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contactOrders_List.py
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contactOrders_List.py
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#!/usr/bin/python
import re,sys
import numpy as Np
def calDist(atm1,atm2):
return(Np.sum((atm1-atm2)**2))
def chainInfo(pdbfl):
'''
pdbfl : opened pdb file in .realines()
'''
pdbfl = open(pdbfl,'r').readlines()
for k in pdbfl:
if re.match(r'^COMPND',k) and re.search(r'CHAIN',k):
chain = k.split(":")[1].strip().strip(";").split(",")
return chain
else:
continue
def getAtomLine(l):
atomDetail = {}
atomDetail['atom_num']=int(l[5:11])
atomDetail['atom_name'] = l[12:16].strip()
atomDetail['res_name'] = l[17:20].strip()
atomDetail['res_num'] = int(l[22:26])
cord = (float(l[30:38]),float(l[38:46]),float(l[46:54]))
atomDetail['cord'] = Np.array(cord)
return atomDetail
def contactParameter(contactMatrix):
"""
S_max,S_min,S_mid
1.RCO: relative contact order,
2.ACO: absolute contact order,
3.SRO: short Range order,(2-4)
4.MRO: Medium Range Order,(5-8)
5.LRO: Long range Order,(>12)
6.TCD: Total Contact Distance, ()
7.N_alpha:
8.Effective Length (L,L^(1/2),L^(2/3),L^(3/5))
From contact matrix get indices(i,j) whose values are not zero. i-j is the sequence separion
between two contacting residues.
"""
from collections import Counter
contactRes_list = []
length = Np.shape(contactMatrix)[0]
print length
for i in range(length-1):
for j in range(i+1,length):
if contactMatrix[j,i]:
#print i,j
contactRes_list.append(abs(j-i))
else:
continue
contactRes_Dic = Counter(contactRes_list)
#print contactRes_list,contactRes_Dic
totalContact = Np.count_nonzero(contactMatrix)
print "Total Contact: %d"%totalContact
sro = []
lro = []
mrc_percent = []
src_percent = []
lrc_percent = []
tcd = []
local_CO = []
nonlc_CO = []
for k in contactRes_Dic.keys():
if k >=2 and k <=8:
local_CO.append(contactRes_Dic[k]*k)
sro.append(contactRes_Dic[k])
if k <= 4:
src_percent.append(contactRes_Dic[k])
else:
mrc_percent.append(contactRes_Dic[k])
elif k >= 12:
nonlc_CO.append(contactRes_Dic[k]*k)
lro.append(contactRes_Dic[k])
elif k >= 3:
tcd.append(contactRes_Dic[k]*k)
#index = 0,1,2,3,4,5,6,
if length and totalContact:
sro_val = sum(sro)/float(length)
lro_val = sum(lro)/float(length)
src_per = (sum(src_percent)/float(totalContact))*100
mrc_per = (sum(mrc_percent)/float(totalContact))*100
lrc_per = (sum(lro)/float(totalContact))*100
localCO_val = sum(local_CO)/float(totalContact)
nonloCO_val = sum(nonlc_CO)/float(totalContact)
tcd_val = (sum(tcd)/float(length*length))
if totalContact:
return totalContact,sro_val,lro_val,src_per,mrc_per,lrc_per,localCO_val,nonloCO_val,tcd_val
else:
return 0,0,0,0,0,0,0,0,0
else:
return 0,0,0,0,0,0,0,0,0
def gen_contactMatrix(pdbfl,chain):
try :
pdbFile = open(pdbfl,'r').readlines()
except:
return (0,0,0,0,0,0,0,0,0,0,0,0,0)
print "processing %s"%pdbfl
#chain = chain
atomList = []
for i in pdbFile:
i = i.rstrip()
if re.match(r'^ATOM',i) and i[21] == chain:
atomList.append(getAtomLine(i))
if re.match(r'^TER',i):
break
if len(atomList):
length = atomList[len(atomList)-1]['res_num'] - atomList[0]['res_num']
else:
return 0,0,0,0
#print atomList
