MaPhi.pyx.bak

import subprocess
import numpy as np
import os
import pathlib
import glob
import contextlib
import multiprocessing
#from gtts import gTTS
import shutil
import pyximport; pyximport.install()
import time
from rdkit import Chem
from mordred import Calculator, descriptors, Polarizability, BCUT
import param
from check_mol import check_mol_struct
from proceed import check_err 
from get_pict import get_pict
from get_pict import get_smile



##############################################################################################
#                                                                                            
#  Modify the following parameter dependig of the calculation that you want to perform.      
#                                                                                            
npro = param.npro                  #Number of processor for orca calculation, see manual        
                                   #(https://sites.google.com/site/orcainputlibrary/setting-up-orca)           
orcaEXE = param.orcaEXE            #orca exe path                                    
mopacEXE = param.mopacEXE          #MOPAC executable                                 
lev_theory = param.lev_theory      #Level of theory check orca manual
basis_set = param.basis_set        #Basis set cheack orca manual            
openbabel = param.openbabel        #OpenBabel executable                                     
#                                                                                            
#                                                                                            
#                                                                                            
#                                                                                            
##############################################################################################

cpu = multiprocessing.cpu_count()
print("Multiprocessing ON"
)


def check_line_mop(pattern):
    with open("molecule_opt.arc") as fp:
        for cnt, line in enumerate(fp):
            if pattern in line:
                return cnt

def create_folder(folder_name):
    if not os.path.exists(folder_name):
        os.mkdir(folder_name)

#Parsing output file
def check_line(fileout,pattern,num,from_st):
    with open(fileout) as fp:
        for cnt, line in enumerate(fp):
            if cnt > from_st and pattern in line:
                return cnt+int(num)

#here fileout file to parsing, param: search word(s), num: num of line after param, ini: starting line
#fin: end line, from_stt: starying parcing from specific line
def get_val(fileout,param,num,ini,fin,from_stt):
    with open(fileout) as fp:
        for cnt, line in enumerate(fp):
            if cnt == check_line(fileout,param,num,from_stt):
                return line[ini:fin]



if __name__ == "__main__":

    if not os.path.exists(param.orcaEXE):
        print("\n\nPlease provide a valid path for orca executable in the param.py file, see orca manual and edit param.py file\n\n")
        exit(1)
    
    if not os.path.exists(param.mopacEXE):
        print("\n\nPlease provide a valid path for MOPAC2016 executable in the param.py file, see MOPAC manual and edit param.py file\n\n")
        exit(1)

    if not os.path.exists(param.openbabel):
        print("\n\nPlease provide a valid path for OpenBabel executable in the param.py file, see OpenBabel manual and edit param.py file\n\n")
        exit(1)

    print("\n\n\n Let's start.....\n\n\n")

    #Checking if there is some valence problem and move those with probles to molecules_error directory

    check_mol_struct(param.openbabel, param.mol_path, param.mopacEXE)

    #If there are any molecule with error fix it or continue calculations

    check_err(param.mol_path)
    
    #warn = "calculation can take longer on very large files, Maphi will take care of it. You can go out and have a life in the meantime!"
    #tts = gTTS(text=warn, lang='en')
    #tts.save('warn.mp3')
    #os.system('mpg321 warn.mp3')


    save_path =  os.getcwd() + "/" + 'electronic_descriptors.csv'



    with contextlib.suppress(FileNotFoundError):
        os.remove(save_path)




    mol_path = param.mol_path

    if not os.path.exists(mol_path):
        #warn = "The path for molecules directory does not exist. Please run the script again and write a correct path in the param.py file!!!!"
        #tts = gTTS(text=warn, lang='en')
        #tts.save('warn.mp3')
        #os.system('mpg321 warn.mp3')
        print("\n\nWarning!!!!!!!\n\n\n\nThe path for molecules directory does not exist, please run the script again and write a correct path in the param.py file!!\n\n\n")
        exit(1)
    else:
        print("This is the path", mol_path)
        res_path=mol_path + "/" + str("Results")
        if os.path.exists(res_path):
            print("\n\n\n\nResults file exist, the program will write new calculation in this folder!!!!\n\n\n\n")
            #warn="Results file exist, the program will write new calculation in this folder"
            #tts = gTTS(text=warn, lang='en')
            #tts.save('warn.mp3')
            #os.system('mpg321 warn.mp3')
            time.sleep(5)
        else:
            create_folder(mol_path + "/" + str("Results"))
        
        res_folder = mol_path + "/" + str("Results")
        mole_all = mol_path + "/" + str("*.mol2")

        
        molecules_F = glob.glob(mole_all)

        print("\n\n\nMolecules will be submitted in the following order :\n")
        time.sleep(5)

        for i in molecules_F:
            print("\n{}".format(i))
        
        with open(save_path,'a+') as data_file:

            data_file.write("Molecule,Smile,Structure,Total Energy [Eh],HOMO[Eh],HOMO-1[Eh],HOMO-2[Eh],LUMO[Eh],LUMO+1[Eh],\
            LUMO+2[Eh],dipole[Debye],quadrupole XX[Debye],quadrupole YY[Debye],quadrupole ZZ[Debye],quadrupole XY[Debye],\
            quadrupole XZ[Debye],quadrupole YZ[Debye],IsotropicQuad,hardness[Eh],electronegativity[Eh],electrophilicity[Eh],\
            Electron_donating_power[Eh],Electron_accepting_power[Eh],Net_electrophilicity[Eh]")

            calc = Calculator(BCUT, ignore_3D=False)
            descript = int(len(Calculator(BCUT, ignore_3D=False).descriptors))

            all_data = np.empty((0, descript))
            #all_data = np.empty((0, 10))
            for k in molecules_F:

                molecule_path, molecule_file = os.path.split(k)

                orb_folder = res_folder + "/" + molecule_file + str("outputs")
                
                
                if os.path.exists(orb_folder):
                    shutil.rmtree(orb_folder)
                
                create_folder(res_folder + "/" + molecule_file + str("outputs"))
                print("\n\n\n***************************Calculations start for molecule : ", molecule_file, "******************************************\n\n\n")

                print("\n\n\nUsing openBabel for molecule convertion...\n\n\n")
                
