generate_mcts.py

#!/usr/bin/env
import torch
import torch.nn.functional as F
import math
import random
import sys
import pandas as pd
from utils.generate_utils import mask_for_de_novo, calculate_cosine_sim, calculate_hamming_dist
from diffusion import Diffusion
from pareto_mcts import Node, MCTS
import hydra
from tqdm import tqdm
from transformers import AutoTokenizer, AutoModel, pipeline
from tokenizer.my_tokenizers import SMILES_SPE_Tokenizer
from helm_tokenizer.helm_tokenizer import HelmTokenizer
from utils.helm_utils import create_helm_from_aa_seq
from utils.app import PeptideAnalyzer
from new_tokenizer.ape_tokenizer import APETokenizer
import matplotlib.pyplot as plt
import os
import seaborn as sns
import pandas as pd
import numpy as np

def save_logs_to_file(config, valid_fraction_log, affinity1_log, affinity2_log, sol_log, hemo_log, nf_log, permeability_log, output_path):
    """
    Saves the logs (valid_fraction_log, affinity1_log, and permeability_log) to a CSV file.
    
    Parameters:
        valid_fraction_log (list): Log of valid fractions over iterations.
        affinity1_log (list): Log of binding affinity over iterations.
        permeability_log (list): Log of membrane permeability over iterations.
        output_path (str): Path to save the log CSV file.
    """
    os.makedirs(os.path.dirname(output_path), exist_ok=True)
    
    if config.mcts.perm:
        # Combine logs into a DataFrame
        log_data = {
            "Iteration": list(range(1, len(valid_fraction_log) + 1)),
            "Valid Fraction": valid_fraction_log,
            "Binding Affinity": affinity1_log,
            "Solubility": sol_log,
            "Hemolysis": hemo_log, 
            "Nonfouling": nf_log,
            "Permeability": permeability_log
        }
    elif config.mcts.dual: 
        log_data = {
            "Iteration": list(range(1, len(valid_fraction_log) + 1)),
            "Valid Fraction": valid_fraction_log,
            "Binding Affinity 1": affinity1_log,
            "Binding Affinity 2": affinity2_log,
            "Solubility": sol_log,
            "Hemolysis": hemo_log, 
            "Nonfouling": nf_log,
            "Permeability": permeability_log
        }
    elif config.mcts.single: 
        log_data = {
            "Iteration": list(range(1, len(valid_fraction_log) + 1)),
            "Valid Fraction": valid_fraction_log,
            "Permeability": permeability_log
        }
    else:
        log_data = {
            "Iteration": list(range(1, len(valid_fraction_log) + 1)),
            "Valid Fraction": valid_fraction_log,
            "Binding Affinity": affinity1_log,
            "Solubility": sol_log,
            "Hemolysis": hemo_log, 
            "Nonfouling": nf_log
        }
        
    df = pd.DataFrame(log_data)
    
    # Save to CSV
    df.to_csv(output_path, index=False)

def plot_data(log1, log2=None, 
                    save_path=None, 
                    label1="Log 1", 
                    label2=None, 
                    title="Fraction of Valid Peptides Over Iterations", 
                    palette=None):
    """
    Plots one or two datasets with their mean values over iterations.

    Parameters:
        log1 (list): The first list of mean values for each iteration.
        log2 (list, optional): The second list of mean values for each iteration. Defaults to None.
        save_path (str): Path to save the plot. Defaults to None.
        label1 (str): Label for the first dataset. Defaults to "Log 1".
        label2 (str, optional): Label for the second dataset. Defaults to None.
        title (str): Title of the plot. Defaults to "Mean Values Over Iterations".
        palette (dict, optional): A dictionary defining custom colors for datasets. Defaults to None.
    """
    # Prepare data for log1
    data1 = pd.DataFrame({
        "Iteration": range(1, len(log1) + 1),
        "Fraction of Valid Peptides": log1,
        "Dataset": label1
    })

