class FcfrpTopolPDB:
def __init__(self, pdbName=None, pathPdb=None, pathOut=None):
self._config = FcfrpConfig("GLOBAL")
self._pdbName = pdbName
if pathPdb == None:
self._pathPdb = self._config.getParameter("Local_PDB_Files")
else:
self._pathPdb = pathPdb
if pathOut == None:
self.pathOut = self._config.getParameter("Local_PDB_Files")
else:
self._pathOut = pathOut
def checkPDB(self):
qt = 0
dell = []
parser = PDBParser()
name = ''
if self._pdbName.__contains__('pdb'):
name = self._pdbName
else:
name = self._pdbName + '.pdb'
structure = parser.get_structure(self._pdbName, os.path.join(self._pathPdb, name))
for model in structure:
for chain in model:
for residue in chain:
qt = 0
for atom in residue:
qt += 1
if qt == 1:
dell.append(str(residue.id[1]))
if dell.__len__() > 1:
self.deleteResidue(dell, name)
def deleteResidue(self, dell, name):
pdbFile = open(os.path.join(self._pathPdb, name))
str = ''
strDell = ''
for line in pdbFile.readlines():
fields = line.split()
if fields[0] == 'ATOM':
num = fields[5]
if num not in dell:
str = str + line
else:
strDell = strDell + line
else:
str = str + line
#print str
print strDell
self.saveFile(name, str)
def saveFile(self, fileName, conteudo):
f = FcfrpFile(self._pathOut, fileName)
f.getAsFile("w")
f.write(conteudo)
f.close()
class FcfrpParse:
def __init__(self, pqrName=None, pathPqr=None, pathOut=None):
self._config = FcfrpConfig("GLOBAL")
self._pqrName = pqrName
#Path where are the input files
if pathPqr == None:
self._pathPqr = self._config.getParameter("Local_PQR_Files")
else:
self._pathPqr = pathPqr
if pathOut == None:
self._pathOut = self._config.getParameter("Local_MEAD_Files")
else:
self._pathOut = pathOut
#Path where are the MEAD Programs
self._pathMEADPrograms = self._config.getParameter("MEAD_Program")
self._inicializated()
def _inicializated(self):
# Titrable residues to Sites file
self.resIonic = ['ASP', 'GLU', 'LYS', 'ARG', 'HIS', 'TYR']
#self.resIonic = ['ASP', 'GLU', 'LYS', 'ARG']
self.positive = ['ARG', 'LYS', 'HIS', 'NT']
self.negative = ['GLU', 'ASP', 'TYR', 'CT']
# Return pka's for individual aminoacids
def getPkas (self, amino):
if amino == 'LYS':
return 10.4
elif amino == 'ASP':
return 4.0
elif amino == 'GLU':
return 4.4
elif amino == 'CT':
return 3.8
elif amino == 'HIS':
return 6.3
elif amino == 'TYR':
return 9.6
elif amino == 'NT':
return 7.5
elif amino == 'ARG':
return 12.0
# Create St files for all ionic residues and N and C Terminal
def createStFiles(self):
sitesFile = open(os.path.join(self._pathPqr, self._pqrName[0:self._pqrName.__len__()-4]+'.sites'))
st = []
linhaCT = 0 # Reference line for the last residue : C-Terminal
lineNT = -1 # Reference line for the first residue: N-Terminal
for line in sitesFile.readlines():
# Build a list for ionic residues (not repeated) plus N and C-Terminal
if not line.split()[1] in st:
st.append(line.split()[1])
amino = line.split()[1]
lineNT = line.split()[0]
lineCT = line.split()[0]
# It creates st files for each residue not repeated in sites file
# Residue as N-Terminal. pk = 7.5
if amino[0:2] == 'NT':
self.createStNT(amino, lineNT)
# Residue as C-Terminal. pk = 3.8
elif amino[0:2] == 'CT':
self.createStCT(amino, lineCT)
# Ionic Residue as N-Terminal. pk = pk_residue
elif amino[3:5] == 'NT':
self.createStNT2(amino, lineNT)
# Ionic Residue as C-Terminal. pk = pk_residue
elif amino[3:5] == 'CT':
self.createStCT2(amino, lineCT)
# Others residuos
self.buildStsFIle()
# It buil N-Terminal st file
def createStNT(self, amino, lineNT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == 'ATOM':
if fields[4] == lineNT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom == 'N' or atom == 'H' or atom == 'H2' or atom == 'H3':
atoms[atom] = str(charge)
else:
atoms[atom] = str(charge)
self.mountStNT(amino, atoms)
