yukti.py

# "yukti": a program, intended for the students of computational biology & bioinformatics; helps its users perform an assisted experiment involving molecular docking simulation techniques

import os;
from shutil import copyfile;
from shutil import rmtree;

print("\nHello user! 'YUKTI' (yukti.py) is running now! Always make sure that you've properly converted all of your targets/proteins & ligands/compounds to the PDBQT file format before using this program in order to avoid any errors!\n\nA recommendation:\n\nIf you run 'YUKTI' more than once in the same folder/directory for any reason, then make sure to remove everything created during its previous run before you run it again because otherwise, it'll all get deleted & also make sure to take a proper look at the \"read me\" file prepared for it. This program's flexibility will keep improving until its development is complete & the preparations required for using it will keep decreasing.\n");

judge1 = os.path.exists("/home/user/YUKTI/target_1");

if judge1 == True:
    rmtree("/home/user/YUKTI/target_1");

os.mkdir("/home/user/YUKTI/target_1");

folders1 = ["{}".format(x) for x in range(11)];
del folders1[0];

for f_variable in folders1:
    os.mkdir(os.path.join("/home/user/YUKTI/target_1", f_variable));

src_path = "/home/user/YUKTI/";
#fileA = "autodock4.exe";
#fileB = "autogrid4.exe";
fileC = "target_1.pdb";
fileD = "target_1.pdbqt";

for f_variable in folders1:
    dst_path = "/home/user/YUKTI/target_1/{}/".format(f_variable);
    #copyfile(src_path+str(fileA), dst_path+str(fileA));
    #copyfile(src_path+str(fileB), dst_path+str(fileB));
    copyfile(src_path+str(fileC), dst_path+str(fileC));
    copyfile(src_path+str(fileD), dst_path+str(fileD));

judge2 = os.path.exists("/home/user/YUKTI/target_2");

if judge2 == True:
    rmtree("/home/user/YUKTI/target_2");

os.mkdir("/home/user/YUKTI/target_2");

folders2 = ["{}".format(x) for x in range(11)];
del folders2[0];

for f_variable in folders2:
    os.mkdir(os.path.join("/home/user/YUKTI/target_2", f_variable));

src_path = "/home/user/YUKTI/";
#fileA = "autodock4.exe";
#fileB = "autogrid4.exe";
fileC = "target_2.pdb";
fileD = "target_2.pdbqt";

for f_variable in folders2:
    dst_path = "/home/user/YUKTI/target_2/{}/".format(f_variable);
    #copyfile(src_path+str(fileA), dst_path+str(fileA));
    #copyfile(src_path+str(fileB), dst_path+str(fileB));
    copyfile(src_path+str(fileC), dst_path+str(fileC));
    copyfile(src_path+str(fileD), dst_path+str(fileD));

folders = ["{}".format(x) for x in range(11)];
del folders[0];

src_path1 = "/home/user/YUKTI/library-pdbqt/";

for f_variable in folders:
    dst_path1 = "/home/user/YUKTI/target_1/{}/".format(f_variable);
    dst_path2 = "/home/user/YUKTI/target_2/{}/".format(f_variable);
    copyfile(src_path1+"compound_"+str(f_variable)+".pdbqt", dst_path1+"compound_"+str(f_variable)+".pdbqt");
    copyfile(src_path1+"compound_"+str(f_variable)+".pdbqt", dst_path2+"compound_"+str(f_variable)+".pdbqt");
    
    copyfile("/home/user/YUKTI/library-pdb/compound_"+str(f_variable)+".pdb", dst_path1+"compound_"+str(f_variable)+".pdb");
    copyfile("/home/user/YUKTI/library-pdb/compound_"+str(f_variable)+".pdb", dst_path2+"compound_"+str(f_variable)+".pdb");

src_path2 = "/home/user/YUKTI/";