    # Prepare data for log2 if provided
    if log2 is not None:
        data2 = pd.DataFrame({
            "Iteration": range(1, len(log2) + 1),
            "Fraction of Valid Peptides": log2,
            "Dataset": label2
        })
        data = pd.concat([data1, data2], ignore_index=True)
    else:
        data = data1

    palette = {
        label1: "#8181ED",  # Default color for log1
        label2: "#D577FF"   # Default color for log2 (if provided)
    }

    # Set Seaborn theme
    sns.set_theme()
    sns.set_context("paper")

    # Create the plot
    sns.lineplot(
        data=data, 
        x="Iteration", 
        y="Fraction of Valid Peptides", 
        hue="Dataset", 
        style="Dataset", 
        markers=True, 
        dashes=False, 
        palette=palette
    )

    # Titles and labels
    plt.title(title)
    plt.xlabel("Iteration")
    plt.ylabel("Fraction of Valid Peptides")

    if save_path:
        plt.savefig(save_path, dpi=300, bbox_inches='tight')
        print(f"Plot saved to {save_path}")
    plt.show()

def plot_data_with_distribution_seaborn(log1, log2=None, 
                                        save_path=None, 
                                        label1=None, 
                                        label2=None, 
                                        title=None):
    """
    Plots one or two datasets with the average values and distributions over iterations using Seaborn.

    Parameters:
        log1 (list of lists): The first list of scores (each element is a list of scores for an iteration).
        log2 (list of lists, optional): The second list of scores (each element is a list of scores for an iteration). Defaults to None.
        save_path (str): Path to save the plot. Defaults to None.
        label1 (str): Label for the first dataset. Defaults to "Fraction of Valid Peptide SMILES".
        label2 (str, optional): Label for the second dataset. Defaults to None.
        title (str): Title of the plot. Defaults to "Fraction of Valid Peptides Over Iterations".
    """
    # Prepare data for log1
    data1 = pd.DataFrame({
        "Iteration": np.repeat(range(1, len(log1) + 1), [len(scores) for scores in log1]),
        "Fraction of Valid Peptides": [score for scores in log1 for score in scores],
        "Dataset": label1,
        "Style": "Log1"
    })

    # Prepare data for log2 if provided
    if log2 is not None:
        data2 = pd.DataFrame({
            "Iteration": np.repeat(range(1, len(log2) + 1), [len(scores) for scores in log2]),
            "Fraction of Valid Peptides": [score for scores in log2 for score in scores],
            "Dataset": label2,
            "Style": "Log2"
        })
        data = pd.concat([data1, data2], ignore_index=True)
    else:
        data = data1
    
    palette = {
        label1: "#8181ED",  # Default color for log1
        label2: "#D577FF"   # Default color for log2 (if provided)
    }

    # Set Seaborn theme
    sns.set_theme()
    sns.set_context("paper")

    # Create the plot
    sns.relplot(
        data=data, 
        kind="line",
        x="Iteration", 
        y="Fraction of Valid Peptides", 
        hue="Dataset", 
        style="Style", 
        markers=True, 
        dashes=True,
        ci="sd",  # Show standard deviation
        height=5, 
        aspect=1.5,
        palette=palette
    )

    # Titles and labels
    plt.title(title)
    plt.xlabel("Iteration")
    plt.ylabel("Fraction of Valid Peptides")

    if save_path:
        plt.savefig(save_path, dpi=300, bbox_inches='tight')
        print(f"Plot saved to {save_path}")
    plt.show()

@torch.no_grad()
def generate_valid_mcts(config, mdlm, prot1=None, prot2=None, filename=None, prot_name1=None, prot_name2 = None):
    tokenizer = mdlm.tokenizer
    max_sequence_length = config.sampling.seq_length
        