                #subprocess.call(openbabel + str("\t-imol2\t") + molecule_path + "/" + molecule_file + str("\t-omol2\t") + molecule_path + "/" + molecule_file, shell=True)
                #subprocess.call(openbabel + str("\t-imol2\t") + molecule_path + "/" + molecule_file + str("\t-omol\t") + "molecule.mol", shell=True)
                

                with open(mol_path + "/" + molecule_file) as fp:
                    for cnt, line in enumerate(fp):
                        if '@<TRIPOS>BOND' in line:
                            last=cnt
                with open(mol_path + "/" + molecule_file) as fp:
                    for cnt, line in enumerate(fp):
                        if '@<TRIPOS>ATOM' in line:
                            ini=cnt
                
                #Extracting geometry from mol2 file
                with open(mol_path + "/" + molecule_file) as fp:
                    struct=[]
                    for cnt, line in enumerate(fp):
                        if cnt > ini and cnt < last:
                            struct.append(line[8:46])
                
                #Generating XYZ coordinates and MOPAC for charge estimatimation
                valuesMatrix = ""
                for i in struct:
                    valuesMatrix += "{}\n".format(str(i))
                    f = open("molecule.mop","w") 
                    f.write("CHARGES\n\nFile generate by El_Dryosa\n{}".format(valuesMatrix))
                    f.close()
                print("\n\n\nComputing total charge for :", molecule_file)
                
                subprocess.call(mopacEXE + str("\tmolecule.mop"), shell=True)


                #Getting total charge from MOPAC output file"molecule.out"
                with open('molecule.out') as fp:
                    for cnt, line in enumerate(fp):
                        if 'COMPUTED CHARGE ON SYSTEM:' in line:
                            charge=int(line[37:39])
                            break
                
                print("\n\n\n\n\nMolecule charge =", charge, "for :", molecule_file, "\n\n\n")


                #generating input file for initial MOPAC optimization using PM7 "See MOPAC manual"
                f_opt = open("molecule_opt.mop","w")
                f_opt.write("PM7 XYZ CHARGE={} Singlet BONDS AUX \n\nFile generated by El_Dryosa\n{}".format(charge,valuesMatrix))
                f_opt.close()

                #Submiting MOPAC optimization
                print("\n\n\nInitial optimization using Mopac PM7\n\n\n")
                subprocess.call(mopacEXE + str("\tmolecule_opt.mop"), shell=True)

                subprocess.call(openbabel + str("\t-imopout\t") + str("molecule_opt.out") + str("\t-omol\t") + "molecule.mol", shell=True)
                subprocess.call(openbabel + str("\t-imopout\t") + str("molecule_opt.out") + str("\t-osmi\t") + "molecule.smi   " + param.ph, shell=True)
                
                smile = get_smile()
                print(smile)
                get_pict("molecule.mol")
                imag_File = res_folder + "/" + molecule_file + str("outputs") + "/" + str("molecule.png")

                mol = Chem.MolFromMolFile('molecule.mol')
                prop=calc(mol)
                numbers=np.array(list(prop.values()))
                all_data = np.append(all_data, [numbers], axis=0)

                print("\n\n\nOptimization with  Mopac PM7 done!!!!!\n\n\n")
                #check line number for optimized coordinates coordinates
                

                #Geting optimized coordinates
                with open("molecule_opt.arc") as fp:
                    struct_opt=[]
                    for cnt, line in enumerate(fp):
                        if cnt > int(check_line_mop("FINAL GEOMETRY OBTAINED"))+3:
                            struct_opt.append(line.replace("+1",""))


                #Generating input for orca
                valuesMatrix_opt = ""
                for i in struct_opt:
                    valuesMatrix_opt += "{}".format(str(i.replace(".0   ","")))
                
                print("Final optimized coordinates from MOPAC PM7!!!\n{}".format(valuesMatrix_opt))

                geome="# Test redundant internal optimization for: {}\n#\n! opt {}\n! PrintBasis {}\n%output\n print[P_MOs]1\n end #output\n* xyz {} 1\n{}*\n%elprop\nQuadrupole True\nend\n%pal\nnprocs {}\
                \nend".format(molecule_file,lev_theory,basis_set,charge,valuesMatrix_opt,npro)
                orca_input = open("orca_input.in",'w')
                orca_input.write(geome)
                orca_input.close()
                print("\norca optimization for: {} using {}/{} start...\n".format(molecule_file,param.lev_theory, param.basis_set))
                subprocess.call(orcaEXE + str("\torca_input.in") + str("\t>") + str("orca_input.out"), shell=True)


                
                normal_term = get_val("orca_input.out","****ORCA TERMINATED NORMALLY****",0,0,-1,1)
                check_norm="                             ****ORCA TERMINATED NORMALLY****"
                conve_term = get_val("orca_input.out","The optimization did not converge",0,0,-1,1)
                check_conve="       The optimization did not converge but reached the maximum number of"
                if normal_term == check_norm and conve_term == None:
                    print("{}\n".format(normal_term))
                    with open('orca_input.out') as fp:
                        for cnt, line in enumerate(fp):
                            if 'NEL' in line:
                                electrons=int(line[-5:-1])
                                break
                    with open('orca_input.out') as fp:
                        for cnt, line in enumerate(fp):
                            if 'SCF CONVERGED AFTER' in line:
                                converg=int(cnt)
                    print("\n\nmolecule {} has {} electrons.\n\n".format(molecule_file,electrons))
                    cube = int((electrons/2))
                    hcube, h1cube, h2cube, lcube, l1cube, l2cube = int(cube-1) , int(cube-2) , int(cube-3) , int(cube) , int(cube+1) , int(cube+2)
                    homo=int((electrons/2))
                    homo1=int(homo-1)
                    homo2=int(homo-2)
                    lumo=int(homo+1)
                    lumo1=int(homo+2)
                    lumo2=int(homo+3)
                    HOMO=float(get_val("orca_input.out","OCC",homo,16,29,converg))
                    HOMO1=float(get_val("orca_input.out","OCC",homo1,16,29,converg))
                    HOMO2=float(get_val("orca_input.out","OCC",homo2,16,29,converg))
                    LUMO=float(get_val("orca_input.out","OCC",lumo,16,29,converg))
                    LUMO1=float(get_val("orca_input.out","OCC",lumo1,16,29,converg))
                    LUMO2=float(get_val("orca_input.out","OCC",lumo2,16,29,converg))
                    hardness = LUMO - HOMO
                    electronegativity = float((LUMO + HOMO)/2)
                    electrophilicity = float(((LUMO + HOMO)**2)/(4*(LUMO-HOMO)))
                    ElectronDonatingPower = (3*float(HOMO)+float(LUMO))**2/(16*hardness)
                    ElectronAcceptingPower = (float(HOMO)+(3*float(LUMO)))**2/(16*hardness)
                    NetElectrophilicity = ElectronDonatingPower + ElectronAcceptingPower

