gpu_filecr.py

import sys
import os
import subprocess
import shutil


if len(sys.argv) == 5:
	prot_name1 = sys.argv[1]
	os.system("python PDB_process.py "+prot_name1)
	prot_name = prot_name1[:-4]+"a.pdb"
	lig_name = sys.argv[2]
	centroid = sys.argv[3]
        nrun = sys.argv[4]
	print(prot_name)
	directory_name = os.getcwd()
	path_out = directory_name+'/'+prot_name[:-4]+'_'+lig_name[:-4]
	if not os.path.exists(path_out):
		os.mkdir(path_out)
	else:
		shutil.rmtree(path_out)
		os.mkdir(path_out)
	shutil.copy(prot_name, path_out)
	shutil.copy(lig_name, path_out)
	shutil.copy(directory_name+'/Repository/autogrid4', path_out)
	shutil.copy(directory_name+'/Repository/autodock_gpu_128wi', path_out)
	os.chdir(path_out)
	try:
		pre_rec = 'python ../Repository/prepare_receptor4.py -r '+prot_name+' -A bonds_hydrogens '
		subprocess.call(pre_rec, shell=True)
	except:
		pre_rec = 'python ../Repository/prepare_receptor4.py -r '+prot_name
		subprocess.call(pre_rec, shell=True)
	try:
		pre_lig = 'python ../Repository/prepare_ligand4.py -l'+lig_name+' -A bonds_hydrogens'
		subprocess.call(pre_lig, shell=True)
	except:
		pre_lig = 'python ../Repository/prepare_ligand4.py -l'+lig_name
		subprocess.call(pre_lig, shell=True)
		
	grid_para = 'python ../Repository/prepare_gpf4.py -l '+lig_name[:-4]+'.pdbqt -r '+prot_name[:-4]+'.pdbqt -p gridcenter='+centroid+' -o grid_pf.gpf'
	subprocess.call(grid_para, shell=True)
        dock_para = 'python ../Repository/prepare_dpf4.py -l '+lig_name[:-4]+'.pdbqt -r '+prot_name[:-4]+'.pdbqt -o dock_pf.dpf'
        subprocess.call(dock_para, shell=True)
        def a():
                a_line = open("dock_pf.dpf", 'r')
                aline = a_line.readlines()
                out = open("dock_pf1.dpf", 'w')
                for line in aline:
                        #print line
                        if line[:6] == "ga_run":
                                a = line[:6]+" 10"+line[10:]
                                out.write(a)
                        else:
                                out.write(line)
                out.close()
        a()
        os.remove('dock_pf.dpf')
        subprocess.call('./autogrid4 -p grid_pf.gpf -l grid_pf.glg ', shell=True)
        os.system("rm autogrid4")
        os.system("./autodock_gpu_128wi --ffile "+prot_name[:-4]+".maps.fld --lfile "+lig_name[:-4]+".pdbqt"+" --nrun "+nrun)
        os.system("rm autodock_gpu_128wi")
        os.chdir(directory_name)
        shutil.copy(path_out+"/"+lig_name[:-4]+".dlg", directory_name)
        os.system("rm "+prot_name)
else:
	print("Usage python gpu_filecr.py <prot_name> <lig_name> <centroid_coordinate> <nrun>")
	sys.exit()