    # generate array of [MASK] tokens
    masked_array = mask_for_de_novo(config, max_sequence_length)
    
    if config.vocab == 'old_smiles':
        # use custom encode function
        inputs = tokenizer.encode(masked_array)
    elif config.vocab == 'new_smiles' or config.vocab == 'selfies':
        inputs = tokenizer.encode_for_generation(masked_array)
    else:
        # custom HELM tokenizer
        inputs = tokenizer(masked_array, return_tensors="pt")
    
    inputs = {key: value.to(mdlm.device) for key, value in inputs.items()}
    
    # initialize root node
    rootNode = Node(config=config, tokens=inputs, timestep=0)
    # initalize tree search algorithm
    
    if config.mcts.perm:
        score_func_names = ['permeability', 'binding_affinity1', 'solubility', 'hemolysis', 'nonfouling']
        num_func = [0, 50, 50, 50, 50]
    elif config.mcts.dual:
        score_func_names = ['binding_affinity1', 'solubility', 'hemolysis', 'nonfouling', 'binding_affinity2']
    elif config.mcts.single:
        score_func_names = ['permeability']
    else: 
        score_func_names = ['binding_affinity1', 'solubility', 'hemolysis', 'nonfouling']  
        
    if not config.mcts.time_dependent:
        num_func = [0] * len(score_func_names)
    
    if prot1 and prot2 is not None:
        mcts = MCTS(config=config, max_sequence_length=max_sequence_length, mdlm=mdlm, score_func_names=score_func_names, prot_seqs=[prot1, prot2], num_func=num_func)
    elif prot1 is not None: 
        mcts = MCTS(config=config, max_sequence_length=max_sequence_length, mdlm=mdlm, score_func_names=score_func_names, prot_seqs=[prot1], num_func=num_func)
    elif config.mcts.single:
        mcts = MCTS(config=config, max_sequence_length=max_sequence_length, mdlm=mdlm, score_func_names=score_func_names, num_func=num_func)
    else:
        mcts = MCTS(config=config, max_sequence_length=max_sequence_length, mdlm=mdlm, score_func_names=score_func_names, num_func=num_func)
    
    paretoFront = mcts.forward(rootNode)
    
    output_log_path = f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/log_{filename}.csv'
    save_logs_to_file(config, mcts.valid_fraction_log, mcts.affinity1_log, mcts.affinity2_log, mcts.sol_log, mcts.hemo_log, mcts.nf_log, mcts.permeability_log, output_log_path)

    if config.mcts.single:
        plot_data_with_distribution_seaborn(log1=mcts.permeability_log,
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/perm_{filename}.png',
                label1="Average Permeability Score",
                title="Average Permeability Score Over Iterations")
    else:
        plot_data(mcts.valid_fraction_log, 
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/valid_{filename}.png')
        plot_data_with_distribution_seaborn(log1=mcts.affinity1_log,
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/binding1_{filename}.png',
                label1="Average Binding Affinity to TfR",
                title="Average Binding Affinity to TfR Over Iterations")
        if config.mcts.dual:
            plot_data_with_distribution_seaborn(log1=mcts.affinity2_log,
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/binding2_{filename}.png',
                label1="Average Binding Affinity to SKP2",
                title="Average Binding Affinity to SKP2 Over Iterations")
        plot_data_with_distribution_seaborn(log1=mcts.sol_log,
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/sol_{filename}.png',
                label1="Average Solubility Score",
                title="Average Solubility Score Over Iterations")
        plot_data_with_distribution_seaborn(log1=mcts.hemo_log,
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/hemo_{filename}.png',
                label1="Average Hemolysis Score",
                title="Average Hemolysis Score Over Iterations")
        plot_data_with_distribution_seaborn(log1=mcts.nf_log,
                save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/nf_{filename}.png',
                label1="Average Nonfouling Score",
                title="Average Nonfouling Score Over Iterations")
        if config.mcts.perm:
            plot_data_with_distribution_seaborn(log1=mcts.permeability_log,
                    save_path=f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/perm_{filename}.png',
                    label1="Average Permeability Score",
                    title="Average Permeability Score Over Iterations")
    