pqrFile.close()
# It buil N-Terminal st file
# N-term is charged positively
def mountStNT(self, amino, atoms):
s = ''
pk = self.getPkas('NT')
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[2:5] + '\t' + a + '\t' + atoms[a] + '\t' + '0.00' + '\n'
self.saveFile(amino+'.st', s)
# It buil N-Terminal st file
# In this case the residue N-Terminal is an ionic residue
def createStNT2(self, amino, lineNT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == "ATOM":
if fields[4] == lineNT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom != 'N' and atom != 'H' and atom != 'H2' and atom != 'H3':
atoms[atom] = str(charge)
self.mountStNT2(amino, atoms)
pqrFile.close()
# It buil N-Terminal st file
# N-term is charged positively
# In this case the residue N-Terminal is an ionic residue
def mountStNT2(self, amino, atoms):
s = ''
pk = self.getPkas(amino[0:3])
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[0:3] + '\t' + a + '\t' + atoms[a] + '\t' + '0.00' + '\n'
self.saveFile(amino+'.st', s)
# It buil C-Terminal st file
# C-term is charged negatively
def createStCT(self, amino, linhaCT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == "ATOM":
if fields[4] == linhaCT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom == 'C' or atom == 'O' or atom == 'OH' or atom == 'OXT':
atoms[atom] = str(charge)
else:
atoms[atom] = str(charge)
self.mountStCT(amino, atoms)
pqrFile.close()
# It buil C-Terminal st file
def mountStCT(self, amino, atoms):
s = ''
pk = self.getPkas('CT')
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[2:5] + '\t' + a + '\t' + '0.00' + '\t' + atoms[a] + '\n'
self.saveFile(amino+'.st', s)
# It buil C-Terminal st file
# In this case the residue C-Terminal is an ionic residue
def createStCT2(self, amino, linhaCT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == "ATOM":
if fields[4] == linhaCT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom != 'C' and atom != 'O' and atom != 'OH' and atom != 'OXT':
atoms[atom] = str(charge)
self.mountStCT2(amino, atoms)
pqrFile.close()
# It buil C-Terminal st file
# C-term is charged negatively
# In this case the residue C-Terminal is an ionic residue
def mountStCT2(self, amino, atoms):
s = ''
pk = self.getPkas(amino[0:3])
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[0:3] + '\t' + a + '\t' + '0.00' + '\t' + atoms[a] + '\n'
self.saveFile(amino+'.st', s)
# It creates a site file
def createSitesFile(self, last):
pqr_file = FcfrpFile(self._pathPqr, self._pqrName + '.renumbered')
record = ''
refLine = -1
NTref = 1
flag = 0
lastResidue = last
for line in pqr_file.readLines():
fields = line.split()
if fields[0] != "END_CHAIN":
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
# It used to insert N Terminal
if flag == 1:
NTref = int(numSeq)
flag = 0
if numRes != refLine:
if int(numSeq) == NTref:
# Get the all (the first and others) N-Terminal
record = self.insertNterminal(numRes, resName, record)
elif resName in self.resIonic:
# It does not insert the last ionic residue
if int(numSeq) == lastResidue:
break
else:
record = record + str(numRes) + " " + str(resName) + '\n'
refLine = numRes
if fields[0] == "END_CHAIN":
# Get the others C-Terminal
record = self.insertCterminal(numRes, resName, record)
flag = 1 # It indicates that the next residue is a N Terminal
# Get the last C-Terminal
record = self.insertCterminal(numRes, resName, record)
self.saveFile(self._pqrName[:self._pqrName.__len__()-3] + 'sites', record)
# Insert C terminal residue in sites file
def insertCterminal(self, numRes, resName, record):
record = record + numRes + " " + 'CT' + resName + '\n'
if resName in self.resIonic:
record = record + numRes + " " + resName + 'CT' + '\n'
return record
# Insert N terminal residue in sites file
def insertNterminal(self, numRes, resName, record):