                    with open('orca_input.out') as fp:
                        for cnt, line in enumerate(fp):
                            if 'FINAL SINGLE POINT ENERGY' in line:
                                tot_e=float(line[-24:-1])
                    dipole = float(get_val("orca_input.out","DIPOLE MOMENT",9,-11,-1,1))
                    quadXX = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,9,22,1))
                    quadYY = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,23,35,1))
                    quadZZ = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,36,48,1))
                    quadXY = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,49,60,1))
                    quadXZ = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,61,74,1))
                    quadYZ = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,75,87,1))
                    quadYZ = float(get_val("orca_input.out","QUADRUPOLE MOMENT (A.U.)",6,75,87,1))
                    IsotropicQuad = float(get_val("orca_input.out","Isotropic quadrupole",0,-11,-1,1))
                    data_file.write("\n{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{}".format(molecule_file,smile,imag_File,\
                    tot_e,HOMO,HOMO1,HOMO2,LUMO,LUMO1,LUMO2,dipole,quadXX,quadYY,quadZZ,quadXY,quadXZ,quadYZ,IsotropicQuad,hardness,electronegativity,electrophilicity,ElectronDonatingPower,ElectronAcceptingPower,NetElectrophilicity))
                    
                    #computing orbital
                    print("\nComputing orbitals (cube format)...")
                    orbCube="""# Test redundant internal optimization for: {}\n#\n! {}\n! PrintBasis {} keepdens\n%output\n print[P_MOs]1\n end #output\n* xyz {} 1\n{}*\n%elprop\nQuadrupole True\nend\n%pal\nnprocs \
                    {}\nend\n%plots\nFormat CUBE\nMO("orcaHOMO-{}.cube",{},0);\nMO("orcaHOMO-1-{}.cube",{},0);\
                    \nMO("orcaHOMO-2-{}.cube",{},0);\nMO("orcaLUMO-{}.cube",{},0);\nMO("orcaLUMO+1-{}.cube",{},0);\
                    \nMO("orcaLUMO+2-{}.cube",{},0);\nend""".format(molecule_file,lev_theory,\
                    basis_set,charge,valuesMatrix_opt,npro,hcube,hcube,h1cube,h1cube,h2cube,h2cube,lcube,lcube,l1cube,l1cube,l2cube,l2cube)
                    orca_orbital = open("orca_orbitals.in",'w')
                    orca_orbital.write(orbCube)
                    orca_orbital.close()
                    
                    subprocess.call(orcaEXE + str("\torca_orbitals.in") + str("\t>") + str("orca_orbitals.out"), shell=True)

                    if os.path.exists(os.getcwd() + "/" + str("orca_input.xyz")):
                        shutil.copy(os.getcwd() + "/" + str("orca_input.xyz"), os.getcwd() + "/" +  str("orca_orbitals.xyz"))
                                
                    files = glob.glob("orca*")
                    for f in files:
                        shutil.move(f, res_folder + "/" + molecule_file + str("outputs"))

                    outputs = glob.glob("molecule*")
                    for f in outputs:
                        shutil.move(f, res_folder + "/" + molecule_file + str("outputs"))
                    print("\n\n\nCalculation ended for molecule:", molecule_file, "\n\n\n")

                    
                else:
                    print("\nMolecule: {}  does not converge data will appear as NAN".format(molecule_file))
                    print("\nPossible problems; bad initial guess, wrong charge multiplicity pair. Remember that the program only works when multiplicity is equal to 1 (singlet state)")
                    print("Send us an email to juvenal.yosa@unisimonbolivar.com with the orca output file and we will improve the code to handle a particular problem\n")
                    data_file.write("\n{},{},{},NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN".format(smile,imag_File,molecule_file))



