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dock_analyse.py
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dock_analyse.py
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import sys
import os
import shutil
if len(sys.argv) == 5:
lig_file = sys.argv[1]
dlg_file = sys.argv[2]
out_fold = sys.argv[3]
prot_file = sys.argv[4]
directory_name = os.getcwd()
path_out = directory_name+'/'+out_fold
if not os.path.exists(path_out):
os.mkdir(path_out)
else:
shutil.rmtree(path_out)
os.mkdir(path_out)
a_line = open(lig_file,"r")
aline = a_line.readlines()
b_line = open(dlg_file, "r")
bline = b_line.readlines()
shutil.copy(directory_name+"/"+lig_file, path_out+"/"+lig_file)
shutil.copy(directory_name+"/"+dlg_file, path_out+"/"+dlg_file)
shutil.copy(directory_name+"/"+prot_file, path_out+"/"+prot_file)
def prot(prot_file):
a_line = open(prot_file, "r")
aline = a_line.readlines()
prt = ""
for line in aline:
prt += line
return prt
prt = prot(prot_file)
def dlg_count(dlg_file):
b_line = open(dlg_file, "r")
bline = b_line.readlines()
count = 0
for line in bline:
if "USER Cluster Rank = " in line:
count += 1
return count
dlg_occ = dlg_count(dlg_file)
#print dlg_occ
def arr_clu_ran(bline, dlg_occ):
arr1 = ""
arr2 = []
cc = 0
cc1 = 1
#out = open("out1","w")
for line in bline:
if cc1 < dlg_occ+1 :
asss =0
if line[:24] == "USER Cluster Rank = "+str(cc1):
print line
cc = 1
#print cc1
if cc == 1:
arr1 += line
if "ENDMDL" in line[:6]:
cc = 0
cc1 += 1
arr2.append(arr1)
arr1 = ""
return arr2
arr2 = arr_clu_ran(bline, dlg_occ)
#print arr2
def fil_op(dlg_occ, arr2):
i = 1
if i < dlg_occ+1:
for line in arr2:
#print line
out = open(directory_name+"/"+out_fold+"/out"+str(i), "w")
out.write(line)
out.close()
i += 1
fil_op(dlg_occ, arr2)
def comp(lig_file, out_fold, prt):
a_line = open(path_out+"/"+lig_file)
aline = a_line.readlines()
dir_lis = os.listdir(path_out)
count = 1
for dir_lis_line in dir_lis:
#print dir_lis_line
if "out" in dir_lis_line[:3]:
out = open(path_out+"/"+str(count)+"doc.pdb", "w")
b_line = open(path_out+"/"+dir_lis_line)
bline = b_line.readlines()
for line1 in aline:
for line2 in bline:
if line1[11:26] == line2[11:26]:
if line1[11:26].count(" ") > 1 :
#print line1[11:26]
#print line1[11:26].count(" ")
out.write(line1[:26]+line2[26:54]+line1[54:])
#out.write("END \n")
out.write(prt)
out.close()
count += 1
def lig_merge():
dir_lis = os.listdir(path_out)
out = open(path_out+"/"+"merge.pdb",'w')
dir_lis1 = []
for l1 in dir_lis:
if l1[:3] == "out":
dir_lis1.append(l1)
dir_lis1 = sorted(dir_lis1, key = lambda x1 : x1[3:])
for line in range(1, len(dir_lis1)+1):
#print line
if "out"+str(line) in dir_lis1:
#print "sgf"
a_line = open(path_out+"/"+"out"+str(line),'r')
aline = a_line.readlines()
for line1 in aline:
if line1[:4] == "ATOM":
line1 = line1.replace("ATOM ","HETATM")
out.write(line1)
out.write("END\n")
out.close()
lig_merge()
else:
print "Usage: python dock_analyse.py ligand.pdb dlg_file output_folder protein.pdb"
sys.exit()