record = record + numRes + " " + 'NT' + resName + '\n'
if resName in self.resIonic:
record = record + numRes + " " + resName + 'NT' + '\n'
return record
# Check the correct charges in N and C-Terminal st files
def checaSt(self):
sites = open(os.path.join(self._pathPqr, self._pqrName[0:self._pqrName.__len__()-4]+'.sites'))
st = []
for line in sites:
tmp = line.split()
residuo = tmp[1]
if residuo not in st:
st.append(residuo)
if residuo[0:2] == 'NT':
self.checaNT(residuo + '.st')
elif residuo[3:5] == 'NT':
self.checaSiteNT(residuo + '.st')
elif residuo[0:2] == 'CT':
self.checaCT(residuo + '.st')
elif residuo[3:5] == 'CT':
self.checaSiteCT(residuo + '.st')
elif residuo in self.resIonic:
self.checaSites(residuo + '.st')
# Check the correct charges in st's file
def checaSites(self, fileName):
st = open(os.path.join(self._pathPqr, fileName))
atomsPROT = {}
atomsDEPROT = {}
s = ''
for line in st:
tmp = line.split()
if tmp.__len__() > 1:
atomsPROT[tmp[1]] = tmp[2]
atomsDEPROT[tmp[1]] = tmp[3]
protonates = 0.0
deprotonates = 0.0
sum = 0.0
for a in atomsPROT:
protonates = protonates + float(atomsPROT[a])
for a in atomsDEPROT:
deprotonates = deprotonates + float(atomsDEPROT[a])
sum = protonates - deprotonates
# Check if the sum of protonated states - the of deprotonated state = 1
sum = float("%.2f" % sum)
if sum != 1.00:
# Check if residue is a positive residue
if fileName[0:3] in self.positive:
correcao = 1.0 - sum
stCorrect = open(os.path.join(self._pathPqr, fileName))
for line in stCorrect:
tmp = line.split()
if tmp.__len__() == 1:
s = s + tmp[0] + '\n'
else:
atm = self.getAtom4chargeInResidue('Residue', fileName)
if tmp[1] == atm:
c = float(tmp[3])+correcao
c = c*(-1.0)
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + str("%.3f" % c) + '\n'
else:
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + tmp[3] + '\n'
# Check if residue is a negative residue
elif fileName[0:3] in self.negative:
correcao = 1.0 + sum
stCorrect = open(os.path.join(self._pathPqr, fileName))
for line in stCorrect:
tmp = line.split()
if tmp.__len__() == 1:
s = s + tmp[0] + '\n'
else:
atm = self.getAtom4chargeInResidue('Residue', fileName)
if tmp[1] == atm:
c = float(tmp[2])+correcao
s = s + tmp[0] + '\t' + tmp[1] + '\t' + str("%.3f" % c) + '\t' + tmp[3] + '\n'
else:
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + tmp[3] + '\n'
self.saveFile(fileName, s)
# Check the correct charges in N-Terminal st file
# Residue is NTres
def checaNT(self, fileName):
st = open(os.path.join(self._pathPqr, fileName))
atoms = {}
s = ''
for line in st:
tmp = line.split()
if tmp.__len__() > 1:
atoms[tmp[1]] = tmp[2]
sum = 0.0
for a in atoms:
sum = sum + float(atoms[a])
# Check if the sum of protonated states - the of deprotonated state = 1
sum = float("%.2f" % sum)
if sum != 1.00:
correcao = 1.0 - sum
stCorrect = open(os.path.join(self._pathPqr, fileName))
for line in stCorrect:
tmp = line.split()
if tmp.__len__() == 1:
s = s + tmp[0] + '\n'
else:
atm = self.getAtom4chargeInResidue('NT', fileName)
if tmp[1] == atm:
c = float(tmp[3])+correcao
c = c*(-1.0)
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + str("%.3f" % c) + '\n'
else:
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + tmp[3] + '\n'
self.saveFile(fileName, s)
# Check the correct charges in N-Terminal st file
# Residue is resNT. In this case the residue has the behavior
# as residue and not like N-Terminal
def checaSiteNT(self, fileName):
st = open(os.path.join(self._pathPqr, fileName))
atomsPROT = {}
atomsDEPROT = {}
s = ''
for line in st:
tmp = line.split()
if tmp.__len__() > 1:
atomsPROT[tmp[1]] = tmp[2] # Charges on the first column
atomsDEPROT[tmp[1]] = tmp[3] # Charges on the second column
sum = 0.0