    header = "ABC,ABCGG,nAcid,nBase,SpAbs_A,SpMax_A,SpDiam_A,SpAD_A,SpMAD_A,LogEE_A,VE1_A,VE2_A,VE3_A,VR1_A,VR2_A,VR3_A,nAromAtom,nAromBond,nAtom,\
    nHeavyAtom,nSpiro,nBridgehead,nHetero,nH,nB,nC,nN,nO,nS,nP,nF,nCl,nBr,nI,nX,ATS0dv,ATS1dv,ATS2dv,ATS3dv,ATS4dv,ATS5dv,ATS6dv,ATS7dv,ATS8dv,ATS0d,\
    ATS1d,ATS2d,ATS3d,ATS4d,ATS5d,ATS6d,ATS7d,ATS8d,ATS0s,ATS1s,ATS2s,ATS3s,ATS4s,ATS5s,ATS6s,ATS7s,ATS8s,ATS0Z,ATS1Z,ATS2Z,ATS3Z,ATS4Z,ATS5Z,ATS6Z,\
    ATS7Z,ATS8Z,ATS0m,ATS1m,ATS2m,ATS3m,ATS4m,ATS5m,ATS6m,ATS7m,ATS8m,ATS0v,ATS1v,ATS2v,ATS3v,ATS4v,ATS5v,ATS6v,ATS7v,ATS8v,ATS0se,ATS1se,ATS2se,\
    ATS3se,ATS4se,ATS5se,ATS6se,ATS7se,ATS8se,ATS0pe,ATS1pe,ATS2pe,ATS3pe,ATS4pe,ATS5pe,ATS6pe,ATS7pe,ATS8pe,ATS0are,ATS1are,ATS2are,ATS3are,ATS4are,\
    ATS5are,ATS6are,ATS7are,ATS8are,ATS0p,ATS1p,ATS2p,ATS3p,ATS4p,ATS5p,ATS6p,ATS7p,ATS8p,ATS0i,ATS1i,ATS2i,ATS3i,ATS4i,ATS5i,ATS6i,ATS7i,ATS8i,\
    AATS0dv,AATS1dv,AATS2dv,AATS3dv,AATS4dv,AATS5dv,AATS6dv,AATS7dv,AATS8dv,AATS0d,AATS1d,AATS2d,AATS3d,AATS4d,AATS5d,AATS6d,AATS7d,AATS8d,AATS0s,\
    AATS1s,AATS2s,AATS3s,AATS4s,AATS5s,AATS6s,AATS7s,AATS8s,AATS0Z,AATS1Z,AATS2Z,AATS3Z,AATS4Z,AATS5Z,AATS6Z,AATS7Z,AATS8Z,AATS0m,AATS1m,AATS2m,\
    AATS3m,AATS4m,AATS5m,AATS6m,AATS7m,AATS8m,AATS0v,AATS1v,AATS2v,AATS3v,AATS4v,AATS5v,AATS6v,AATS7v,AATS8v,AATS0se,AATS1se,AATS2se,AATS3se,\
    AATS4se,AATS5se,AATS6se,AATS7se,AATS8se,AATS0pe,AATS1pe,AATS2pe,AATS3pe,AATS4pe,AATS5pe,AATS6pe,AATS7pe,AATS8pe,AATS0are,AATS1are,AATS2are,\
    AATS3are,AATS4are,AATS5are,AATS6are,AATS7are,AATS8are,AATS0p,AATS1p,AATS2p,AATS3p,AATS4p,AATS5p,AATS6p,AATS7p,AATS8p,AATS0i,AATS1i,AATS2i,\
    AATS3i,AATS4i,AATS5i,AATS6i,AATS7i,AATS8i,ATSC0c,ATSC1c,ATSC2c,ATSC3c,ATSC4c,ATSC5c,ATSC6c,ATSC7c,ATSC8c,ATSC0dv,ATSC1dv,ATSC2dv,ATSC3dv,\
    ATSC4dv,ATSC5dv,ATSC6dv,ATSC7dv,ATSC8dv,ATSC0d,ATSC1d,ATSC2d,ATSC3d,ATSC4d,ATSC5d,ATSC6d,ATSC7d,ATSC8d,ATSC0s,ATSC1s,ATSC2s,ATSC3s,ATSC4s,ATSC5s\
    ,ATSC6s,ATSC7s,ATSC8s,ATSC0Z,ATSC1Z,ATSC2Z,ATSC3Z,ATSC4Z,ATSC5Z,ATSC6Z,ATSC7Z,ATSC8Z,ATSC0m,ATSC1m,ATSC2m,ATSC3m,ATSC4m,ATSC5m,ATSC6m,ATSC7m,\
    ATSC8m,ATSC0v,ATSC1v,ATSC2v,ATSC3v,ATSC4v,ATSC5v,ATSC6v,ATSC7v,ATSC8v,ATSC0se,ATSC1se,ATSC2se,ATSC3se,ATSC4se,ATSC5se,ATSC6se,ATSC7se,ATSC8se,\
    ATSC0pe,ATSC1pe,ATSC2pe,ATSC3pe,ATSC4pe,ATSC5pe,ATSC6pe,ATSC7pe,ATSC8pe,ATSC0are,ATSC1are,ATSC2are,ATSC3are,ATSC4are,ATSC5are,ATSC6are,ATSC7are,\
    ATSC8are,ATSC0p,ATSC1p,ATSC2p,ATSC3p,ATSC4p,ATSC5p,ATSC6p,ATSC7p,ATSC8p,ATSC0i,ATSC1i,ATSC2i,ATSC3i,ATSC4i,ATSC5i,ATSC6i,ATSC7i,ATSC8i,AATSC0c,\
    AATSC1c,AATSC2c,AATSC3c,AATSC4c,AATSC5c,AATSC6c,AATSC7c,AATSC8c,AATSC0dv,AATSC1dv,AATSC2dv,AATSC3dv,AATSC4dv,AATSC5dv,AATSC6dv,AATSC7dv,AATSC8dv,\
    AATSC0d,AATSC1d,AATSC2d,AATSC3d,AATSC4d,AATSC5d,AATSC6d,AATSC7d,AATSC8d,AATSC0s,AATSC1s,AATSC2s,AATSC3s,AATSC4s,AATSC5s,AATSC6s,AATSC7s,AATSC8s,\
    AATSC0Z,AATSC1Z,AATSC2Z,AATSC3Z,AATSC4Z,AATSC5Z,AATSC6Z,AATSC7Z,AATSC8Z,AATSC0m,AATSC1m,AATSC2m,AATSC3m,AATSC4m,AATSC5m,AATSC6m,AATSC7m,AATSC8m,\
    AATSC0v,AATSC1v,AATSC2v,AATSC3v,AATSC4v,AATSC5v,AATSC6v,AATSC7v,AATSC8v,AATSC0se,AATSC1se,AATSC2se,AATSC3se,AATSC4se,AATSC5se,AATSC6se,AATSC7se,\
    AATSC8se,AATSC0pe,AATSC1pe,AATSC2pe,AATSC3pe,AATSC4pe,AATSC5pe,AATSC6pe,AATSC7pe,AATSC8pe,AATSC0are,AATSC1are,AATSC2are,AATSC3are,AATSC4are,\
    AATSC5are,AATSC6are,AATSC7are,AATSC8are,AATSC0p,AATSC1p,AATSC2p,AATSC3p,AATSC4p,AATSC5p,AATSC6p,AATSC7p,AATSC8p,AATSC0i,AATSC1i,AATSC2i,AATSC3i,\
    AATSC4i,AATSC5i,AATSC6i,AATSC7i,AATSC8i,MATS1c,MATS2c,MATS3c,MATS4c,MATS5c,MATS6c,MATS7c,MATS8c,MATS1dv,MATS2dv,MATS3dv,MATS4dv,MATS5dv,MATS6dv,\
    MATS7dv,MATS8dv,MATS1d,MATS2d,MATS3d,MATS4d,MATS5d,MATS6d,MATS7d,MATS8d,MATS1s,MATS2s,MATS3s,MATS4s,MATS5s,MATS6s,MATS7s,MATS8s,MATS1Z,MATS2Z,\
