def __init__(self,pdbfile,user_params={},reporter_groups=None):
"""Read the pdbfile and the wild type pKa values
Define the reporter groups"""
# Topdir
import os
self.topdir=os.getcwd()
#
# Set the PDB file name
#
self.pdbfile=os.path.join(self.topdir,pdbfile)
import Protool
self.PI=Protool.structureIO()
self.PI.readpdb(self.pdbfile)
#
# Get the defaults from Design_pKa
#
import Design_pKa
defaults=Design_pKa.get_defaults()
self.params={}
for key in defaults.keys():
self.params[key]=defaults[key][0]
self.params['pKMCsteps']=20000
self.params['recalc_intpka']=True
self.params['recalc_intpka_dist']=20.0
self.params['save_temp_files']=False
#
# Change the values that the user specified
#
for u_par in user_params.keys():
self.params[u_par]=user_params[u_par]
#
# Set the pKa calc parms as a subset
#
self.pKarun_params={}
include=['indi','dbcrit','ion','allow_unknown_atoms','unknown_crg','unknown_rad']
import copy
for key in include:
self.pKarun_params[key]=copy.copy(self.params[key])
#
# Set the output handler
#
self.O=Design_pKa.verbose(self.params['verbose'])
#
# Instantiate the pKa_info class and instruct it to save nothing
#
import Design_pKa_help
print 'pKa_info, PDB file',self.pdbfile
self.pKa_info=Design_pKa_help.pKa_info(pdbfile=self.pdbfile,parent=self,PBEsolver=self.params['PBEsolver'],save_file=False)
#
# Set the calculation routine to CPP
#
import pKa_MC
self.pKaCALC=pKa_MC.pKa_calculation_class(pdbfile=self.pdbfile,pKa_info=self.pKa_info,params=self.params,parent=self)
self.pKaCALC.set_MC_CPP()
#
# Re-calculate the wild type pKa values
#
print 'Calculating wild type pKa values'
self.wt_pKas,self.wt_prot_states=self.pKaCALC.calc_wt_pkas()
#
# Set the reporter groups
#
if reporter_groups:
self.reporter_groups=reporter_groups
else:
self.reporter_groups=self.wt_pKas.keys()
return
def __init__(self, pdbfile, user_params={}, reporter_groups=None):
"""Read the pdbfile and the wild type pKa values
Define the reporter groups"""
# Topdir
import os
self.topdir = os.getcwd()
#
# Set the PDB file name
#
self.pdbfile = os.path.join(self.topdir, pdbfile)
import Protool
self.PI = Protool.structureIO()
self.PI.readpdb(self.pdbfile)
#
# Get the defaults from Design_pKa
#
import Design_pKa
defaults = Design_pKa.get_defaults()
self.params = {}
for key in defaults.keys():
self.params[key] = defaults[key][0]
self.params['pKMCsteps'] = 20000
self.params['recalc_intpka'] = True
self.params['recalc_intpka_dist'] = 20.0
self.params['save_temp_files'] = False
#
# Change the values that the user specified
#
for u_par in user_params.keys():
self.params[u_par] = user_params[u_par]
#
# Set the pKa calc parms as a subset
#
self.pKarun_params = {}
include = [
'indi', 'dbcrit', 'ion', 'allow_unknown_atoms', 'unknown_crg',
'unknown_rad'
]
import copy
for key in include:
self.pKarun_params[key] = copy.copy(self.params[key])
#
# Set the output handler
#
self.O = Design_pKa.verbose(self.params['verbose'])
#
# Instantiate the pKa_info class and instruct it to save nothing
#
import Design_pKa_help
print 'pKa_info, PDB file', self.pdbfile
self.pKa_info = Design_pKa_help.pKa_info(
pdbfile=self.pdbfile,
parent=self,
PBEsolver=self.params['PBEsolver'],
save_file=False)