# Checking id contact or not
resDictionary = {}
for k in atomList:
resDictionary[k['res_num']] = len(resDictionary.keys()) -1
contacts = 0
sequenceDist = 0
residueContact = Np.zeros((length+1,length+1))
for atom1 in atomList:
for atom2 in atomList:
seqDist = atom1['res_num']-atom2['res_num']
if seqDist > 2: # calculating non-adjecent residues
dist = calDist(atom1['cord'],atom2['cord'])
if dist < 36: # 6*6 d comare with square dist
contacts +=1
sequenceDist += seqDist
residueContact[resDictionary[atom1['res_num']],resDictionary[atom2['res_num']]]=1
print "Analyzing contact"
#import ipdb;ipdb.set_trace()
if length and contacts:
totalRes_Contact,sro,lro,src_per,mrc_per,lrc_per,lCO,nloCO,tcd = contactParameter(residueContact)
#print sro,lro,src_per,mrc_per,lrc_per,lCO,nloCO,tcd
rco_fl = sequenceDist/float(length*contacts)
absCO_fl = rco_fl*length
#print contacts,sequenceDist, rco
#print length
#longContactRes = Np.count_nonzero(residueContact)/float(length)
# import ipdb; ipdb.set_trace()
return (length,contacts,totalRes_Contact,rco_fl,absCO_fl,sro,lro,src_per,mrc_per,lrc_per,lCO,nloCO,tcd)
else:
return (0,0,0,0,0,0,0,0,0,0,0,0,0)
if __name__ == '__main__':
"""
contact order parameters (relative and absolute) for pdbids
Length
Atom Contacts
Residue contacts
Relative contact order, Absolute contact order
"""
import argparse
parse = argparse.ArgumentParser()
parse.add_argument('-p',action='store',dest='pdbFl',help='pdb file and chain')
parse.add_argument('-d',dest='pdbDir',action='store',help='PDB directory As in Only Beta: /home/taushif/ThesisWork/allPDbs/Data/PDB_files/')
parse.add_argument('-o',dest='outfl',action='store',help='output file name')
presult = parse.parse_args()
print "pdb file with pid and chain:"+presult.pdbFl
pfl = open(presult.pdbFl,'r').readlines()
ofl = open(presult.outfl,'w')
elog = open("error.log",'w')
ofl.write("p.ID\tChain\tlength\tAtom_Con\tRes_Cont\tRCO\tACO\tSRO\tLRO\tSR_per\tMR_per\tLR_per\tLCO\tNlCO\tTCD\n")
pdbDir = presult.pdbDir
#pdbDir = "/home/taushif/ThesisWork/Codes_Data/alphaWork/Data2_7June/PDB/"
#pdbDir = "/home/taushif/PyCodes/ContactOrders/pdbs/"
#pdbDir = "/home/taushif/PyCodes/ContactOrders/kineticDataset/pdbs/"
chainCount_suc = 0
chainCount_fail = 0
for k in pfl:
k = k.strip().split()
#dbfl = pdbDir+"pdb"+k[0]+".ent"
pdbfl = pdbDir+k[0]+".pdb"
#chain = chainInfo(pdbfl)
#print chain
chain = k[1]
# for c in chain:
res = gen_contactMatrix(pdbfl,chain)
#protl,tAContact,tRContact,rco_fl,absCo_fl,sro,lro,src_p,mrc_p,lrc_p,lCO,nloCO,tcd
if res[0]:
print "%d\t%d\t%d\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.6f\t"\
%(res[0],res[1],res[2],res[3],res[4],res[5],res[6],res[7],res[8],res[9],res[10],res[11],res[12])
ofl.write("%s\t%s\t%d\t%d\t%d\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.3f\t%0.6f\n"\
%(k[0],chain,res[0],res[1],res[2],res[3],res[4],res[5],res[6],res[7],res[8],res[9],res[10],res[11],res[12]))
chainCount_suc += 1
else:
print "problem in protein %s"%k
chainCount_fail += 1
#elog.write("%s\t%s\n"%(k[0],k[1]))
elog.write("%s\n"%(k))
continue
print "\nDONE : [%d/%d] FAIL: [%d/%d]\n"%(chainCount_suc,len(pfl),chainCount_fail,len(pfl))
#import ipdb; ipdb.set_trace()
ofl.close()
elog.close()