def main():
parser=argparse.ArgumentParser()
parser.add_argument('-path', action='store', required=True, dest='pathfile',
help='pathfile is a textfile of name of pdb')
inputs=parser.parse_args()
pathfile=inputs.pathfile
file_pathfile=open(pathfile)
loop=0
complexddg=[]
for line in file_pathfile: # caculate the value of ddg before mutation
line=line.strip('\n')
print "caulate of %s ddg" % line
#removeantibody1(line,loop)
os.system('./removebody.sh '+line+' '+str(loop))
removeTER(line)
os.system('./interface.sh '+line)
dirname=os.getcwd()
dirname+='/interface_analyzer/'+line+'.sc'
theline=linecache.getline(dirname,3)
theline=theline.strip('\n')
thelinesplit=theline.split(' ',1000)
for i in thelinesplit:
if i=='':
thelinesplit.remove(i)
dirname=os.getcwd()+'/interface_analyzer/'+line.split('.')[0]+'_sc.txt'
f_file=open(dirname,'w')
f_file.write(line+':'+thelinesplit[5]+'\n')
complexddg.append(thelinesplit[5])
f_file.close()
loop+=1
file_pathfile.close()
loop=0
file_pathfile=open(pathfile)
for line in file_pathfile:
line=line.strip('\n')
pdbfileselect=line.split('.')
#removeantibody1(line)
pdbantigenfile=pdbfileselect[0]+'_antigen.pdb'
caculateasa(line,0)
caculateasa(pdbantigenfile,1)
file1=caculatecomplexandantigen(line,pdbantigenfile)
shutil.move('./interface_analyzer/pdbdata/'+pdbantigenfile,'./interface_analyzer/pdbdata/file/'+pdbantigenfile)
print "*************the asa caculation have done****************"
file2=caculatedistance(line)
print "*******the distance of 4.0 caculation have done*********"
mutatelistfile=getmutatelist(file2,file1,line)
print"*************************%sbegin mutate************" % line
f_mutate=open(mutatelistfile)
for linemutate in f_mutate:
linemutate=linemutate.strip('\n')
linemutatesplit=linemutate.split(':')
print "mutate chain %s %s" % (linemutatesplit[0],linemutatesplit[1])
beginmutate(pdbfileselect[0],linemutatesplit[1],linemutatesplit[0])
aftermutatefile=pdbfileselect[0]+'ALA'+linemutatesplit[0]+linemutatesplit[1]+'.pdb'
caculatemethod1(aftermutatefile,line,complexddg[loop])
shutil.move('./interface_analyzer/pdbdata/'+aftermutatefile,'./interface_analyzer/pdbdata/file/'+aftermutatefile)
f_mutate.close()
loop+=1
file_pathfile.close()
print "the program caculate over"
def main():
parser=argparse.ArgumentParser()
parser.add_argument('-path', action='store', required=True, dest='pathfile',
help='pathfile is a textfile of name of pdb')
#parser.add_argument('-c1', action='store', required=True, dest='chain_a',
# help='pathfile is a textfile of name of pdb')
#parser.add_argument('-c2', action='store', required=True, dest='chain_b',
#help='pathfile is a textfile of name of pdb')
inputs=parser.parse_args()
pathfile=inputs.pathfile
file_pathfile=open(pathfile)
loop=0
complexddg=[]
scorecomplex=[]
for line1 in file_pathfile: # caculate the value of ddg before mutation
line1=line1.strip('\n')
fixedchains=''
line=line1.split(':',2)
os.system('./removefile.sh '+line[0].split('.')[0])
print "caulate of %s ddg" % line[0]
#removeantibody1(line,loop)
os.system('./removebody.sh '+line[0]+' '+str(loop)+' '+line[1]+' '+line[2])
removeTER(line[0])
if '+' in line[2]:
line3=line[2].split('+',100)
#fixedchains=' -fixedchains '
for i in xrange(len(line3)):
fixedchains=fixedchains+line3[i]+':'
print'%s'%fixedchains
os.system('./interface1.sh '+line[0]+' '+fixedchains)
else:
os.system('./interface.sh '+line[0])
os.system('./score.sh '+line[0])
dirname=os.getcwd()
dirname+='/interface_analyzer/'+line[0]+'.sc'
theline=linecache.getline(dirname,3)
theline=theline.strip('\n')
thelinesplit=theline.split(' ',1000)
for i in thelinesplit:
if i=='':
thelinesplit.remove(i)
dirname+='ore'
theline=linecache.getline(dirname,2)
theline=theline.strip('\n')
thelinesplit1=theline.split(' ')
for i in thelinesplit1:
if i=='':
thelinesplit1.remove(i)
dirname=os.getcwd()+'/interface_analyzer/'+line[0].split('.')[0]+'_sc.txt'
f_file=open(dirname,'w')
f_file.write(line[0]+':'+thelinesplit[5]+':'+thelinesplit1[1]+'\n')
complexddg.append(thelinesplit[5])
scorecomplex.append(thelinesplit1[1])
f_file.close()
loop+=1
file_pathfile.close()
loop=0
file_pathfile=open(pathfile)
for line1 in file_pathfile:
line1=line1.strip('\n')
line=line1.split(':',2)
pdbfileselect=line[0].split('.')
#removeantibody1(line)
pdbantigenfile=pdbfileselect[0]+'_antigen.pdb'
caculateasa(line[0],0)
caculateasa(pdbantigenfile,1)
file1=caculatecomplexandantigen(line[0],pdbantigenfile)
shutil.move('./interface_analyzer/pdbdata/'+pdbantigenfile,'./interface_analyzer/pdbdata/file/'+pdbantigenfile)
print "*************the asa caculation have done****************"
file2=caculatedistance(line[0],line[1],line[2])
print "*******the distance of 4.0 caculation have done*********"
mutatelistfile=getmutatelist(file2,file1,line[0])
print"*************************%sbegin mutate************" % line
f_mutate=open(mutatelistfile)
for linemutate in f_mutate:
linemutate=linemutate.strip('\n')
linemutatesplit=linemutate.split(':')
print "mutate chain %s %s" % (linemutatesplit[0],linemutatesplit[1])
beginmutate(pdbfileselect[0],linemutatesplit[1],linemutatesplit[0])
aftermutatefile=pdbfileselect[0]+'ALA'+linemutatesplit[0]+linemutatesplit[1]
#print "begin idealstructure"
#os.system('./ideal.sh '+aftermutatefile)
#print "structure is get ideal"
aftermutatefile1=pdbfileselect[0]+'ALA'+linemutatesplit[0]+linemutatesplit[1]+'.pdb'
caculatemethod1(aftermutatefile1,line[0],line[2],complexddg[loop],scorecomplex[loop])
shutil.move('./interface_analyzer/pdbdata/'+aftermutatefile1,'./interface_analyzer/pdbdata/file/'+aftermutatefile1)
f_mutate.close()
loop+=1
file_pathfile.close()
print "the program caculate over"