#
# Set the calculation routine to CPP
#
import pKa_MC
self.pKaCALC = pKa_MC.pKa_calculation_class(pdbfile=self.pdbfile,
pKa_info=self.pKa_info,
params=self.params,
parent=self)
self.pKaCALC.set_MC_CPP()
#
# Re-calculate the wild type pKa values
#
print 'Calculating wild type pKa values'
self.wt_pKas, self.wt_prot_states = self.pKaCALC.calc_wt_pkas()
#
# Set the reporter groups
#
if reporter_groups:
self.reporter_groups = reporter_groups
else:
self.reporter_groups = self.wt_pKas.keys()
return
def calculate_insystem_dpKas(self):
"""Calculate the dpKas for all residues"""
import pKarun.pKa_utility_functions as pKa_utility_functions
import os
groups = self.wt_pKas.keys()
groups.sort()
self.in_data = {}
count = 1
for group in groups:
print 'Group: %s (%3d of %3d)' % (group, count, len(groups))
count = count + 1
dirname = os.path.join(self.topdir, 'in_system')
if not os.path.isdir(dirname):
os.mkdir(dirname)
filename = os.path.join(dirname, group + '.DAT')
data = None
if os.path.isfile(filename):
try:
fd = open(filename)
import cPickle
data = cPickle.load(fd)
fd.close()
self.in_data[group] = data
print 'Loaded in_system data for %s' % group
except:
data = None
#
# If we don't have the data calculate it
#
if data is None:
print 'Calculating in_system dpKas when removing: %s' % group
import pKa_MC
pKa_params = {
'pHstart': self.pHstart,
'pHstop': self.pHend,
'pHstep': self.pHstep,
'pKMCsteps': self.MCsteps,
'verbose': 1
}
self.pKaCALC = pKa_MC.pKa_calculation_class(self.pdbfile,
pKa_info=None,
params=pKa_params,
parent=self)
self.pKaCALC.set_MC_CPP()
reporter_groups = groups[:]
reporter_groups.remove(group)
self.pKaCALC.set_reporter_groups(reporter_groups)
self.pKaCALC.remove_interactions_with(group)
pkas, titcurvs = self.pKaCALC.calc_wt_pkas()
self.in_data[group] = titcurvs
print 'I got %d titration curves' % (len(titcurvs.keys()))
#
# Save the data
#
fd = open(filename, 'w')
import cPickle
data = cPickle.dump(titcurvs, fd)
fd.close()
print 'done'
print
print
#
# Integrate differences from wild type titration curve
#
data = {}
rgroups = self.in_data.keys()
rgroups.sort()
for removed_group in rgroups:
data[removed_group] = {}
tgroups = self.in_data[removed_group].keys()
tgroups.sort()
for tgroup in tgroups:
if removed_group == tgroup:
continue
pH_values = self.in_data[removed_group][tgroup].keys()
pH_values.sort()
pH_values.remove('pKa')
pH_step = pH_values[1] - pH_values[0]
diff = 0.0
for pH in pH_values:
diff = diff + (self.in_data[removed_group][tgroup][pH] -
self.wt_titcurv[tgroup][pH]) * pH_step
if abs(diff) < 0.1:
diff = 0.0
data[removed_group][tgroup] = diff
return data
def __init__(self, params):
#
# Initialise
#
self.params = params
import pKaTool.pKaIO as pKaIO
self.pdbfile = self.params['pdb']
self.MCsteps = int(self.params['MCsteps'])
self.pHstep = float(self.params['pHstep'])
self.pHstart = float(self.params['pHstart'])
self.pHend = float(self.params['pHend'])
IO = pKaIO.pKaIO(self.pdbfile)
#
# Define the tmpdir for all our calcs
#
import os
self.topdir = os.path.split(self.pdbfile)[0]
self.topdir = os.path.join(
self.topdir, '%s_autonomy' % os.path.split(self.pdbfile)[1])
if not os.path.isdir(self.topdir):
os.mkdir(self.topdir)