    MATS3Z,MATS4Z,MATS5Z,MATS6Z,MATS7Z,MATS8Z,MATS1m,MATS2m,MATS3m,MATS4m,MATS5m,MATS6m,MATS7m,MATS8m,MATS1v,MATS2v,MATS3v,MATS4v,MATS5v,MATS6v,\
    MATS7v,MATS8v,MATS1se,MATS2se,MATS3se,MATS4se,MATS5se,MATS6se,MATS7se,MATS8se,MATS1pe,MATS2pe,MATS3pe,MATS4pe,MATS5pe,MATS6pe,MATS7pe,MATS8pe,\
    MATS1are,MATS2are,MATS3are,MATS4are,MATS5are,MATS6are,MATS7are,MATS8are,MATS1p,MATS2p,MATS3p,MATS4p,MATS5p,MATS6p,MATS7p,MATS8p,MATS1i,MATS2i,\
    MATS3i,MATS4i,MATS5i,MATS6i,MATS7i,MATS8i,GATS1c,GATS2c,GATS3c,GATS4c,GATS5c,GATS6c,GATS7c,GATS8c,GATS1dv,GATS2dv,GATS3dv,GATS4dv,GATS5dv,\
    GATS6dv,GATS7dv,GATS8dv,GATS1d,GATS2d,GATS3d,GATS4d,GATS5d,GATS6d,GATS7d,GATS8d,GATS1s,GATS2s,GATS3s,GATS4s,GATS5s,GATS6s,GATS7s,GATS8s,\
    GATS1Z,GATS2Z,GATS3Z,GATS4Z,GATS5Z,GATS6Z,GATS7Z,GATS8Z,GATS1m,GATS2m,GATS3m,GATS4m,GATS5m,GATS6m,GATS7m,GATS8m,GATS1v,GATS2v,GATS3v,GATS4v,\
    GATS5v,GATS6v,GATS7v,GATS8v,GATS1se,GATS2se,GATS3se,GATS4se,GATS5se,GATS6se,GATS7se,GATS8se,GATS1pe,GATS2pe,GATS3pe,GATS4pe,GATS5pe,GATS6pe,\
    GATS7pe,GATS8pe,GATS1are,GATS2are,GATS3are,GATS4are,GATS5are,GATS6are,GATS7are,GATS8are,GATS1p,GATS2p,GATS3p,GATS4p,GATS5p,GATS6p,GATS7p,\
    GATS8p,GATS1i,GATS2i,GATS3i,GATS4i,GATS5i,GATS6i,GATS7i,GATS8i,BCUTc-1h,BCUTc-1l,BCUTdv-1h,BCUTdv-1l,BCUTd-1h,BCUTd-1l,BCUTs-1h,BCUTs-1l,\
    BCUTZ-1h,BCUTZ-1l,BCUTm-1h,BCUTm-1l,BCUTv-1h,BCUTv-1l,BCUTse-1h,BCUTse-1l,BCUTpe-1h,BCUTpe-1l,BCUTare-1h,BCUTare-1l,BCUTp-1h,BCUTp-1l,\
    BCUTi-1h,BCUTi-1l,BalabanJ,SpAbs_DzZ,SpMax_DzZ,SpDiam_DzZ,SpAD_DzZ,SpMAD_DzZ,LogEE_DzZ,SM1_DzZ,VE1_DzZ,VE2_DzZ,VE3_DzZ,VR1_DzZ,VR2_DzZ,VR3_DzZ,\
    SpAbs_Dzm,SpMax_Dzm,SpDiam_Dzm,SpAD_Dzm,SpMAD_Dzm,LogEE_Dzm,SM1_Dzm,VE1_Dzm,VE2_Dzm,VE3_Dzm,VR1_Dzm,VR2_Dzm,VR3_Dzm,SpAbs_Dzv,SpMax_Dzv,\
    SpDiam_Dzv,SpAD_Dzv,SpMAD_Dzv,LogEE_Dzv,SM1_Dzv,VE1_Dzv,VE2_Dzv,VE3_Dzv,VR1_Dzv,VR2_Dzv,VR3_Dzv,SpAbs_Dzse,SpMax_Dzse,SpDiam_Dzse,SpAD_Dzse,\
    SpMAD_Dzse,LogEE_Dzse,SM1_Dzse,VE1_Dzse,VE2_Dzse,VE3_Dzse,VR1_Dzse,VR2_Dzse,VR3_Dzse,SpAbs_Dzpe,SpMax_Dzpe,SpDiam_Dzpe,SpAD_Dzpe,SpMAD_Dzpe,\
    LogEE_Dzpe,SM1_Dzpe,VE1_Dzpe,VE2_Dzpe,VE3_Dzpe,VR1_Dzpe,VR2_Dzpe,VR3_Dzpe,SpAbs_Dzare,SpMax_Dzare,SpDiam_Dzare,SpAD_Dzare,SpMAD_Dzare,\
    LogEE_Dzare,SM1_Dzare,VE1_Dzare,VE2_Dzare,VE3_Dzare,VR1_Dzare,VR2_Dzare,VR3_Dzare,SpAbs_Dzp,SpMax_Dzp,SpDiam_Dzp,SpAD_Dzp,SpMAD_Dzp,LogEE_Dzp,\
    SM1_Dzp,VE1_Dzp,VE2_Dzp,VE3_Dzp,VR1_Dzp,VR2_Dzp,VR3_Dzp,SpAbs_Dzi,SpMax_Dzi,SpDiam_Dzi,SpAD_Dzi,SpMAD_Dzi,LogEE_Dzi,SM1_Dzi,VE1_Dzi,VE2_Dzi,\
    VE3_Dzi,VR1_Dzi,VR2_Dzi,VR3_Dzi,BertzCT,nBonds,nBondsO,nBondsS,nBondsD,nBondsT,nBondsA,nBondsM,nBondsKS,nBondsKD,PNSA1,PNSA2,PNSA3,PNSA4,PNSA5,\
    PPSA1,PPSA2,PPSA3,PPSA4,PPSA5,DPSA1,DPSA2,DPSA3,DPSA4,DPSA5,FNSA1,FNSA2,FNSA3,FNSA4,FNSA5,FPSA1,FPSA2,FPSA3,FPSA4,FPSA5,WNSA1,WNSA2,WNSA3,\
    WNSA4,WNSA5,WPSA1,WPSA2,WPSA3,WPSA4,WPSA5,RNCG,RPCG,RNCS,RPCS,TASA,TPSA,RASA,RPSA,C1SP1,C2SP1,C1SP2,C2SP2,C3SP2,C1SP3,C2SP3,C3SP3,C4SP3,\
    HybRatio,FCSP3,Xch-3d,Xch-4d,Xch-5d,Xch-6d,Xch-7d,Xch-3dv,Xch-4dv,Xch-5dv,Xch-6dv,Xch-7dv,Xc-3d,Xc-4d,Xc-5d,Xc-6d,Xc-3dv,Xc-4dv,Xc-5dv,Xc-6dv,\
    Xpc-4d,Xpc-5d,Xpc-6d,Xpc-4dv,Xpc-5dv,Xpc-6dv,Xp-0d,Xp-1d,Xp-2d,Xp-3d,Xp-4d,Xp-5d,Xp-6d,Xp-7d,AXp-0d,AXp-1d,AXp-2d,AXp-3d,AXp-4d,AXp-5d,AXp-6d,\
    AXp-7d,Xp-0dv,Xp-1dv,Xp-2dv,Xp-3dv,Xp-4dv,Xp-5dv,Xp-6dv,Xp-7dv,AXp-0dv,AXp-1dv,AXp-2dv,AXp-3dv,AXp-4dv,AXp-5dv,AXp-6dv,AXp-7dv,SZ,Sm,Sv,Sse,\
    Spe,Sare,Sp,Si,MZ,Mm,Mv,Mse,Mpe,Mare,Mp,Mi,SpAbs_Dt,SpMax_Dt,SpDiam_Dt,SpAD_Dt,SpMAD_Dt,LogEE_Dt,SM1_Dt,VE1_Dt,VE2_Dt,VE3_Dt,VR1_Dt,VR2_Dt,\
    VR3_Dt,DetourIndex,SpAbs_D,SpMax_D,SpDiam_D,SpAD_D,SpMAD_D,LogEE_D,VE1_D,VE2_D,VE3_D,VR1_D,VR2_D,VR3_D,NsLi,NssBe,NssssBe,NssBH,NsssB,NssssB,\