    return paretoFront, inputs


@hydra.main(version_base=None, config_path='/home/st512/peptune/scripts/peptide-mdlm-mcts', config_name='config')
def main(config):
    prot_name1 = "time_dependent"
    prot_name2 = "skp2"
    mode = "2"
    model = "mcts"
    length = "100"
    epoch = "7"
    
    filename = f'{mode}_{model}_length_{length}_epoch_{epoch}'

    if config.vocab == 'new_smiles':
        tokenizer = APETokenizer()
        tokenizer.load_vocabulary('/home/st512/peptune/scripts/peptide-mdlm-mcts/new_tokenizer/peptide_smiles_600_vocab.json')
    elif config.vocab == 'old_smiles':
        tokenizer = SMILES_SPE_Tokenizer('/home/st512/peptune/scripts/peptide-mdlm-mcts/tokenizer/new_vocab.txt', 
                                    '/home/st512/peptune/scripts/peptide-mdlm-mcts/tokenizer/new_splits.txt')
    elif config.vocab == 'selfies':
        tokenizer = APETokenizer()
        tokenizer.load_vocabulary('/home/st512/peptune/scripts/peptide-mdlm-mcts/new_tokenizer/peptide_selfies_600_vocab.json')
    elif config.vocab == 'helm':
        tokenizer = HelmTokenizer('/home/st512/peptune/scripts/peptide-mdlm-mcts/helm_tokenizer/monomer_vocab.txt')
    
    mdlm = Diffusion.load_from_checkpoint(config.eval.checkpoint_path, config=config, tokenizer=tokenizer, strict=False)
    
    mdlm.eval()
    device = torch.device('cuda' if torch.cuda.is_available() else "cpu")
    mdlm.to(device)
    

    print("loaded models...")
    analyzer = PeptideAnalyzer()
    