protonates = 0.0
deprotonates = 0.0
for a in atomsPROT:
protonates = protonates + float(atomsPROT[a])
for a in atomsDEPROT:
deprotonates = deprotonates + float(atomsDEPROT[a])
sum = protonates - deprotonates
# Check if the sum of protonated states - the of deprotonated state = 1
sum = float("%.2f" % sum)
if sum != 1.00:
stCorrect = open(os.path.join(self._pathPqr, fileName))
for line in stCorrect:
tmp = line.split()
if tmp.__len__() == 1:
s = s + tmp[0] + '\n'
else:
atm = self.getAtom4chargeInResidue('ResidueNT', fileName)
if tmp[1] == atm:
# Check if residue is positive
if fileName[0:3] in self.positive:
correcao = 1.0 - sum
c = float(tmp[3])+correcao
c = c*(-1.0)
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + str("%.3f" % c) + '\n'
# Check if residue is negative
elif fileName[0:3] in self.negative:
correcao = 1.0 + sum
c = float(tmp[2])+correcao
s = s + tmp[0] + '\t' + tmp[1] + '\t' + str("%.3f" % c) + '\t' + tmp[3] + '\n'
else:
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + tmp[3] + '\n'
self.saveFile(fileName, s)
# Check the correct charges in C-Terminal st file
# Residue is CTres
def checaCT(self, fileName):
st = open(os.path.join(self._pathPqr, fileName))
atoms = {}
s = ''
for line in st:
tmp = line.split()
if tmp.__len__() > 1:
atoms[tmp[1]] = tmp[3]
sum = 0.0
for a in atoms:
sum = sum + float(atoms[a])
# Check if the sum of protonated states - the of deprotonated state = 1
sum = float("%.2f" % sum)
if sum != -1.00:
correcao = 1.0 + sum
stCorrect = open(os.path.join(self._pathPqr, fileName))
for line in stCorrect:
tmp = line.split()
if tmp.__len__() == 1:
s = s + tmp[0] + '\n'
else:
atm = self.getAtom4chargeInResidue('CT', fileName)
if tmp[1] == atm:
c = float(tmp[2])+correcao
s = s + tmp[0] + '\t' + tmp[1] + '\t' + str("%.3f" % c) + '\t' + tmp[3] + '\n'
else:
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + tmp[3] + '\n'
self.saveFile(fileName, s)
# Check the correct charges in C-Terminal st file
# Residue is resCT
def checaSiteCT(self, fileName):
st = open(os.path.join(self._pathPqr, fileName))
atoms = {}
s = ''
for line in st:
tmp = line.split()
if tmp.__len__() > 1:
atoms[tmp[1]] = tmp[3]
sum = 0.0
for a in atoms:
sum = sum + float(atoms[a])
# Check if the sum of protonated states - the of deprotonated state = 1
sum = float("%.2f" % sum)
if sum != -1.00:
correcao = 1.0 + sum
stCorrect = open(os.path.join(self._pathPqr, fileName))
for line in stCorrect:
tmp = line.split()
if tmp.__len__() == 1:
s = s + tmp[0] + '\n'
else:
atm = self.getAtom4chargeInResidue('ResidueCT', fileName)
print atm
if tmp[1] == atm:
c = float(tmp[3])+correcao
s = s + tmp[0] + '\t' + tmp[1] + '\t' + str("%.3f" % c) + '\t' + tmp[3] + '\n'
else:
s = s + tmp[0] + '\t' + tmp[1] + '\t' + tmp[2] + '\t' + tmp[3] + '\n'
self.saveFile(fileName, s)
# Build the OGM file
def createOGM(self, p1=41, p2=8.0, p3=2.0, p4=0.25):
#box = int(self.getRaioProtein(self._pqrName[0:self._pqrName.__len__()-4]))
#if box % 2 == 0:
#box += 1
#p1 = box
s = ''
fileName = self._pqrName[0:self._pqrName.__len__()-4] + ".ogm"
Origin = "ON_ORIGIN "+ str(p1) + " " + str(p2)
Center = "ON_CENT_OF_INTR "+ str(p1) + " " + str(p3)
Center2 = "ON_CENT_OF_INTR "+ str(p1) + " " + str(p4)
s = s + Origin + '\n'
s = s + Center + '\n'
s = s + Center2 + '\n'
self.saveFile(fileName, s)
# Build the MGM file
def createMGM(self, p1=41, p2=8.0, p3=2.0, p4=0.25):
#box = int(self.getRaioProtein(self._pqrName[0:self._pqrName.__len__()-4]))
#if box % 2 == 0:
#box += 1
#p1 = box
s = ''
fileName = self._pqrName[0:self._pqrName.__len__()-4] + ".mgm"
Origin = "ON_GEOM_CENT "+ str(p1) + " " + str(p2)
Center = "ON_CENT_OF_INTR "+ str(p1) + " " + str(p3)
Center2 = "ON_CENT_OF_INTR "+ str(p1) + " " + str(p4)
s = s + Origin + '\n'
s = s + Center + '\n'