for f_variable in folders:
    dst_path1 = "/home/user/YUKTI/target_1/{}/".format(f_variable);
    dst_path2 = "/home/user/YUKTI/target_2/{}/".format(f_variable);
    copyfile(src_path2+"prepare_gpf4.py", dst_path1+"prepare_gpf4.py");
    copyfile(src_path2+"prepare_gpf4.py", dst_path2+"prepare_gpf4.py");
    copyfile(src_path2+"prepare_dpf4.py", dst_path1+"prepare_dpf4.py");
    copyfile(src_path2+"prepare_dpf4.py", dst_path2+"prepare_dpf4.py");
    #copyfile(src_path2+"sunya.py", dst_path1+"sunya.py");
    #copyfile(src_path2+"sunya.py", dst_path2+"sunya.py");

index = list(range(0, 10));

location1 = "/home/user/YUKTI/target_1";

folders1 = ["{}".format(x) for x in range(11)];
del folders1[0];

for i_variable1 in index:
    folders1[i_variable1] = os.path.join(location1, folders1[i_variable1]);

location2 = "/home/user/YUKTI/target_2";

folders2 = ["{}".format(x) for x in range(11)];
del folders2[0];

for i_variable2 in index:
    folders2[i_variable2] = os.path.join(location2, folders2[i_variable2]);

numbers = list(range(0, 11));
del numbers[0];

autopython = "/home/user/mgltools_x86_64Linux2_1.5.6/bin/pythonsh"; # location of 'pythonsh' 

for i_variable in index:
    
    holderA = autopython+" "+folders1[i_variable]+"/prepare_gpf4.py -l "+folders1[i_variable]+"/compound_"+str(numbers[i_variable])+".pdbqt -r "+folders1[i_variable]+"/target_1.pdbqt -p npts=\'60,60,60\' -p gridcenter=\'11.112,-7.196,1.36\' -o \'"+folders1[i_variable]+"/target.gpf\'";
    os.system(holderA);
    holderB = autopython+" "+folders1[i_variable]+"/prepare_dpf4.py -l "+folders1[i_variable]+"/compound_"+str(numbers[i_variable])+".pdbqt -r "+folders1[i_variable]+"/target_1.pdbqt -o \'"+folders1[i_variable]+"/compound_target.dpf\'";
    os.system(holderB);
    #holderC = "python3 "+folders1[i_variable]+"/sunya.py";
    #os.system(holderC);
    
    # insert replacement code to get rid of 'sunya.py'
    
    tempaddr = folders1[i_variable] + "/";
    #retrieved_address = __file__;
    #retrieved_address = retrieved_address.replace("sunya.py", "");
    retrieved_address = tempaddr;
    file_path = retrieved_address+"compound_target.dpf";

    fin = open(file_path, "rt");
    data = fin.read();
    data = data.replace('extended', 'bound');
    fin.close();

    fin = open(file_path, "wt");
    fin.write(data);
    fin.close();
    
    os.chdir(folders1[i_variable]);
    
    holderD = "autogrid4 -p "+folders1[i_variable]+"/target.gpf -l "+folders1[i_variable]+"/protein.glg";
    os.system(holderD);
    holderE = "autodock4 -p "+folders1[i_variable]+"/compound_target.dpf -l "+folders1[i_variable]+"/protein.dlg";
    os.system(holderE);
    
    with open('protein.dlg', 'r') as  f:
        content = f.read();
        holder1 = content.index("\n\nMODEL       ");
        holder2 = content.index("TER\nENDMDL\n");
        holder3 = content[holder1+1:holder2+11];
        
        output = open("bestmodel.pdb", "w");
        output.write(holder3);
        output.close();
        
        print("\nTarget 1's Compound "+str(i_variable+1)+" is done!\n");
        
    holderA = autopython+" "+folders2[i_variable]+"/prepare_gpf4.py -l "+folders2[i_variable]+"/compound_"+str(numbers[i_variable])+".pdbqt -r "+folders2[i_variable]+"/target_2.pdbqt -p npts=\'82,42,126\' -o \'"+folders2[i_variable]+"/target.gpf\'";
    os.system(holderA);
    holderB = autopython+" "+folders2[i_variable]+"/prepare_dpf4.py -l "+folders2[i_variable]+"/compound_"+str(numbers[i_variable])+".pdbqt -r "+folders2[i_variable]+"/target_2.pdbqt -o \'"+folders2[i_variable]+"/compound_target.dpf\'";
    os.system(holderB);
    #holderC = "python3 "+folders2[i_variable]+"/sunya.py";
    #os.system(holderC);
    