    NsCH3,NdCH2,NssCH2,NtCH,NdsCH,NaaCH,NsssCH,NddC,NtsC,NdssC,NaasC,NaaaC,NssssC,NsNH3,NsNH2,NssNH2,NdNH,NssNH,NaaNH,NtN,NsssNH,NdsN,NaaN,NsssN,\
    NddsN,NaasN,NssssN,NsOH,NdO,NssO,NaaO,NsF,NsSiH3,NssSiH2,NsssSiH,NssssSi,NsPH2,NssPH,NsssP,NdsssP,NsssssP,NsSH,NdS,NssS,NaaS,NdssS,NddssS,NsCl,\
    NsGeH3,NssGeH2,NsssGeH,NssssGe,NsAsH2,NssAsH,NsssAs,NsssdAs,NsssssAs,NsSeH,NdSe,NssSe,NaaSe,NdssSe,NddssSe,NsBr,NsSnH3,NssSnH2,NsssSnH,NssssSn,\
    NsI,NsPbH3,NssPbH2,NsssPbH,NssssPb,SsLi,SssBe,SssssBe,SssBH,SsssB,SssssB,SsCH3,SdCH2,SssCH2,StCH,SdsCH,SaaCH,SsssCH,SddC,StsC,SdssC,SaasC,SaaaC,\
    SssssC,SsNH3,SsNH2,SssNH2,SdNH,SssNH,SaaNH,StN,SsssNH,SdsN,SaaN,SsssN,SddsN,SaasN,SssssN,SsOH,SdO,SssO,SaaO,SsF,SsSiH3,SssSiH2,SsssSiH,SssssSi,\
    SsPH2,SssPH,SsssP,SdsssP,SsssssP,SsSH,SdS,SssS,SaaS,SdssS,SddssS,SsCl,SsGeH3,SssGeH2,SsssGeH,SssssGe,SsAsH2,SssAsH,SsssAs,SsssdAs,SsssssAs,SsSeH,\
    SdSe,SssSe,SaaSe,SdssSe,SddssSe,SsBr,SsSnH3,SssSnH2,SsssSnH,SssssSn,SsI,SsPbH3,SssPbH2,SsssPbH,SssssPb,MAXsLi,MAXssBe,MAXssssBe,MAXssBH,MAXsssB,\
    MAXssssB,MAXsCH3,MAXdCH2,MAXssCH2,MAXtCH,MAXdsCH,MAXaaCH,MAXsssCH,MAXddC,MAXtsC,MAXdssC,MAXaasC,MAXaaaC,MAXssssC,MAXsNH3,MAXsNH2,MAXssNH2,MAXdNH,\
    MAXssNH,MAXaaNH,MAXtN,MAXsssNH,MAXdsN,MAXaaN,MAXsssN,MAXddsN,MAXaasN,MAXssssN,MAXsOH,MAXdO,MAXssO,MAXaaO,MAXsF,MAXsSiH3,MAXssSiH2,MAXsssSiH,\
    MAXssssSi,MAXsPH2,MAXssPH,MAXsssP,MAXdsssP,MAXsssssP,MAXsSH,MAXdS,MAXssS,MAXaaS,MAXdssS,MAXddssS,MAXsCl,MAXsGeH3,MAXssGeH2,MAXsssGeH,MAXssssGe,\
    MAXsAsH2,MAXssAsH,MAXsssAs,MAXsssdAs,MAXsssssAs,MAXsSeH,MAXdSe,MAXssSe,MAXaaSe,MAXdssSe,MAXddssSe,MAXsBr,MAXsSnH3,MAXssSnH2,MAXsssSnH,MAXssssSn,\
    MAXsI,MAXsPbH3,MAXssPbH2,MAXsssPbH,MAXssssPb,MINsLi,MINssBe,MINssssBe,MINssBH,MINsssB,MINssssB,MINsCH3,MINdCH2,MINssCH2,MINtCH,MINdsCH,MINaaCH,\
    MINsssCH,MINddC,MINtsC,MINdssC,MINaasC,MINaaaC,MINssssC,MINsNH3,MINsNH2,MINssNH2,MINdNH,MINssNH,MINaaNH,MINtN,MINsssNH,MINdsN,MINaaN,MINsssN,\
    MINddsN,MINaasN,MINssssN,MINsOH,MINdO,MINssO,MINaaO,MINsF,MINsSiH3,MINssSiH2,MINsssSiH,MINssssSi,MINsPH2,MINssPH,MINsssP,MINdsssP,MINsssssP,\
    MINsSH,MINdS,MINssS,MINaaS,MINdssS,MINddssS,MINsCl,MINsGeH3,MINssGeH2,MINsssGeH,MINssssGe,MINsAsH2,MINssAsH,MINsssAs,MINsssdAs,MINsssssAs,\
    MINsSeH,MINdSe,MINssSe,MINaaSe,MINdssSe,MINddssSe,MINsBr,MINsSnH3,MINssSnH2,MINsssSnH,MINssssSn,MINsI,MINsPbH3,MINssPbH2,MINsssPbH,MINssssPb,\
    ECIndex,ETA_alpha,AETA_alpha,ETA_shape_p,ETA_shape_y,ETA_shape_x,ETA_beta,AETA_beta,ETA_beta_s,AETA_beta_s,ETA_beta_ns,AETA_beta_ns,ETA_beta_ns_d,\
    AETA_beta_ns_d,ETA_eta,AETA_eta,ETA_eta_L,AETA_eta_L,ETA_eta_R,AETA_eta_R,ETA_eta_RL,AETA_eta_RL,ETA_eta_F,AETA_eta_F,ETA_eta_FL,AETA_eta_FL,\
    ETA_eta_B,AETA_eta_B,ETA_eta_BR,AETA_eta_BR,ETA_dAlpha_A,ETA_dAlpha_B,ETA_epsilon_1,ETA_epsilon_2,ETA_epsilon_3,ETA_epsilon_4,ETA_epsilon_5,\
    ETA_dEpsilon_A,ETA_dEpsilon_B,ETA_dEpsilon_C,ETA_dEpsilon_D,ETA_dBeta,AETA_dBeta,ETA_psi_1,ETA_dPsi_A,ETA_dPsi_B,fragCpx,fMF,GeomDiameter,\
    GeomRadius,GeomShapeIndex,GeomPetitjeanIndex,GRAV,GRAVH,GRAVp,GRAVHp,nHBAcc,nHBDon,IC0,IC1,IC2,IC3,IC4,IC5,TIC0,TIC1,TIC2,TIC3,TIC4,TIC5,SIC0,\
    SIC1,SIC2,SIC3,SIC4,SIC5,BIC0,BIC1,BIC2,BIC3,BIC4,BIC5,CIC0,CIC1,CIC2,CIC3,CIC4,CIC5,MIC0,MIC1,MIC2,MIC3,MIC4,MIC5,ZMIC0,ZMIC1,ZMIC2,ZMIC3,\
    ZMIC4,ZMIC5,Kier1,Kier2,Kier3,Lipinski,GhoseFilter,FilterItLogS,VMcGowan,Mor01,Mor02,Mor03,Mor04,Mor05,Mor06,Mor07,Mor08,Mor09,Mor10,Mor11,\
    Mor12,Mor13,Mor14,Mor15,Mor16,Mor17,Mor18,Mor19,Mor20,Mor21,Mor22,Mor23,Mor24,Mor25,Mor26,Mor27,Mor28,Mor29,Mor30,Mor31,Mor32,Mor01m,Mor02m,\
