def read_WIfile(self,lines,dict,format):
"""
# Read a DESOLV file or a BACKGR file
"""
import string
x=1
done=None
Nterm=0
while not done:
x=x+1
#
# Read first line for this residue
#
term=None
if lines[x].strip()=='TERMINAL GROUP:':
Nterm=abs(Nterm-1)
term=True
x=x+1
nline=string.replace(lines[x],'(','')
nline=string.replace(nline,')','')
list=string.split(nline)
resid=pKaUT.getWI_resid2(lines[x])
if term:
#
# Replace the residue name by the terminal name
#
resname=resid.split(':')[-1]
d={1:'NTERM',0:'CTERM'}
resid=resid.replace(resname,d[Nterm])
#
dict[resid]=string.atof(list[-1])
if string.strip(lines[x+1])=='End of file':
done=1
return dict
def read_WIfile(self, lines, dict, format):
"""
# Read a DESOLV file or a BACKGR file
"""
import string
x = 1
done = None
Nterm = 0
while not done:
x = x + 1
#
# Read first line for this residue
#
term = None
if lines[x].strip() == 'TERMINAL GROUP:':
Nterm = abs(Nterm - 1)
term = True
x = x + 1
nline = string.replace(lines[x], '(', '')
nline = string.replace(nline, ')', '')
list = string.split(nline)
resid = pKaUT.getWI_resid2(lines[x])
if term:
#
# Replace the residue name by the terminal name
#
resname = resid.split(':')[-1]
d = {1: 'NTERM', 0: 'CTERM'}
resid = resid.replace(resname, d[Nterm])
#
dict[resid] = string.atof(list[-1])
if string.strip(lines[x + 1]) == 'End of file':
done = 1
return dict
def read_matrix(self,filename=None):
"""
# This subroutine read a MATRIX file
"""
if not filename:
if self.matrix_file:
filename=self.matrix_file
else:
raise Exception('No matrix filename given')
#
import os, string
if not os.path.isfile(filename):
raise Exception("File not found: "+filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
#
# Initialise dictionary
#
self.matrix={}
#
# Read title lines
#
if string.lower(string.strip(lines[0]))==string.lower('WHAT IF Interaction Matrix File'):
format='WHAT IF'
elif string.lower(string.strip(lines[0]))==string.lower('pdb2pka Interaction Matrix File'):
format='WHAT IF'
elif lines[2].strip()=='#pKa initialization':
return self.read_MEADfile(lines,mode='matrix')
else:
raise Exception('Unknown format')
if not string.strip(lines[1])=='Format 1.0':
raise Exception('Wrong format'+str(lines[1]))
x=1
done=None
partners=None
Nterm=0
while not done:
x=x+1
#
# Read first line for this partner residue
#
if format=='WHAT IF':
term=None
if string.strip(lines[x])=='TERMINAL GROUP:':
term=1
Nterm=abs(Nterm-1)
x=x+1
nline=string.replace(lines[x],'(','')
nline=string.replace(nline,')','')
resid=pKaUT.getWI_resid2(lines[x])
if term:
#
# Replace the residue name by the terminal name
#
resname=resid.split(':')[-1]
d={1:'NTERM',0:'CTERM'}
resid=resid.replace(resname,d[Nterm])
#
# Get the number of interaction partners
#
np=int(float(nline.split()[-1]))
if not partners:
partners=np
else:
if partners!=np:
raise Exception('Number of partners changes: %d' %np)
self.matrix[resid]={}
#
# Now read all the interactions with the partners
#
Nterm_partner=0
for count in range(partners):
x=x+1
term2=None
if string.strip(lines[x])=='TERMINAL GROUP:':
Nterm_partner=abs(Nterm_partner-1)
term2=1
x=x+1
nline=string.replace(lines[x],'(','')
nline=string.replace(nline,')','')
list=string.split(nline)
partid=pKaUT.getWI_resid2(lines[x])
if term2:
#
# Replace the residue name by the terminal name
#
resname=partid.split(':')[-1]
d={1:'NTERM',0:'CTERM'}
partid=partid.replace(resname,d[Nterm_partner])