#
# Did we find a completed pKa calculation for the PDB file
#
if IO.calculation_completed:
#
# All files found
#
print 'pKa calculation files found'
else:
print
print 'I could not find a completed pKa calculation for the specified PDB file'
print 'Please complete the pKa calculation first'
print
raise Exception()
#
# Get the wild type titration curves calculated with WHAT IF
#
import pKaTool.pKaIO
IO = pKaTool.pKaIO.pKaIO(self.pdbfile)
self.wt_titcurv = IO.read_titration_curve()
self.wt_pKas = IO.readpka()
#
# Recalculate titration curves with the CPP algorithm
#
import os
dirname = os.path.join(self.topdir, 'wt_recalc')
if not os.path.isdir(dirname):
os.mkdir(dirname)
filename = os.path.join(dirname, 'WT.DAT')
data = None
if os.path.isfile(filename):
try:
fd = open(filename)
import cPickle
data = cPickle.load(fd)
fd.close()
self.wtpkas = data['pkas']
self.wt_titcurv = data['titcurv']
print 'Loaded wild type recalculated titration curves'
print 'Loaded %d titration curves' % (len(
self.wt_titcurv.keys()))
except:
data = None
#
# If we don't have the data calculate it
#
if data is None:
import pKa_MC
print 'Recalculating wild type titration curves'
pKa_params = {
'pHstart': self.pHstart,
'pHstop': self.pHend,
'pHstep': self.pHstep,
'pKMCsteps': self.MCsteps,
'verbose': 1
}
self.pKaCALC = pKa_MC.pKa_calculation_class(self.pdbfile,
pKa_info=None,
params=pKa_params,
parent=self)
self.pKaCALC.set_MC_CPP()
self.pKaCALC.set_reporter_groups(self.wt_pKas.keys())
self.wtpkas, self.wt_titcurv = self.pKaCALC.calc_wt_pkas()
#
# Save the data
#
fd = open(filename, 'w')
import cPickle
data = cPickle.dump(
{
'pkas': self.wtpkas,
'titcurv': self.wt_titcurv
}, fd)
fd.close()
print 'done'
print
print 'Calculated %d titration curves' % (len(
self.wt_titcurv.keys()))
#
# Get the in_system energies
#
self.in_data = self.calculate_insystem_dpKas()
#
# Get the ex_data
#
self.ex_data = self.calculate_exsystem_dpKas()
return
def calculate_insystem_dpKas(self):
"""Calculate the dpKas for all residues"""
import pKarun.pKa_utility_functions as pKa_utility_functions
import os
groups=self.wt_pKas.keys()
groups.sort()
self.in_data={}
count=1
for group in groups:
print 'Group: %s (%3d of %3d)' %(group,count,len(groups))
count=count+1
dirname=os.path.join(self.topdir,'in_system')
if not os.path.isdir(dirname):
os.mkdir(dirname)
filename=os.path.join(dirname,group+'.DAT')
data=None
if os.path.isfile(filename):
try:
fd=open(filename)
import cPickle
data=cPickle.load(fd)
fd.close()
self.in_data[group]=data
print 'Loaded in_system data for %s' %group
except:
data=None
#
# If we don't have the data calculate it
#
if data is None:
print 'Calculating in_system dpKas when removing: %s' %group
import pKa_MC
pKa_params={'pHstart':self.pHstart,'pHstop':self.pHend,'pHstep':self.pHstep,'pKMCsteps':self.MCsteps,'verbose':1}
self.pKaCALC=pKa_MC.pKa_calculation_class(self.pdbfile,pKa_info=None,params=pKa_params,parent=self)
self.pKaCALC.set_MC_CPP()
reporter_groups=groups[:]
reporter_groups.remove(group)
self.pKaCALC.set_reporter_groups(reporter_groups)
self.pKaCALC.remove_interactions_with(group)
pkas,titcurvs=self.pKaCALC.calc_wt_pkas()
self.in_data[group]=titcurvs