    # insert replacement code to get rid of 'sunya.py'
    
    tempaddr = folders2[i_variable] + "/";
    #retrieved_address = __file__;
    #retrieved_address = retrieved_address.replace("sunya.py", "");
    retrieved_address = tempaddr;
    file_path = retrieved_address+"compound_target.dpf";

    fin = open(file_path, "rt");
    data = fin.read();
    data = data.replace('extended', 'bound');
    fin.close();

    fin = open(file_path, "wt");
    fin.write(data);
    fin.close();
    
    os.chdir(folders2[i_variable]);
    
    holderD = "autogrid4 -p "+folders2[i_variable]+"/target.gpf -l "+folders2[i_variable]+"/protein.glg";
    os.system(holderD);
    holderE = "autodock4 -p "+folders2[i_variable]+"/compound_target.dpf -l "+folders2[i_variable]+"/protein.dlg";
    os.system(holderE);
    
    with open('protein.dlg', 'r') as  f:
        content = f.read();
        holder1 = content.index("\n\nMODEL       ");
        holder2 = content.index("TER\nENDMDL\n");
        holder3 = content[holder1+1:holder2+11];
        
        output = open("bestmodel.pdb", "w");
        output.write(holder3);
        output.close();
        
        print("\nTarget 2's Compound "+str(i_variable+1)+" is done!\n");

index = list(range(0, 10));
values1 = list(range(0, 10));
values2 = list(range(0, 10));

location1 = "/home/user/YUKTI/target_1";

folders1 = ["{}".format(x) for x in range(11)];
del folders1[0];

for i_variable1 in index:
    folders1[i_variable1] = os.path.join(location1, folders1[i_variable1]);

location2 = "/home/user/YUKTI/target_2";

folders2 = ["{}".format(x) for x in range(11)];
del folders2[0];

for i_variable2 in index:
    folders2[i_variable2] = os.path.join(location2, folders2[i_variable2]);

for i_variable in index:
	
    os.chdir(folders1[i_variable]);
    x = "target 1";
    y = "compound "+str(i_variable+1);
    with open('protein.dlg', 'r') as  f:
        content = f.read();
        holderA = content.index("|___________\n");
        holderB = content[holderA+35:holderA+43];
        #print("Binding Energy for "+x+"\'s "+y+"\'s best model: "+holderB);

        values1[index[i_variable]] = float(holderB);
	
    os.chdir(folders2[i_variable]);
    x = "target 2";
    y = "compound "+str(i_variable+1);
    with open('protein.dlg', 'r') as  f:
        content = f.read();
        holderA = content.index("|___________\n");
        holderC = content[holderA+35:holderA+43];
        #print("Binding Energy for "+x+"\'s "+y+"\'s best model: "+holderC);

        values2[index[i_variable]] = float(holderC);
	
dex = list(range(0, 10));
take1 = list(range(0, 10));
take2 = list(range(0, 10));

v1 = sorted(values1); #print(values1); print(v1);
v11 = sorted(values11); #print(values11); print(v11);

numbers1 = list(range(0, 10));
numbers11 = list(range(0, 10));


# first ranker starts here onwards


repeat1S = [];
repeat2S = [];
repeat1Z = [];
repeat2Z = [];
repeat1J = [];
repeat2J = [];

for d in dex:
    if d != 0:
        if numbers1[d-1] == values1.index(v1[d])+1:
            #repeat1S = [];
            for i in range(0, len(values1)) : 
                if values1[i] == v1[d]:
                    repeat1S.append(i);
            numbers1[d] = values1.index(v1[d])+1;
        else:
            numbers1[d] = values1.index(v1[d])+1;
    else:
        numbers1[d] = values1.index(v1[d])+1;

grrrr = []

for i in range(0, len(repeat1S)) :
    j = (len(repeat1S)/2)+i;
    j = int(j);
    if j < len(repeat1S):
        if repeat1S[i] == repeat1S[j]:
            grrrr.append(j);

for i in range(0, len(grrrr)) :
    del repeat1S[i];