    # proteins
    amhr = 'MLGSLGLWALLPTAVEAPPNRRTCVFFEAPGVRGSTKTLGELLDTGTELPRAIRCLYSRCCFGIWNLTQDRAQVEMQGCRDSDEPGCESLHCDPSPRAHPSPGSTLFTCSCGTDFCNANYSHLPPPGSPGTPGSQGPQAAPGESIWMALVLLGLFLLLLLLLGSIILALLQRKNYRVRGEPVPEPRPDSGRDWSVELQELPELCFSQVIREGGHAVVWAGQLQGKLVAIKAFPPRSVAQFQAERALYELPGLQHDHIVRFITASRGGPGRLLSGPLLVLELHPKGSLCHYLTQYTSDWGSSLRMALSLAQGLAFLHEERWQNGQYKPGIAHRDLSSQNVLIREDGSCAIGDLGLALVLPGLTQPPAWTPTQPQGPAAIMEAGTQRYMAPELLDKTLDLQDWGMALRRADIYSLALLLWEILSRCPDLRPDSSPPPFQLAYEAELGNTPTSDELWALAVQERRRPYIPSTWRCFATDPDGLRELLEDCWDADPEARLTAECVQQRLAALAHPQESHPFPESCPRGCPPLCPEDCTSIPAPTILPCRPQRSACHFSVQQGPCSRNPQPACTLSPV'
    tfr = 'MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAVDEEENADNNTKANVTKPKRCSGSICYGTIAVIVFFLIGFMIGYLGYCKGVEPKTECERLAGTESPVREEPGEDFPAARRLYWDDLKRKLSEKLDSTDFTGTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIKLTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF'
    gfap = 'MERRRITSAARRSYVSSGEMMVGGLAPGRRLGPGTRLSLARMPPPLPTRVDFSLAGALNAGFKETRASERAEMMELNDRFASYIEKVRFLEQQNKALAAELNQLRAKEPTKLADVYQAELRELRLRLDQLTANSARLEVERDNLAQDLATVRQKLQDETNLRLEAENNLAAYRQEADEATLARLDLERKIESLEEEIRFLRKIHEEEVRELQEQLARQQVHVELDVAKPDLTAALKEIRTQYEAMASSNMHEAEEWYRSKFADLTDAAARNAELLRQAKHEANDYRRQLQSLTCDLESLRGTNESLERQMREQEERHVREAASYQEALARLEEEGQSLKDEMARHLQEYQDLLNVKLALDIEIATYRKLLEGEENRITIPVQTFSNLQIRETSLDTKSVSEGHLKRNIVVKTVEMRDGEVIKESKQEHKDVM'
    glp1 = 'MAGAPGPLRLALLLLGMVGRAGPRPQGATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEESKRGERSSPEEQLLFLYIIYTVGYALSFSALVIASAILLGFRHLHCTRNYIHLNLFASFILRALSVFIKDAALKWMYSTAAQQHQWDGLLSYQDSLSCRLVFLLMQYCVAANYYWLLVEGVYLYTLLAFSVLSEQWIFRLYVSIGWGVPLLFVVPWGIVKYLYEDEGCWTRNSNMNYWLIIRLPILFAIGVNFLIFVRVICIVVSKLKANLMCKTDIKCRLAKSTLTLIPLLGTHEVIFAFVMDEHARGTLRFIKLFTELSFTSFQGLMVAILYCFVNNEVQLEFRKSWERWRLEHLHIQRDSSMKPLKCPTSSLSSGATAGSSMYTATCQASCS'
    glast = 'MTKSNGEEPKMGGRMERFQQGVRKRTLLAKKKVQNITKEDVKSYLFRNAFVLLTVTAVIVGTILGFTLRPYRMSYREVKYFSFPGELLMRMLQMLVLPLIISSLVTGMAALDSKASGKMGMRAVVYYMTTTIIAVVIGIIIVIIIHPGKGTKENMHREGKIVRVTAADAFLDLIRNMFPPNLVEACFKQFKTNYEKRSFKVPIQANETLVGAVINNVSEAMETLTRITEELVPVPGSVNGVNALGLVVFSMCFGFVIGNMKEQGQALREFFDSLNEAIMRLVAVIMWYAPVGILFLIAGKIVEMEDMGVIGGQLAMYTVTVIVGLLIHAVIVLPLLYFLVTRKNPWVFIGGLLQALITALGTSSSSATLPITFKCLEENNGVDKRVTRFVLPVGATINMDGTALYEALAAIFIAQVNNFELNFGQIITISITATAASIGAAGIPQAGLVTMVIVLTSVGLPTDDITLIIAVDWFLDRLRTTTNVLGDSLGAGIVEHLSRHELKNRDVEMGNSVIEENEMKKPYQLIAQDNETEKPIDSETKM'
    ncam = 'LQTKDLIWTLFFLGTAVSLQVDIVPSQGEISVGESKFFLCQVAGDAKDKDISWFSPNGEKLTPNQQRISVVWNDDSSSTLTIYNANIDDAGIYKCVVTGEDGSESEATVNVKIFQKLMFKNAPTPQEFREGEDAVIVCDVVSSLPPTIIWKHKGRDVILKKDVRFIVLSNNYLQIRGIKKTDEGTYRCEGRILARGEINFKDIQVIVNVPPTIQARQNIVNATANLGQSVTLVCDAEGFPEPTMSWTKDGEQIEQEEDDEKYIFSDDSSQLTIKKVDKNDEAEYICIAENKAGEQDATIHLKVFAKPKITYVENQTAMELEEQVTLTCEASGDPIPSITWRTSTRNISSEEKASWTRPEKQETLDGHMVVRSHARVSSLTLKSIQYTDAGEYICTASNTIGQDSQSMYLEVQYAPKLQGPVAVYTWEGNQVNITCEVFAYPSATISWFRDGQLLPSSNYSNIKIYNTPSASYLEVTPDSENDFGNYNCTAVNRIGQESLEFILVQADTPSSPSIDQVEPYSSTAQVQFDEPEATGGVPILKYKAEWRAVGEEVWHSKWYDAKEASMEGIVTIVGLKPETTYAVRLAALNGKGLGEISAASEF'
    cereblon = 'MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL'
    ligase = 'MASQPPEDTAESQASDELECKICYNRYNLKQRKPKVLECCHRVCAKCLYKIIDFGDSPQGVIVCPFCRFETCLPDDEVSSLPDDNNILVNLTCGGKGKKCLPENPTELLLTPKRLASLVSPSHTSSNCLVITIMEVQRESSPSLSSTPVVEFYRPASFDSVTTVSHNWTVWNCTSLLFQTSIRVLVWLLGLLYFSSLPLGIYLLVSKKVTLGVVFVSLVPSSLVILMVYGFCQCVCHEFLDCMAPPS'
    skp2 = 'MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLGHPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQKPSCL'
    