print 'I got %d titration curves' %(len(titcurvs.keys()))
#
# Save the data
#
fd=open(filename,'w')
import cPickle
data=cPickle.dump(titcurvs,fd)
fd.close()
print 'done'
print
print
#
# Integrate differences from wild type titration curve
#
data={}
rgroups=self.in_data.keys()
rgroups.sort()
for removed_group in rgroups:
data[removed_group]={}
tgroups=self.in_data[removed_group].keys()
tgroups.sort()
for tgroup in tgroups:
if removed_group==tgroup:
continue
pH_values=self.in_data[removed_group][tgroup].keys()
pH_values.sort()
pH_values.remove('pKa')
pH_step=pH_values[1]-pH_values[0]
diff=0.0
for pH in pH_values:
diff=diff+(self.in_data[removed_group][tgroup][pH]-self.wt_titcurv[tgroup][pH])*pH_step
if abs(diff)<0.1:
diff=0.0
data[removed_group][tgroup]=diff
return data
def __init__(self,params):
#
# Initialise
#
self.params=params
import pKaTool.pKaIO as pKaIO
self.pdbfile=self.params['pdb']
self.MCsteps=int(self.params['MCsteps'])
self.pHstep=float(self.params['pHstep'])
self.pHstart=float(self.params['pHstart'])
self.pHend=float(self.params['pHend'])
IO=pKaIO.pKaIO(self.pdbfile)
#
# Define the tmpdir for all our calcs
#
import os
self.topdir=os.path.split(self.pdbfile)[0]
self.topdir=os.path.join(self.topdir,'%s_autonomy' %os.path.split(self.pdbfile)[1])
if not os.path.isdir(self.topdir):
os.mkdir(self.topdir)
#
# Did we find a completed pKa calculation for the PDB file
#
if IO.calculation_completed:
#
# All files found
#
print 'pKa calculation files found'
else:
print
print 'I could not find a completed pKa calculation for the specified PDB file'
print 'Please complete the pKa calculation first'
print
raise Exception()
#
# Get the wild type titration curves calculated with WHAT IF
#
import pKaTool.pKaIO
IO=pKaTool.pKaIO.pKaIO(self.pdbfile)
self.wt_titcurv=IO.read_titration_curve()
self.wt_pKas=IO.readpka()
#
# Recalculate titration curves with the CPP algorithm
#
import os
dirname=os.path.join(self.topdir,'wt_recalc')
if not os.path.isdir(dirname):
os.mkdir(dirname)
filename=os.path.join(dirname,'WT.DAT')
data=None
if os.path.isfile(filename):
try:
fd=open(filename)
import cPickle
data=cPickle.load(fd)
fd.close()
self.wtpkas=data['pkas']
self.wt_titcurv=data['titcurv']
print 'Loaded wild type recalculated titration curves'
print 'Loaded %d titration curves' %(len(self.wt_titcurv.keys()))
except:
data=None
#
# If we don't have the data calculate it
#
if data is None:
import pKa_MC
print 'Recalculating wild type titration curves'
pKa_params={'pHstart':self.pHstart,'pHstop':self.pHend,'pHstep':self.pHstep,'pKMCsteps':self.MCsteps,'verbose':1}
self.pKaCALC=pKa_MC.pKa_calculation_class(self.pdbfile,pKa_info=None,params=pKa_params,parent=self)
self.pKaCALC.set_MC_CPP()
self.pKaCALC.set_reporter_groups(self.wt_pKas.keys())
self.wtpkas,self.wt_titcurv=self.pKaCALC.calc_wt_pkas()
#
# Save the data
#
fd=open(filename,'w')
import cPickle
data=cPickle.dump({'pkas':self.wtpkas,'titcurv':self.wt_titcurv},fd)
fd.close()
print 'done'
print
print 'Calculated %d titration curves' %(len(self.wt_titcurv.keys()))
#
# Get the in_system energies
#
self.in_data=self.calculate_insystem_dpKas()
#
# Get the ex_data
#
self.ex_data=self.calculate_exsystem_dpKas()
return