#print("first repeat1S: "); print(repeat1S); print("first repeat1Z: "); print(repeat1Z); print("first repeat1J: "); print(repeat1J);

for i in range(0, len(repeat1S)) :
    if values1[repeat1S[0]] != values1[repeat1S[-1]]:
        repeat1Z.insert(0, repeat1S[-1]); # added from front
        if repeat1S[-1] == repeat1Z[0]:
            del repeat1S[-1]; # substracted from back

for i in range(0, len(repeat1Z)) :
    if values1[repeat1Z[0]] != values1[repeat1Z[-1]]:
        repeat1J.insert(0, repeat1Z[-1]); # added from front
        if repeat1Z[-1] == repeat1J[0]:
            del repeat1Z[-1]; # substracted from back

#print("first repeat1S: "); print(repeat1S); print("first repeat1Z: "); print(repeat1Z); print("first repeat1J: "); print(repeat1J);

for i in range(1, len(numbers1)) :
    if numbers1[i] == numbers1[i-1]:
        repeat2S.append(i);

#print("first repeat2S: "); print(repeat2S); print("first repeat2Z: "); print(repeat2Z); print("first repeat2J: "); print(repeat2J);

for i in range(0, len(repeat2S)) :
    if v1[repeat2S[0]] != v1[repeat2S[-1]]:
        repeat2Z.insert(0, repeat2S[-1]); # added from front
        if repeat2S[-1] == repeat2Z[0]:
            del repeat2S[-1]; # substracted from back

for i in range(0, len(repeat2Z)) :
    if v1[repeat2Z[0]] != v1[repeat2Z[-1]]:
        repeat2J.insert(0, repeat2Z[-1]); # added from front
        if repeat2Z[-1] == repeat2J[0]:
            del repeat2Z[-1]; # substracted from back

#print("first repeat2S: "); print(repeat2S); print("first repeat2Z: "); print(repeat2Z); print("first repeat2J: "); print(repeat2J);

if repeat1S[0] > repeat1S[1]:
    repeat1S.sort();

holdin = 1;

if holdin < len(repeat1S):
    numbers1[repeat2S[holdin-1]] = repeat1S[holdin]+1;

if holdin < len(repeat1Z):
    numbers1[repeat2Z[holdin-1]] = repeat1Z[holdin]+1;

if holdin < len(repeat1J):
    numbers1[repeat2J[holdin-1]] = repeat1J[holdin]+1;

holdin = 2;

if holdin < len(repeat1S):
    numbers1[repeat2S[holdin-1]] = repeat1S[holdin]+1;

if holdin < len(repeat1Z):
    numbers1[repeat2Z[holdin-1]] = repeat1Z[holdin]+1;

if holdin < len(repeat1J):
    numbers1[repeat2J[holdin-1]] = repeat1J[holdin]+1;

#print(values1); print(v1); print(numbers1);


# second ranker starts here onwards


repeat1S = [];
repeat2S = [];
repeat1Z = [];
repeat2Z = [];
repeat1J = [];
repeat2J = [];

for d in dex:
    if d != 0:
        if numbers11[d-1] == values11.index(v11[d])+1:
            #repeat1S = [];
            for i in range(0, len(values11)) : 
                if values11[i] == v11[d]:
                    repeat1S.append(i);
            numbers11[d] = values11.index(v11[d])+1;
        else:
            numbers11[d] = values11.index(v11[d])+1;
    else:
        numbers11[d] = values11.index(v11[d])+1;

grrrr = []

for i in range(0, len(repeat1S)) :
    j = (len(repeat1S)/2)+i;
    j = int(j);
    if j < len(repeat1S):
        if repeat1S[i] == repeat1S[j]:
            grrrr.append(j);

for i in range(0, len(grrrr)) :
    del repeat1S[i];

