Molecular Docking

printstyled("\n Triple Negative Brest Cancer 🦚\n\n",color=:green)
current_path = pwd()
energy_minimize_structures_path = String("$current_path/energy-minimize-structures")
 
@info "Current path : $current_path"
@info "Energy Minimize structres path : $energy_minimize_structures_path "
 
# get all list of structures
all_mol2_structures = readdir(energy_minimize_structures_path)
name_folder = "converted"
 
function CreateFolder()
    current_folder_list = readdir(pwd())
    for i in current_folder_list
        if i === name_folder
            return
        end
    end
        mkdir(name_folder)
end
CreateFolder() # to check whether folder is already there or not
 
for structure in all_mol2_structures
    # to convert spelling into lowercase and remove mol2 extension
    name = lowercase(split(structure,".")[1])
    printstyled("Started working on $structure \t",color=:light_cyan)
    structure_path = "$energy_minimize_structures_path/$structure"
 
    # to run the command line tool
    run(`obabel.exe -i mol2 $structure_path -o pdbqt -O ./converted/$name.pdbqt`)
 
    printstyled("Compeleted $structure 🦚\n",color=:green)
end

using DelimitedFiles
 
println("Autodock")
 
current_path = pwd()
autodock_path = "$current_path/middleware"
all_structures_path = "$current_path/converted"
 
all_structures = readdir("$all_structures_path")
docked_folder = "docked"
rececptor_name = "7AAD.pdbqt"
 
function CreateFolder(name_folder,path)
    allFolder = readdir("$path")
 
    for dir in allFolder
        if dir === name_folder
            return
        end
    end
    mkdir("$current_path/$name_folder")
end
CreateFolder(docked_folder,current_path)
 
print(all_structures)
 
function CreateConfigFile(name_of_ligand,rececptor_name,path)
    touch("$path/$name_of_ligand-config.txt")
    open("$path/$name_of_ligand-config.txt","w") do io
        writedlm(io,["ligand = $all_structures_path/$name_of_ligand.pdbqt" ,
        "receptor = $rececptor_name",
        "center_x = 20.262",
        "center_y = 35.132",
        "center_z = 21.294",
 
        "size_x = 54",
        "size_y = 54",
        "size_z = 54",
 
        "energy_range = 3 ",
        "exhaustiveness = 8",
        "num_modes = 10  "
        ])
    end
    printstyled("Created Comfig File for $name_of_ligand",color=:light_cyan)
end
 
for structure in all_structures
    println("\n")
    structure_name = lowercase(split("$structure",".")[1])
 
    path = mkdir("$current_path/$docked_folder/$structure_name")
    @info "Folder Created $path"
 
    # create a config file for structure
    CreateConfigFile("$structure_name",rececptor_name,"$path")
 
    run(`$autodock_path/vina.exe --config $path/$structure_name-config.txt --log $path/$structure_name-output.txt`)
 
    # command line tool
    printstyled("Completed docking of $structure_name \n\n")
end

current_path = pwd()
docked_folder_path = "$current_path/docked"
 
get_all_folders_in_docked = readdir(docked_folder_path)
 
 
 
function ExtractFile(f,structure_name)
    line = 0
 
    println("```powershell filename=\"$structure_name\"")
    for i in  eachline(f)
        line = line + 1
        if line >= 25
            println(i)
 
        end
    end
    println("```\n\n")
end
 
# loop all folders
 
for dir in get_all_folders_in_docked
    # printstyled("\n name of folder $dir \n\n",color=:light_yellow)
    get_all_files = readdir("$docked_folder_path/$dir")
 
    # loop through all files
    done = 0
    for files in get_all_files
        f = open("$docked_folder_path/$dir/$dir-output.txt","r")
        if done < 1
            ExtractFile(f,dir)
           done = done + 1
 
        end
    end
end

path = "./lig/ligand.txt"
f = open(path,"r")
 
function finalFunction()
    line = 0
    for i in  eachline(f)
        line = line + 1
        if line >= 25
            println(i)
        end
    end
end

🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚🦚
mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1         -7.0      0.000      0.000
   2         -6.9      2.092      2.744
   3         -6.9      9.159      9.848
   4         -6.9      1.687      3.128
   5         -6.8      9.484     11.275
   6         -6.7      9.748     12.336
   7         -6.7      1.616      3.040
   8         -6.7     15.879     18.360
   9         -6.6      2.286      7.916
  10         -6.6      7.649     12.197
Writing output ... done.