
    
    Returns:
        pd.Index: The indices of the test set.
    """
    tanimoto_groups = pd.cut(active_df['Avg Tanimoto'], bins=n_bins_tanimoto).copy()
    encoder = OrdinalEncoder()
    active_df['Tanimoto Group'] = encoder.fit_transform(tanimoto_groups.values.reshape(-1, 1)).astype(int)
    # Sort the groups so that samples with the highest tanimoto similarity,
    # i.e., the "less similar" ones, are placed in the test set first
    tanimoto_groups = active_df.groupby('Tanimoto Group')['Avg Tanimoto'].mean().sort_values(ascending=False).index

    test_df = []
    # For each group, get the number of active and inactive entries. Then, add those
    # entries to the test_df if: 1) the test_df lenght + the group entries is less
    # 20% of the active_df lenght, and 2) the percentage of True and False entries
    # in the active_col in test_df is roughly 50%.
    for group in tanimoto_groups:
        group_df = active_df[active_df['Tanimoto Group'] == group]
        if test_df == []:
            test_df.append(group_df)
            continue
        
        num_entries = len(group_df)
        num_active_group = group_df[active_col].sum()
        num_inactive_group = num_entries - num_active_group

        tmp_test_df = pd.concat(test_df)
        num_entries_test = len(tmp_test_df)
        num_active_test = tmp_test_df[active_col].sum()
        num_inactive_test = num_entries_test - num_active_test
        
        # Check if the group entries can be added to the test_df
        if num_entries_test + num_entries < test_split * len(active_df):
            # Add anything at the beggining
            if num_entries_test + num_entries < test_split / 2 * len(active_df):
                test_df.append(group_df)
                continue
            # Be more selective and make sure that the percentage of active and
            # inactive is balanced
            if (num_active_group + num_active_test) / (num_entries_test + num_entries) < 0.6:
                if (num_inactive_group + num_inactive_test) / (num_entries_test + num_entries) < 0.6:
                    test_df.append(group_df)
    test_df = pd.concat(test_df)
    return test_df.index


def get_target_split_indices(active_df: pd.DataFrame, active_col: str, test_split: float) -> pd.Index:
    """ Get the indices of the test set using the target-based split.

    Args:
        active_df (pd.DataFrame): The DataFrame containing the active PROTACs.
        active_col (str): The column containing the active/inactive information.
        test_split (float): The percentage of the active PROTACs to use as the test set.

    Returns:
        pd.Index: The indices of the test set.
    """
    encoder = OrdinalEncoder()
    active_df['Uniprot Group'] = encoder.fit_transform(active_df[['Uniprot']]).astype(int)

    test_df = []
    # For each group, get the number of active and inactive entries. Then, add those
    # entries to the test_df if: 1) the test_df lenght + the group entries is less
    # 20% of the active_df lenght, and 2) the percentage of True and False entries
    # in the active_col in test_df is roughly 50%.
    # Start the loop from the groups containing the smallest number of entries.
    for group in reversed(active_df['Uniprot'].value_counts().index):
        group_df = active_df[active_df['Uniprot'] == group]
        if test_df == []:
            test_df.append(group_df)
            continue
        
        num_entries = len(group_df)
        num_active_group = group_df[active_col].sum()
        num_inactive_group = num_entries - num_active_group

        tmp_test_df = pd.concat(test_df)
        num_entries_test = len(tmp_test_df)
        num_active_test = tmp_test_df[active_col].sum()
        num_inactive_test = num_entries_test - num_active_test
        
        # Check if the group entries can be added to the test_df
        if num_entries_test + num_entries < test_split * len(active_df):
            # Add anything at the beggining
            if num_entries_test + num_entries < test_split / 2 * len(active_df):
                test_df.append(group_df)
                continue
            # Be more selective and make sure that the percentage of active and
            # inactive is balanced
            if (num_active_group + num_active_test) / (num_entries_test + num_entries) < 0.6:
                if (num_inactive_group + num_inactive_test) / (num_entries_test + num_entries) < 0.6:
                    test_df.append(group_df)
    test_df = pd.concat(test_df)
    return test_df.index


def main(
    active_col: str = 'Active (Dmax 0.6, pDC50 6.0)',
    test_split: float = 0.1,
    studies: str | Literal['all', 'standard', 'e3_ligase', 'similarity', 'target'] = 'all',
):
    """ Get and save the datasets for the different studies.
    
    Args:
        active_col (str): The column containing the active/inactive information. It should be in the format 'Active (Dmax N, pDC50 M)', where N and M are the thresholds float values for Dmax and pDC50, respectively.
        test_split (float): The percentage of the active PROTACs to use as the test set.
        studies (str): The type of studies to save dataset for. Options: 'all', 'standard', 'e3_ligase', 'similarity', 'target'.
    """
    pl.seed_everything(42)

    # Set the Column to Predict
    active_name = active_col.replace(' ', '_').replace('(', '').replace(')', '').replace(',', '')

    # Get Dmax_threshold from the active_col
    Dmax_threshold = float(active_col.split('Dmax')[1].split(',')[0].strip('(').strip(')').strip())
    pDC50_threshold = float(active_col.split('pDC50')[1].strip('(').strip(')').strip())

    # Load the PROTAC dataset
    protac_df = pd.read_csv('../data/PROTAC-Degradation-DB.csv')
    # Map E3 Ligase Iap to IAP
    protac_df['E3 Ligase'] = protac_df['E3 Ligase'].str.replace('Iap', 'IAP')
    protac_df[active_col] = protac_df.apply(
        lambda x: pdp.is_active(x['DC50 (nM)'], x['Dmax (%)'], pDC50_threshold=pDC50_threshold, Dmax_threshold=Dmax_threshold), axis=1
    )
    _, protac_df = get_smiles2fp_and_avg_tanimoto(protac_df)

    ## Get the test sets
    test_indeces = {}
    active_df = protac_df[protac_df[active_col].notna()].copy()

    # Remove legacy column 'Active - OR' if it exists
    if 'Active - OR' in active_df.columns:
        active_df.drop(columns='Active - OR', inplace=True)
    
    if studies == 'standard' or studies == 'all':
        test_indeces['standard'] = get_random_split_indices(active_df, test_split)
    if studies == 'target' or studies == 'all':
        test_indeces['target'] = get_target_split_indices(active_df, active_col, test_split)
    if studies == 'e3_ligase' or studies == 'all':
        test_indeces['e3_ligase'] = get_e3_ligase_split_indices(active_df)
    if studies == 'similarity' or studies == 'all':
        test_indeces['similarity'] = get_tanimoto_split_indices(active_df, active_col, test_split)

    # Make directory for studies datasets if it does not exist
    data_dir = '../data/studies'
    if not os.path.exists(data_dir):
        os.makedirs(data_dir)

    # Cross-Validation Training
    for split_type, indeces in test_indeces.items():
        test_df = active_df.loc[indeces].copy()
        train_val_df = active_df[~active_df.index.isin(test_df.index)].copy()

        # Save the datasets

        train_val_perc = f'{int((1 - test_split) * 100)}'
        test_perc = f'{int(test_split * 100)}'

        train_val_filename = f'{data_dir}/{split_type}_train_val_{train_val_perc}split_{active_name}.csv'
        test_filename = f'{data_dir}/{split_type}_test_{test_perc}split_{active_name}.csv'

        print('')
        print(f'Saving train_val datasets as: {train_val_filename}')
        print(f'Saving test datasets as:      {test_filename}')

        train_val_df.to_csv(train_val_filename, index=False)
        test_df.to_csv(test_filename, index=False)


if __name__ == '__main__':
    main()