s = s + Center2 + '\n'
self.saveFile(fileName, s)
# Change the PQR file to permit various N and C Terminal
# When the sites file
def changePQR(self):
# Create a copy from genuine pqr file
shutil.copy2(os.path.join(self._pathPqr, self._pqrName), os.path.join(self._pathPqr, self._pqrName + '.bkp'))
self.cleanPQR()
self.insertChainRemark()
lastResidue = self.renumberPQR()
return lastResidue
# Remove from pqr file all fields that not is 'ATOM'
def cleanPQR(self):
pqr = open(os.path.join(self._pathPqr, self._pqrName))
s = ''
for line in pqr:
tmp = line.split()
if tmp[0] == 'ATOM':
s = s + line
self.saveFile(self._pqrName + '.clean', s)
# Insert the remark 'END_CHAIN' to indicate the end of each chain
def insertChainRemark(self):
pqr = open(os.path.join(self._pathPqr, self._pqrName + '.clean'))
s = ''
endLine = False
first = True
firstLine = pqr.readlines()[0]
back = int(firstLine.split()[4])
pqr = open(os.path.join(self._pathPqr, self._pqrName + '.clean'))
for line in pqr:
tmp = line.split()
if int(tmp[4]) < back:
s = s + 'END_CHAIN' + '\n'
s = s + line
back = -1
endLine = True
elif int(tmp[4]) == 1 and endLine == False and first == False:
s = s + 'END_CHAIN' + '\n'
s = s + line
endLine = True
first = True
else:
s = s + line
if int(tmp[4]) != 1:
endLine = False
first = False
self.saveFile(self._pqrName + '.endChain', s)
# Change the number order of numRes (if necessary)
# The numRes numbering is always sequential.
def renumberPQR(self):
# Format field
ATOM_FORMAT="%-8s %-4s %-5s %-3s %-4s %8.3f%8.3f%8.3f %7.3f%6.3f \n"
pqr = open(os.path.join(self._pathPqr, self._pqrName + '.endChain'))
s = ''
numResREF = 0
i = 0
lastResidue = -1 # numSeq of the last residue. These residue will be use in method to create sites file
for line in pqr:
tmp = line.split()
if tmp[0] == 'END_CHAIN':
s = s + line
else:
# New numbering for residues in pqr file
# Start in 1 and go to N
if numResREF != int(tmp[4]):
numResREF = int(tmp[4])
i += 1
lastResidue = int(tmp[1])
campo = tmp[0]
numSeq = tmp[1]
atom = tmp[2]
resName = tmp[3]
numRes = str(i)
px = float(tmp[5])
py = float(tmp[6])
pz = float(tmp[7])
charge = float(tmp[8])
radii = float(tmp[9])
values = (campo, numSeq, atom, resName, numRes, px, py, pz, charge, radii)
s = s + (ATOM_FORMAT % values)
self.saveFile(self._pqrName + '.renumbered', s)
return lastResidue
# Return the atoms or list of atom witch will receive the charges
# for a correct build of st's file
def getAtom4chargeInResidue(self, type, residue):
# If residue is a N-Terminal as N-Terminal
if type == 'NT':
return 'N'
# If residue is a C-Terminal as C-Terminal
elif type == 'CT':
return 'O'
# If residue is a N-Terminal as Residue
elif type == 'ResidueNT':
if residue.__contains__('LYS'):
return 'NZ'
elif residue.__contains__('GLU'):
return None
elif residue.__contains__('HIS'):
return None
elif residue.__contains__('ARG'):
return 'NE'
elif residue.__contains__('ASP'):
return 'O'
elif residue.__contains__('CYS'):
return None
elif residue.__contains__('TYR'):
return None
# If residue is a C-Terminal as Residue
elif type == 'ResidueCT':
if residue.__contains__('LYS'):
return 'NZ'
elif residue.__contains__('GLU'):
return 'N'
elif residue.__contains__('HIS'):
return None
elif residue.__contains__('ARG'):
return 'NE'
elif residue.__contains__('ASP'):
return 'O'
elif residue.__contains__('CYS'):
return None
elif residue.__contains__('TYR'):
return 'N'
# Just single residue
elif type == 'Residue':
if residue.__contains__('LYS'):
return 'NZ'
elif residue.__contains__('GLU'):
return 'CD'
elif residue.__contains__('HIS'):
return 'NE2'
elif residue.__contains__('ARG'):
return 'NE'
elif residue.__contains__('ASP'):
return 'CG'
elif residue.__contains__('CYS'):
return None
elif residue.__contains__('TYR'):
return 'N'