    Mor03m,Mor04m,Mor05m,Mor06m,Mor07m,Mor08m,Mor09m,Mor10m,Mor11m,Mor12m,Mor13m,Mor14m,Mor15m,Mor16m,Mor17m,Mor18m,Mor19m,Mor20m,Mor21m,Mor22m,\
    Mor23m,Mor24m,Mor25m,Mor26m,Mor27m,Mor28m,Mor29m,Mor30m,Mor31m,Mor32m,Mor01v,Mor02v,Mor03v,Mor04v,Mor05v,Mor06v,Mor07v,Mor08v,Mor09v,Mor10v,\
    Mor11v,Mor12v,Mor13v,Mor14v,Mor15v,Mor16v,Mor17v,Mor18v,Mor19v,Mor20v,Mor21v,Mor22v,Mor23v,Mor24v,Mor25v,Mor26v,Mor27v,Mor28v,Mor29v,Mor30v,\
    Mor31v,Mor32v,Mor01se,Mor02se,Mor03se,Mor04se,Mor05se,Mor06se,Mor07se,Mor08se,Mor09se,Mor10se,Mor11se,Mor12se,Mor13se,Mor14se,Mor15se,Mor16se,\
    Mor17se,Mor18se,Mor19se,Mor20se,Mor21se,Mor22se,Mor23se,Mor24se,Mor25se,Mor26se,Mor27se,Mor28se,Mor29se,Mor30se,Mor31se,Mor32se,Mor01p,\
    Mor02p,Mor03p,Mor04p,Mor05p,Mor06p,Mor07p,Mor08p,Mor09p,Mor10p,Mor11p,Mor12p,Mor13p,Mor14p,Mor15p,Mor16p,Mor17p,Mor18p,Mor19p,Mor20p,Mor21p,\
    Mor22p,Mor23p,Mor24p,Mor25p,Mor26p,Mor27p,Mor28p,Mor29p,Mor30p,Mor31p,Mor32p,LabuteASA,PEOE_VSA1,PEOE_VSA2,PEOE_VSA3,PEOE_VSA4,PEOE_VSA5,\
    PEOE_VSA6,PEOE_VSA7,PEOE_VSA8,PEOE_VSA9,PEOE_VSA10,PEOE_VSA11,PEOE_VSA12,PEOE_VSA13,SMR_VSA1,SMR_VSA2,SMR_VSA3,SMR_VSA4,SMR_VSA5,SMR_VSA6,\
    SMR_VSA7,SMR_VSA8,SMR_VSA9,SlogP_VSA1,SlogP_VSA2,SlogP_VSA3,SlogP_VSA4,SlogP_VSA5,SlogP_VSA6,SlogP_VSA7,SlogP_VSA8,SlogP_VSA9,SlogP_VSA10,\
    SlogP_VSA11,EState_VSA1,EState_VSA2,EState_VSA3,EState_VSA4,EState_VSA5,EState_VSA6,EState_VSA7,EState_VSA8,EState_VSA9,EState_VSA10,\
    VSA_EState1,VSA_EState2,VSA_EState3,VSA_EState4,VSA_EState5,VSA_EState6,VSA_EState7,VSA_EState8,VSA_EState9,MDEC-11,MDEC-12,MDEC-13,MDEC-14,\
    MDEC-22,MDEC-23,MDEC-24,MDEC-33,MDEC-34,MDEC-44,MDEO-11,MDEO-12,MDEO-22,MDEN-11,MDEN-12,MDEN-13,MDEN-22,MDEN-23,MDEN-33,MID,AMID,MID_h,AMID_h,\
    MID_C,AMID_C,MID_N,AMID_N,MID_O,AMID_O,MID_X,AMID_X,MOMI-X,MOMI-Y,MOMI-Z,MPC2,MPC3,MPC4,MPC5,MPC6,MPC7,MPC8,MPC9,MPC10,TMPC10,piPC1,piPC2,\
    piPC3,piPC4,piPC5,piPC6,piPC7,piPC8,piPC9,piPC10,TpiPC10,apol,bpol,nRing,n3Ring,n4Ring,n5Ring,n6Ring,n7Ring,n8Ring,n9Ring,n10Ring,n11Ring,\
    n12Ring,nG12Ring,nHRing,n3HRing,n4HRing,n5HRing,n6HRing,n7HRing,n8HRing,n9HRing,n10HRing,n11HRing,n12HRing,nG12HRing,naRing,n3aRing,n4aRing,\
    n5aRing,n6aRing,n7aRing,n8aRing,n9aRing,n10aRing,n11aRing,n12aRing,nG12aRing,naHRing,n3aHRing,n4aHRing,n5aHRing,n6aHRing,n7aHRing,n8aHRing,\
    n9aHRing,n10aHRing,n11aHRing,n12aHRing,nG12aHRing,nARing,n3ARing,n4ARing,n5ARing,n6ARing,n7ARing,n8ARing,n9ARing,n10ARing,n11ARing,n12ARing,\
    nG12ARing,nAHRing,n3AHRing,n4AHRing,n5AHRing,n6AHRing,n7AHRing,n8AHRing,n9AHRing,n10AHRing,n11AHRing,n12AHRing,nG12AHRing,nFRing,n4FRing,\
    n5FRing,n6FRing,n7FRing,n8FRing,n9FRing,n10FRing,n11FRing,n12FRing,nG12FRing,nFHRing,n4FHRing,n5FHRing,n6FHRing,n7FHRing,n8FHRing,n9FHRing,\
    n10FHRing,n11FHRing,n12FHRing,nG12FHRing,nFaRing,n4FaRing,n5FaRing,n6FaRing,n7FaRing,n8FaRing,n9FaRing,n10FaRing,n11FaRing,n12FaRing,\
    nG12FaRing,nFaHRing,n4FaHRing,n5FaHRing,n6FaHRing,n7FaHRing,n8FaHRing,n9FaHRing,n10FaHRing,n11FaHRing,n12FaHRing,nG12FaHRing,nFARing,\
    n4FARing,n5FARing,n6FARing,n7FARing,n8FARing,n9FARing,n10FARing,n11FARing,n12FARing,nG12FARing,nFAHRing,n4FAHRing,n5FAHRing,n6FAHRing,\
    n7FAHRing,n8FAHRing,n9FAHRing,n10FAHRing,n11FAHRing,n12FAHRing,nG12FAHRing,nRot,RotRatio,SLogP,SMR,TopoPSA(NO),TopoPSA,GGI1,GGI2,GGI3,\
    GGI4,GGI5,GGI6,GGI7,GGI8,GGI9,GGI10,JGI1,JGI2,JGI3,JGI4,JGI5,JGI6,JGI7,JGI8,JGI9,JGI10,JGT10,Diameter,Radius,TopoShapeIndex,PetitjeanIndex,\
    Vabc,VAdjMat,MWC01,MWC02,MWC03,MWC04,MWC05,MWC06,MWC07,MWC08,MWC09,MWC10,TMWC10,SRW02,SRW03,SRW04,SRW05,SRW06,SRW07,SRW08,SRW09,SRW10,\
    TSRW10,MW,AMW,WPath,WPol,Zagreb1,Zagreb2,mZagreb1,mZagreb2"

