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DLA-Ranker
Commit 901a69e1 by DLA-Ranker
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parent aca0ece6
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Representation/scr.py 0 → 100644
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 4 23:49:27 2021
@author: yasser
"""
import re
import os
import sys
from os import path, remove
#sys.path.insert(1, '../lib/')
#import tools as tl
NACCESS_PATH = 'naccess'
def rimcoresup(rsa_rec,rsa_lig,rsa_complex):
'''INPUT: file rsa da NACCESS.
###rASAm: relative ASA in monomer
###rASAc: relative ASA in complex
###Levy model
###deltarASA=rASAm-rASAc
###RIM deltarASA > 0 and rASAc >= 25 and rASAm >= 25 ###corretto da rASAc > 25 and rASAm > 25
###CORE deltarASA > 0 and rASAm >= 25 and rASAc < 25 ###corretto da rASAm > 25 and rASAc <= 25
###SUPPORT deltarASA > 0 and rASAc < 25 and rASAm < 25
OUTPUT:rim, core, support'''
ASA1=[]
resNUMasa1=0
lines = [line.rstrip('\n') for line in open(rsa_rec)]
for lineee in lines:
a=re.split(' ',lineee)
a=list(filter(None, a))
if a[0] == 'RES' and len(a) == 14:
resNUMasa1=(resNUMasa1)+1
restype=a[1]
chain=a[2]
resnumb=a[3]
resnumb=re.findall('\d+', resnumb)
resnumb=resnumb[0]
rASAm=a[5]
ASA1.append((restype,chain,int(resnumb),rASAm,'receptor'))
elif a[0] == 'RES' and len(a) == 13:
resNUMasa1=(resNUMasa1)+1
restype=a[1]
testchain=re.findall('\d+|\D+', a[2])
if len(testchain) == 1:
chain=''
resnumb=int(testchain[0])
elif len(testchain) == 2:
primoterm=testchain[0]
if primoterm.isdigit():
chain=''
resnumb=int(testchain[0])
else:
chain=testchain[0]
resnumb=int(testchain[1])
#resnumb=re.findall('\d+', resnumb)
#resnumb=resnumb[0]
rASAm=a[4]
ASA1.append((restype,chain,int(resnumb),rASAm,'receptor'))
ASA2=[]
resNUMasa2=0
lines = [line.rstrip('\n') for line in open(rsa_lig)]
for lineee in lines:
a=re.split(' ',lineee)
a=list(filter(None, a))
if a[0] == 'RES' and len(a) == 14:
resNUMasa2=(resNUMasa2)+1
restype=a[1]
chain=a[2]
resnumb=a[3]
resnumb=re.findall('\d+', resnumb)
resnumb=resnumb[0]
rASAm=a[5]
ASA2.append((restype,chain,int(resnumb),rASAm,'ligand'))
elif a[0] == 'RES' and len(a) == 13:
resNUMasa2=(resNUMasa2)+1
restype=a[1]
testchain=re.findall('\d+|\D+', a[2])
if len(testchain) == 1:
chain=''
resnumb=int(testchain[0])
elif len(testchain) == 2:
primoterm=testchain[0]
if primoterm.isdigit():
chain=''
resnumb=int(testchain[0])
else:
chain=testchain[0]
resnumb=int(testchain[1])
#resnumb=re.findall('\d+', resnumb)
#resnumb=resnumb[0]
rASAm=a[4]
ASA2.append((restype,chain,int(resnumb),rASAm,'ligand'))
ASAfull=[]
resNUMasafull=0
lines = [line.rstrip('\n') for line in open(rsa_complex)]
for lineee in lines:
a=re.split(' ',lineee)
a=list(filter(None, a))
if a[0] == 'RES' and len(a) == 14:
resNUMasafull=resNUMasafull+1
restype=a[1]
chain=a[2]
resnumb=a[3]
resnumb=re.findall('\d+', resnumb)
resnumb=resnumb[0]
rASAm=a[5]
if resNUMasafull <= len(ASA1):
filename='receptor'
else:
filename='ligand'
ASAfull.append((restype,chain,int(resnumb),rASAm,filename))
elif a[0] == 'RES' and len(a) == 13:
resNUMasafull=resNUMasafull+1
restype=a[1]
testchain=re.findall('\d+|\D+', a[2])
if len(testchain) == 1:
chain=''
resnumb=int(testchain[0])
elif len(testchain) == 2:
primoterm=testchain[0]
if primoterm.isdigit():
chain=''
resnumb=int(testchain[0])
else:
chain=testchain[0]
resnumb=int(testchain[1])
#resnumb=re.findall('\d+', resnumb)
#resnumb=resnumb[0]
rASAm=a[4]
if resNUMasafull <= len(ASA1):
filename='receptor'
else:
filename='ligand'
ASAfull.append((restype,chain,int(resnumb),rASAm,filename))
rim=[]
core=[]
support=[]
for elements in ASAfull:
for x in ASA1:
if elements[0:3] == x[0:3] and elements[4] == x[4]:
rASAm=float(x[3])
rASAc=float(elements[3])
deltarASA=rASAm-rASAc
if deltarASA > 0:
if rASAm < 25:# and rASAc < 25:
support.append(x)
elif rASAm > 25:
if rASAc <= 25:
core.append(x)
else:
rim.append(x)
for x in ASA2:
if elements[0:3] == x[0:3] and elements[4] == x[4]:
rASAm=float(x[3])
rASAc=float(elements[3])
deltarASA=rASAm-rASAc
if deltarASA > 0:
if rASAm < 25:# and rASAc < 25:
support.append(x)
elif rASAm > 25:
if rASAc <= 25:
core.append(x)
else:
rim.append(x)
return rim, core, support
def get_scr(rec, lig, com, name):
#print('rec', path.basename(rec.replace('pdb', 'rsa')))
cmdcompl=NACCESS_PATH + ' ' + com
os.system(cmdcompl)
cmdrec=NACCESS_PATH + ' ' + rec
os.system(cmdrec)
cmdlig=NACCESS_PATH + ' ' + lig
os.system(cmdlig)
# ('GLN', 'B', '44', '55.7', 'receptor')
rim,core,support = rimcoresup(path.basename(rec.replace('pdb', 'rsa')), path.basename(lig.replace('pdb', 'rsa')), path.basename(com.replace('pdb', 'rsa')))
outprimcoresup = open(name+'_rimcoresup.csv', 'w')
for elementrim in rim:
outprimcoresup.write(str((' '.join(map(str,elementrim)))+" R")+"\n") #Rim
for elementcore in core:
outprimcoresup.write(str((' '.join(map(str,elementcore)))+" C")+"\n") #Core
for elementsup in support:
outprimcoresup.write(str((' '.join(map(str,elementsup)))+" S")+"\n") #Support
outprimcoresup.close()
remove(path.basename(rec.replace('pdb', 'rsa')))
remove(path.basename(rec.replace('pdb', 'asa')))
remove(path.basename(rec.replace('pdb', 'log')))
remove(path.basename(lig.replace('pdb', 'rsa')))
remove(path.basename(lig.replace('pdb', 'asa')))
remove(path.basename(lig.replace('pdb', 'log')))
remove(path.basename(com.replace('pdb', 'rsa')))
remove(path.basename(com.replace('pdb', 'asa')))
remove(path.basename(com.replace('pdb', 'log')))
########################
\ No newline at end of file
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