#
# New name?
#
chacha=string.atof(string.strip(list[-1]))
x=x+1
i2=float(lines[x])
x=x+1
i3=float(lines[x])
x=x+1
i4=float(lines[x])
energies=[chacha,i2,i3,i4]
self.matrix[resid][partid]=energies
term2=None
elif format=='pdb2pka':
#
# pseudo-pdb2pka format
#
list=lines[x].split()
resid=string.strip(list[0])
self.matrix[resid]={}
partners=int(float(list[-1]))
#
# Now read all the interactions with the partners
#
for count in range(partners):
x=x+1
list=lines[x].split()
partid=list[0]
chacha=string.atof(string.strip(list[-1]))
x=x+1
i2=string.atof(lines[x])
x=x+1
i3=string.atof(lines[x])
x=x+1
i4=string.atof(lines[x])
energies=[chacha,i2,i3,i4]
self.matrix[resid][partid]=energies
x=x+1
if string.strip(lines[x+1])=='End of file':
done=1
return self.matrix
def readtitcurv(self,filename=None):
#
# Syntax: readtitcurv(self,<titration curve filename>)
# This function reads a WHAT IF titration curve file and
# creates self.titdata, which is a dictionary:
# self.titdata={<residue>:{'pKa':<pka>,<ph1>:<charge1>,<ph2>:<charge2>.....}}
#
if not filename:
filename=self.titcurvfile
import os, string
if not os.path.isfile(filename):
raise Exception('File does not exist: %s' %filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
#
# Parse
#
if string.lower(string.strip(lines[0]))==string.lower('WHAT IF Titration Curve File'):
format='WHAT IF'
elif string.lower(string.strip(lines[0]))==string.lower('pdb2pka Titration Curve File'):
format='WHAT IF'
elif lines[2].strip()=='#pKa initialization':
return self.read_MEADfile(lines,mode='titcurv')
else:
raise Exception('Unknown format')
if string.lower(string.strip(lines[1]))!=string.lower('Format 1.0'):
raise Exception('unknown format: '+str(lines[1]))
#
# Get the pH start, stop and step
#
phvals=string.split(lines[2])
phstart=string.atof(phvals[0])
phend=string.atof(phvals[1])
phstep=string.atof(phvals[2])
titdata={}
linenumber=3
done=0
terms=['NTERM','CTERM']
term_count=-1
while not done:
Term=False
if string.strip(lines[linenumber])=='TERMINAL GROUP:':
linenumber=linenumber+1
Term=1
residue=pKaUT.getWI_resid2(lines[linenumber],format)
if Term:
term_count=term_count+1
#
# Get rid of the residue name and just add the term
#
aaname=residue.split(':')[-1]
residue=residue.replace(aaname,terms[term_count])
if term_count==1:
term_count=-1
pKa=float(string.split(lines[linenumber])[-1])
linenumber=linenumber+1
#
# --------------
#
charge={'pKa':pKa}
for pH in range(int(100*phstart),int(100*phend+100*phstep),int(100*phstep)):
rpH=float(pH)/100.0
line=string.split(lines[linenumber])
if string.atof(line[0])==rpH:
charge[rpH]=string.atof(line[1])
linenumber=linenumber+1
titdata[residue]=charge
linenumber=linenumber+1
if string.strip(string.lower(lines[linenumber]))==string.lower('End of file'):
done=1
self.titdata=titdata
return self.titdata
def read_matrix(self, filename=None):
"""
# This subroutine read a MATRIX file
"""
if not filename:
if self.matrix_file:
filename = self.matrix_file
else:
raise Exception('No matrix filename given')
#
import os, string
if not os.path.isfile(filename):
raise Exception("File not found: " + filename)
fd = open(filename)
lines = fd.readlines()
fd.close()
#
# Initialise dictionary
#
self.matrix = {}
#
# Read title lines
#
if string.lower(string.strip(
lines[0])) == string.lower('WHAT IF Interaction Matrix File'):
format = 'WHAT IF'
elif string.lower(string.strip(
lines[0])) == string.lower('pdb2pka Interaction Matrix File'):
format = 'WHAT IF'
elif lines[2].strip() == '#pKa initialization':
return self.read_MEADfile(lines, mode='matrix')
else:
raise Exception('Unknown format')
if not string.strip(lines[1]) == 'Format 1.0':
raise Exception('Wrong format' + str(lines[1]))
x = 1
done = None
partners = None
Nterm = 0
while not done:
x = x + 1
#
# Read first line for this partner residue
#
if format == 'WHAT IF':
term = None
if string.strip(lines[x]) == 'TERMINAL GROUP:':
term = 1
Nterm = abs(Nterm - 1)
x = x + 1
nline = string.replace(lines[x], '(', '')
nline = string.replace(nline, ')', '')
resid = pKaUT.getWI_resid2(lines[x])
if term:
#
# Replace the residue name by the terminal name
#
resname = resid.split(':')[-1]
d = {1: 'NTERM', 0: 'CTERM'}
resid = resid.replace(resname, d[Nterm])
#
# Get the number of interaction partners
#
np = int(float(nline.split()[-1]))
if not partners:
partners = np
else:
if partners != np:
raise Exception('Number of partners changes: %d' % np)
self.matrix[resid] = {}
#
# Now read all the interactions with the partners
#
Nterm_partner = 0
for count in range(partners):
x = x + 1
term2 = None
if string.strip(lines[x]) == 'TERMINAL GROUP:':
Nterm_partner = abs(Nterm_partner - 1)
term2 = 1
x = x + 1
nline = string.replace(lines[x], '(', '')
nline = string.replace(nline, ')', '')
list = string.split(nline)
partid = pKaUT.getWI_resid2(lines[x])
if term2:
#
# Replace the residue name by the terminal name
#
resname = partid.split(':')[-1]
d = {1: 'NTERM', 0: 'CTERM'}
partid = partid.replace(resname, d[Nterm_partner])