# Save pqr.renumbered file as pqr file for to be used by mead.
# Save a pqr file without END_CHAIN remark
def saveNewPQRfile(self):
s = ''
pqrRenum = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
for line in pqrRenum.readlines():
if not line.__contains__('END_CHAIN'):
s = s + line
self.saveFile(self._pqrName, s)
def buildStsFIle(self):
self.buildARGst()
self.buildASPst()
self.buildGLUst()
self.buildHISst()
self.buildLYSst()
self.buildTYRst()
# It buil N-Terminal st file
def createStNT(self, amino, lineNT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == 'ATOM':
if fields[4] == lineNT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom == 'N' or atom == 'H' or atom == 'H2' or atom == 'H3':
atoms[atom] = str(charge)
else:
atoms[atom] = str(charge)
self.mountStNT(amino, atoms)
pqrFile.close()
# It buil N-Terminal st file
# N-term is charged positively
def mountStNT(self, amino, atoms):
s = ''
pk = self.getPkas('NT')
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[2:5] + '\t' + a + '\t' + atoms[a] + '\t' + '0.00' + '\n'
self.saveFile(amino+'.st', s)
# It buil N-Terminal st file
# In this case the residue N-Terminal is an ionic residue
def createStNT2(self, amino, lineNT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == "ATOM":
if fields[4] == lineNT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom != 'N' and atom != 'H' and atom != 'H2' and atom != 'H3':
atoms[atom] = str(charge)
self.mountStNT2(amino, atoms)
pqrFile.close()
# It buil N-Terminal st file
# N-term is charged positively
# In this case the residue N-Terminal is an ionic residue
def mountStNT2(self, amino, atoms):
s = ''
pk = self.getPkas(amino[0:3])
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[0:3] + '\t' + a + '\t' + atoms[a] + '\t' + '0.00' + '\n'
self.saveFile(amino+'.st', s)
# It buil C-Terminal st file
# C-term is charged negatively
def createStCT(self, amino, linhaCT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == "ATOM":
if fields[4] == linhaCT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom == 'C' or atom == 'O' or atom == 'OH' or atom == 'OXT':
atoms[atom] = str(charge)
else:
atoms[atom] = str(charge)
self.mountStCT(amino, atoms)
pqrFile.close()
# It buil C-Terminal st file
def mountStCT(self, amino, atoms):
s = ''
pk = self.getPkas('CT')
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[2:5] + '\t' + a + '\t' + '0.00' + '\t' + atoms[a] + '\n'
self.saveFile(amino+'.st', s)
# It buil C-Terminal st file
# In this case the residue C-Terminal is an ionic residue
def createStCT2(self, amino, linhaCT):
pqrFile = open(os.path.join(self._pathPqr, self._pqrName + '.renumbered'))
atoms = {}
for line in pqrFile.readlines():
fields = line.split()
if fields[0] == "ATOM":