#print("second repeat1S: "); print(repeat1S); print("second repeat1Z: "); print(repeat1Z); print("second repeat1J: "); print(repeat1J);

for i in range(0, len(repeat1S)) :
    if values11[repeat1S[0]] != values11[repeat1S[-1]]:
        repeat1Z.insert(0, repeat1S[-1]); # added from front
        if repeat1S[-1] == repeat1Z[0]:
            del repeat1S[-1]; # substracted from back

for i in range(0, len(repeat1Z)) :
    if values11[repeat1Z[0]] != values11[repeat1Z[-1]]:
        repeat1J.insert(0, repeat1Z[-1]); # added from front
        if repeat1Z[-1] == repeat1J[0]:
            del repeat1Z[-1]; # substracted from back

#print("second repeat1S: "); print(repeat1S); print("second repeat1Z: "); print(repeat1Z); print("second repeat1J: "); print(repeat1J);

for i in range(1, len(numbers11)) :
    if numbers11[i] == numbers11[i-1]:
        repeat2S.append(i);

#print("second repeat2S: "); print(repeat2S); print("second repeat2Z: "); print(repeat2Z); print("second repeat2J: "); print(repeat2J);

for i in range(0, len(repeat2S)) :
    if v11[repeat2S[0]] != v11[repeat2S[-1]]:
        repeat2Z.insert(0, repeat2S[-1]); # added from front
        if repeat2S[-1] == repeat2Z[0]:
            del repeat2S[-1]; # substracted from back

for i in range(0, len(repeat2Z)) :
    if v11[repeat2Z[0]] != v11[repeat2Z[-1]]:
        repeat2J.insert(0, repeat2Z[-1]); # added from front
        if repeat2Z[-1] == repeat2J[0]:
            del repeat2Z[-1]; # substracted from back

#print("second repeat2S: "); print(repeat2S); print("second repeat2Z: "); print(repeat2Z); print("second repeat2J: "); print(repeat2J);

if repeat1S[0] > repeat1S[1]:
    repeat1S.sort();

holdin = 1;

if holdin < len(repeat1S):
    numbers11[repeat2S[holdin-1]] = repeat1S[holdin]+1;

if holdin < len(repeat1Z):
    numbers11[repeat2Z[holdin-1]] = repeat1Z[holdin]+1;

if holdin < len(repeat1J):
    numbers11[repeat2J[holdin-1]] = repeat1J[holdin]+1;

holdin = 2;

if holdin < len(repeat1S):
    numbers11[repeat2S[holdin-1]] = repeat1S[holdin]+1;

if holdin < len(repeat1Z):
    numbers11[repeat2Z[holdin-1]] = repeat1Z[holdin]+1;

if holdin < len(repeat1J):
    numbers11[repeat2J[holdin-1]] = repeat1J[holdin]+1;

#print(values11); print(v11); print(numbers11);

for d in dex:
    take1[d] = "Compound "+str(numbers1[d])+" at "+str(v1[d]);
    take2[d] = "Compound "+str(numbers11[d])+" at "+str(v11[d]);

print("Top 10 results in our library of ligands for Target 1 in ascending order:");
for d in dex:
    print(str(d+1)+". "+take1[d]);
print("Top 10 results in our library of ligands for Target 2 in ascending order:");
for d in dex:
    print(str(d+1)+". "+take2[d]);
print("The result rankings will also be available as \"top_results.txt\" and will be updated every time this program is run.\n");

os.chdir("/home/user/YUKTI");

output = open("top_results.txt", "w");

output.write("Top 10 results in our library of ligands for Target 1 in ascending order:\n");
for d in dex:
    output.write(str(d+1)+". "+take1[d]+"\n");
output.write("Top 10 results in our library of ligands for Target 2 in ascending order:\n");
for d in dex:
    output.write(str(d+1)+". "+take2[d]+"\n");
output.write("The result rankings will also be presented on the console and will be updated every time this program is run.\n");

output.close();