#
# New name?
#
chacha = string.atof(string.strip(list[-1]))
x = x + 1
i2 = float(lines[x])
x = x + 1
i3 = float(lines[x])
x = x + 1
i4 = float(lines[x])
energies = [chacha, i2, i3, i4]
self.matrix[resid][partid] = energies
term2 = None
elif format == 'pdb2pka':
#
# pseudo-pdb2pka format
#
list = lines[x].split()
resid = string.strip(list[0])
self.matrix[resid] = {}
partners = int(float(list[-1]))
#
# Now read all the interactions with the partners
#
for count in range(partners):
x = x + 1
list = lines[x].split()
partid = list[0]
chacha = string.atof(string.strip(list[-1]))
x = x + 1
i2 = string.atof(lines[x])
x = x + 1
i3 = string.atof(lines[x])
x = x + 1
i4 = string.atof(lines[x])
energies = [chacha, i2, i3, i4]
self.matrix[resid][partid] = energies
x = x + 1
if string.strip(lines[x + 1]) == 'End of file':
done = 1
return self.matrix
def readtitcurv(self, filename=None):
#
# Syntax: readtitcurv(self,<titration curve filename>)
# This function reads a WHAT IF titration curve file and
# creates self.titdata, which is a dictionary:
# self.titdata={<residue>:{'pKa':<pka>,<ph1>:<charge1>,<ph2>:<charge2>.....}}
#
if not filename:
filename = self.titcurvfile
import os, string
if not os.path.isfile(filename):
raise Exception('File does not exist: %s' % filename)
fd = open(filename)
lines = fd.readlines()
fd.close()
#
# Parse
#
if string.lower(string.strip(
lines[0])) == string.lower('WHAT IF Titration Curve File'):
format = 'WHAT IF'
elif string.lower(string.strip(
lines[0])) == string.lower('pdb2pka Titration Curve File'):
format = 'WHAT IF'
elif lines[2].strip() == '#pKa initialization':
return self.read_MEADfile(lines, mode='titcurv')
else:
raise Exception('Unknown format')
if string.lower(string.strip(lines[1])) != string.lower('Format 1.0'):
raise Exception('unknown format: ' + str(lines[1]))
#
# Get the pH start, stop and step
#
phvals = string.split(lines[2])
phstart = string.atof(phvals[0])
phend = string.atof(phvals[1])
phstep = string.atof(phvals[2])
titdata = {}
linenumber = 3
done = 0
terms = ['NTERM', 'CTERM']
term_count = -1
while not done:
Term = False
if string.strip(lines[linenumber]) == 'TERMINAL GROUP:':
linenumber = linenumber + 1
Term = 1
residue = pKaUT.getWI_resid2(lines[linenumber], format)
if Term:
term_count = term_count + 1
#
# Get rid of the residue name and just add the term
#
aaname = residue.split(':')[-1]
residue = residue.replace(aaname, terms[term_count])
if term_count == 1:
term_count = -1
pKa = float(string.split(lines[linenumber])[-1])
linenumber = linenumber + 1
#
# --------------
#
charge = {'pKa': pKa}
for pH in range(int(100 * phstart),
int(100 * phend + 100 * phstep),
int(100 * phstep)):
rpH = float(pH) / 100.0
line = string.split(lines[linenumber])
if string.atof(line[0]) == rpH:
charge[rpH] = string.atof(line[1])
linenumber = linenumber + 1
titdata[residue] = charge
linenumber = linenumber + 1
if string.strip(string.lower(
lines[linenumber])) == string.lower('End of file'):
done = 1
self.titdata = titdata
return self.titdata