if fields[4] == linhaCT:
campo = fields[0]
numSeq = fields[1]
atom = fields[2]
resName = fields[3]
numRes = fields[4]
px = fields[5]
py = fields[6]
pz = fields[7]
charge = fields[8]
radii = fields[9]
if resName in self.resIonic:
if atom != 'C' and atom != 'O' and atom != 'OH' and atom != 'OXT':
atoms[atom] = str(charge)
self.mountStCT2(amino, atoms)
pqrFile.close()
# It buil C-Terminal st file
# C-term is charged negatively
# In this case the residue C-Terminal is an ionic residue
def mountStCT2(self, amino, atoms):
s = ''
pk = self.getPkas(amino[0:3])
s = s + str(pk) + '\n'
for a in atoms:
s = s + amino[0:3] + '\t' + a + '\t' + '0.00' + '\t' + atoms[a] + '\n'
self.saveFile(amino+'.st', s)
# Build st file of residue ARG
# ARG is a POSITIVE residue
def buildARGst(self):
s = ''
s = s + '12.0 \n'
s = s + 'ARG N -0.400 -0.400 \n'
s = s + 'ARG CA -0.000 -0.000 \n'
s = s + 'ARG HN 0.400 0.400 \n'
s = s + 'ARG HA 0.000 0.000 \n'
s = s + 'ARG C 0.550 0.550 \n'
s = s + 'ARG O -0.550 -0.550 \n'
s = s + 'ARG CB 0.000 0.000 \n'
s = s + 'ARG HB1 0.000 0.000 \n'
s = s + 'ARG HB2 0.000 0.000 \n'
s = s + 'ARG CG 0.000 0.000 \n'
s = s + 'ARG HG1 0.000 0.000 \n'
s = s + 'ARG HG2 0.000 0.000 \n'
s = s + 'ARG CD 0.350 0.280 \n'
s = s + 'ARG HD1 0.000 0.000 \n'
s = s + 'ARG HD2 0.000 0.000 \n'
s = s + 'ARG NE -0.350 -0.560 \n'
s = s + 'ARG CZ 0.350 0.280 \n'
s = s + 'ARG NH1 -0.700 -0.750 \n'
s = s + 'ARG NH2 -0.700 -0.750 \n'
s = s + 'ARG HE 0.450 0.000 \n'
s = s + 'ARG HH1 0.400 0.375 \n'
s = s + 'ARG HH2 0.400 0.375 \n'
s = s + 'ARG HH11 0.400 0.375 \n'
s = s + 'ARG HH12 0.400 0.375 \n'
s = s + 'ARG HH21 0.400 0.375 \n'
s = s + 'ARG HH22 0.400 0.375 \n'
self.saveFile('ARG.st', s)
# Build st file of residue GLU
# GLU is a NEAGTIVE residue
def buildGLUst(self):
s = ''
s = s + '4.4 \n'
s = s + 'GLU N -0.400 -0.400 \n'
s = s + 'GLU CA -0.000 -0.000 \n'
s = s + 'GLU HN 0.400 0.400 \n'
s = s + 'GLU HA 0.000 0.000 \n'
s = s + 'GLU C 0.550 0.550 \n'
s = s + 'GLU O -0.550 -0.550 \n'
s = s + 'GLU CB 0.000 0.000 \n'
s = s + 'GLU HB1 0.000 0.000 \n'
s = s + 'GLU HB2 0.000 0.000 \n'
s = s + 'GLU CG 0.000 -0.000 \n'
s = s + 'GLU HG1 0.000 0.000 \n'
s = s + 'GLU HG2 0.000 0.000 \n'
s = s + 'GLU CD 0.550 0.100 \n'
s = s + 'GLU OE1 -0.495 -0.550 \n'
s = s + 'GLU OE2 -0.490 -0.550 \n'
s = s + 'GLU HE2 0.435 0.000 \n'
self.saveFile('GLU.st', s)
# Build st file of residue HIS
# HIS is a POSITIVE residue
def buildHISst(self):
s = ''
s = s + '6.3 \n'
s = s + 'HIS N -0.400 -0.400 \n'
s = s + 'HIS CA -0.000 -0.000 \n'
s = s + 'HIS HN 0.400 0.400 \n'
s = s + 'HIS HA 0.000 0.000 \n'
s = s + 'HIS C 0.550 0.550 \n'
s = s + 'HIS O -0.550 -0.550 \n'
s = s + 'HIS CB 0.125 0.125 \n'
s = s + 'HIS CG 0.142 0.155 \n'
s = s + 'HIS ND1 -0.350 -0.560 \n'