    paretoFront, input_array = generate_valid_mcts(config, mdlm, gfap, None, filename, prot_name1, None)
    generation_results = []
    
    for sequence, v in paretoFront.items():
        generated_array = v['token_ids'].to(mdlm.device)
        
        # compute perplexity
        perplexity = mdlm.compute_masked_perplexity(generated_array, input_array['input_ids'])
        perplexity = round(perplexity, 4)
        
        aa_seq, seq_length = analyzer.analyze_structure(sequence)
        scores = v['scores']
        
        if config.mcts.single == False:
            binding1 = scores[0]
            solubility = scores[1]
            hemo = scores[2]
            nonfouling = scores[3]
        
        if config.mcts.perm:
            permeability = scores[4]
            generation_results.append([sequence, perplexity, aa_seq, binding1, solubility, hemo, nonfouling, permeability])
            print(f"perplexity: {perplexity} | length: {seq_length} | smiles sequence: {sequence} | amino acid sequence: {aa_seq} | Binding Affinity: {binding1} | Solubility: {solubility} | Hemolysis: {hemo} | Nonfouling: {nonfouling} | Permeability: {permeability}")
        elif config.mcts.dual:
            binding2 = scores[4]
            generation_results.append([sequence, perplexity, aa_seq, binding1, binding2, solubility, hemo, nonfouling])
            print(f"perplexity: {perplexity} | length: {seq_length} | smiles sequence: {sequence} | amino acid sequence: {aa_seq} | Binding Affinity 1: {binding1} | Binding Affinity 2: {binding2} | Solubility: {solubility} | Hemolysis: {hemo} | Nonfouling: {nonfouling}")
        elif config.mcts.single:
            permeability = scores[0]
        else: 
            generation_results.append([sequence, perplexity, aa_seq, binding1, solubility, hemo, nonfouling])
            print(f"perplexity: {perplexity} | length: {seq_length} | smiles sequence: {sequence} | amino acid sequence: {aa_seq} | Binding Affinity: {binding1} | Solubility: {solubility} | Hemolysis: {hemo} | Nonfouling: {nonfouling}")

        sys.stdout.flush()

    if config.mcts.perm:
        df = pd.DataFrame(generation_results, columns=['Generated SMILES', 'Perplexity', 'Peptide Sequence', 'Binding Affinity', 'Solubility', 'Hemolysis', 'Nonfouling', 'Permeability'])
    elif config.mcts.dual:
        df = pd.DataFrame(generation_results, columns=['Generated SMILES', 'Perplexity', 'Peptide Sequence', 'Binding Affinity 1', 'Binding Affinity 2', 'Solubility', 'Hemolysis', 'Nonfouling'])
    elif config.mcts.single:
        df = pd.DataFrame(generation_results, columns=['Generated SMILES', 'Perplexity', 'Peptide Sequence', 'Permeability'])
    else: 
        df = pd.DataFrame(generation_results, columns=['Generated SMILES', 'Perplexity', 'Peptide Sequence', 'Binding Affinity', 'Solubility', 'Hemolysis', 'Nonfouling'])

    df.to_csv(f'/home/st512/peptune/scripts/peptide-mdlm-mcts/benchmarks/{prot_name1}/{filename}.csv', index=False)
        
    
if __name__ == "__main__":
    main()