    file_non_elect = "non_electronic_descriptors.csv"

    with contextlib.suppress(FileNotFoundError):
        os.remove(file_non_elect)

    np.savetxt("non_electronic_descriptors.csv", all_data, delimiter=',', header=header, comments="")


    if os.path.exists(os.getcwd() + "/" + str("electronic_descriptors.csv")):
        shutil.move(os.getcwd() + "/" + str("electronic_descriptors.csv"), res_folder + "/" +  str("electronic_descriptors.csv"))

    if os.path.exists(os.getcwd() + "/" + str("non_electronic_descriptors.csv")):
        shutil.move(os.getcwd() + "/" + str("non_electronic_descriptors.csv"), res_folder + "/" +  str("non_electronic_descriptors.csv"))


    print("\n\n\n\nAll calculation are done. Have an awesome analysis. Cheers!\n\n\n")
    #warn = "All calculation are done. Have an awesome analysis. Cheers!"
    #tts = gTTS(text=warn, lang='en')
    #tts.save('warn.mp3')
    os.system('mpg321 warn.mp3')
    os.remove("warn.mp3")
    res=res_folder + "/" +  str("electronic_descriptors.csv")
    res2=res_folder + "/" +  str("non_electronic_descriptors.csv")
    print("\nYou will find a csv file with the results in: {}, {}\n\n".format(res,res2))