s = s + 'HIS CE1 0.141 0.155 \n'
s = s + 'HIS NE2 -0.350 -0.400 \n'
s = s + 'HIS CD2 0.142 -0.125 \n'
s = s + 'HIS HB1 0.000 0.000 \n'
s = s + 'HIS HB2 0.000 0.000 \n'
s = s + 'HIS HD1 0.450 0.000 \n'
s = s + 'HIS HE1 0.125 0.125 \n'
s = s + 'HIS HE2 0.450 0.400 \n'
s = s + 'HIS HD2 0.125 0.125 \n'
self.saveFile('HIS.st', s)
# Build st file of residue LYS
# LYS is a POSITIVE residue
def buildLYSst(self):
s = ''
s = '10.4 \n'
s = s + 'LYS N -0.400 -0.400 \n'
s = s + 'LYS CA -0.000 -0.000 \n'
s = s + 'LYS HN 0.400 0.400 \n'
s = s + 'LYS HA 0.000 0.000 \n'
s = s + 'LYS C 0.550 0.550 \n'
s = s + 'LYS O -0.550 -0.550 \n'
s = s + 'LYS CB 0.000 0.000 \n'
s = s + 'LYS HB1 0.000 0.000 \n'
s = s + 'LYS HB2 0.000 0.000 \n'
s = s + 'LYS CG 0.000 0.000 \n'
s = s + 'LYS HG1 0.000 0.000 \n'
s = s + 'LYS HG2 0.000 0.000 \n'
s = s + 'LYS CD 0.000 0.000 \n'
s = s + 'LYS HD1 0.000 0.000 \n'
s = s + 'LYS HD2 0.000 0.000 \n'
s = s + 'LYS CE 0.330 0.000 \n'
s = s + 'LYS HE1 0.000 0.000 \n'
s = s + 'LYS HE2 0.000 0.000 \n'
s = s + 'LYS NZ -0.320 -0.780 \n'
s = s + 'LYS HZ1 0.330 0.390 \n'
s = s + 'LYS HZ2 0.330 0.390 \n'
s = s + 'LYS HZ3 0.330 0.000 \n'
self.saveFile('LYS.st', s)
# Build st file of residue TYR
# TYR is a NEAGTIVE residue
def buildTYRst(self):
s = ''
s = s + '9.6 \n'
s = s + 'TYR N -0.400 -0.400 \n'
s = s + 'TYR CA -0.000 -0.000 \n'
s = s + 'TYR HN 0.400 0.400 \n'
s = s + 'TYR HA 0.000 0.000 \n'
s = s + 'TYR C 0.550 0.550 \n'
s = s + 'TYR O -0.550 -0.550 \n'
s = s + 'TYR CB 0.125 0.125 \n'
s = s + 'TYR HB1 0.000 0.000 \n'
s = s + 'TYR HB2 0.000 0.000 \n'
s = s + 'TYR CG -0.125 -0.195 \n'
s = s + 'TYR CD1 -0.125 -0.195 \n'
s = s + 'TYR HD1 0.125 0.125 \n'
s = s + 'TYR CE1 -0.125 -0.195 \n'
s = s + 'TYR HE1 0.125 0.125 \n'
s = s + 'TYR CZ 0.055 -0.070 \n'
s = s + 'TYR OH -0.490 -0.580 \n'
s = s + 'TYR HH 0.435 0.000 \n'
s = s + 'TYR CE2 -0.125 -0.195 \n'
s = s + 'TYR HE2 0.125 0.125 \n'
s = s + 'TYR CD2 -0.125 -0.195 \n'
s = s + 'TYR HD2 0.125 0.125 \n'
self.saveFile('TYR.st', s)
# Build st file of residue ASP
# ASP is a NEAGTIVE residue
def buildASPst(self):
s = ''
s = s + '4.0 \n'
s = s + 'ASP N -0.400 -0.400 \n'
s = s + 'ASP CA -0.000 -0.000 \n'
s = s + 'ASP HN 0.400 0.400 \n'
s = s + 'ASP HA 0.000 0.000 \n'
s = s + 'ASP C 0.550 0.550 \n'
s = s + 'ASP O -0.550 -0.550 \n'
s = s + 'ASP CB 0.000 0.000 \n'
s = s + 'ASP HB1 0.000 0.000 \n'
s = s + 'ASP HB2 0.000 0.000 \n'
s = s + 'ASP CG 0.550 0.100 \n'
s = s + 'ASP OD1 -0.495 -0.550 \n'
s = s + 'ASP OD2 -0.490 -0.550 \n'
s = s + 'ASP HD2 0.435 0.000 \n'
self.saveFile('ASP.st', s)
# Save some file in somewhere
def saveFile(self, fileName, conteudo):
f = FcfrpFile(self._pathOut, fileName)
f.getAsFile("w")
f.write(conteudo)
f.close()