def titrate_one_group(name,intpkas,is_charged,acidbase):
"""Titrate a single group and return the pKa value for it"""
names=[name]
num_states=len(intpkas)
state_counter=[num_states]
linear=[] # The linear matrix
for group2 in range(1):
for state1 in range(num_states):
for state2 in range(num_states):
linear.append(0.0)
#
# Set the MC parameters
#
mcsteps=5000
phstart=0.1
phend=20.0
phstep=0.1
#
# Call our little C++ module
#
import pMC_mult
FAST=pMC_mult.MC(intpkas,linear,acidbase,state_counter,is_charged)
FAST.set_MCsteps(int(mcsteps))
print 'Calculating intrinsic pKa value'
pKavals=FAST.calc_pKas(phstart,phend,phstep)
count=0
intpka=pKavals[0]
print 'Simulated intrinsic pKa value: %5.2f' %intpka
count=1
#
# Get the charges
#
charges={}
pH_start=pKavals[count]
pH_step=pKavals[count+1]
num_pHs=pKavals[count+2]
count=count+2
pHs=[]
charges=[]
pH=pH_start
for x in range(int(num_pHs)):
count=count+1
pHs.append(pKavals[count])
count=count+1
charges.append(pKavals[count])
pH=pH+pH_step
if pKavals[count+1]==999.0 and pKavals[count+2]==-999.0:
count=count+2
else:
print 'Something is wrong'
print pKavals[count:count+30]
raise Exception('Incorrect data format from pMC_mult')
return intpka
#
for group2 in range(groups):
for state1 in range(states):
for state2 in range(states):
if state1 == 0 and state2 == 0 and group != group2:
linear.append(-2.3)
else:
linear.append(0.0)
mcsteps = 50000
phstart = 2.0
phend = 14.0
phstep = 0.1
#
# Call our little C++ module
#
FAST = pMC_mult.MC(intpkas, linear, acidbase, state_counter,
is_charged_state)
FAST.set_MCsteps(int(mcsteps))
print 'Starting to calculate pKa values'
pKavals = FAST.calc_pKas(phstart, phend, phstep)
count = 0
print '\n****************************'
print 'Final pKa values'
pkas = {}
for name in names:
pkas[name] = {'pKa': pKavals[count]}
print '%s pKa: %5.2f ' % (name, pKavals[count])
count = count + 1
#
# Write the WHAT IF pKa file
#
for name in names:
def _calc_pKas(self,
mcsteps=200000,
phstep=0.1,
phstart=1.0,
phend=20.0,
verbose=1,
complete_pka=None,
exp_pHs=[]):
"""Do the pKa calculation with the CPP module"""
#
# Do specific CPP_Mult setup
#
import time
starttime = time.time()
#
# Get the number of groups
#
residues = self.intrinsic_pKa.keys()
residues.sort()
#
# num_states holds the number of states for each group
# charged_state identified whether a state is charged or neutral
#
intpkas = []
acidbase = []
num_states = []
linear_charged_state = []
for residue in residues:
num_states.append(len(self.intrinsic_pKa[residue]))
#this_state=[]
state_count = 0
for state in self.intrinsic_pKa[residue]:
intpkas.append(float(state))
acidbase.append(int(self.acid_base[residue]))
linear_charged_state.append(
self.charged_state[residue][state_count])
state_count = state_count + 1
#
# Linearise the matrix
#
linear_matrix = self.make_matrix_linear()
#
# Import the C++ module and run pKa calc from there
#
import time, math
import pMC_mult
FAST = pMC_mult.MC(intpkas, linear_matrix, acidbase, num_states,
linear_charged_state)
loadtime = time.time()
#print 'CPP calculations starting at',time.strftime('%d/%m-%Y %H:%M',time.localtime(loadtime))
FAST.set_MCsteps(int(mcsteps))
#print 'phstart: %f, phend: %f, phstep: %f' %(phstart,phend,phstep)
pKa_values = FAST.calc_pKas(phstart, phend, phstep)
#
# Put the pKa values back in a dictionary
#
pkavalues = {}
count = 0
for residue in residues:
pkavalues[residue] = pKa_values[count]
if pKa_values[count] < -100.0:
pkavalues[residue] = -9999.9
count = count + 1
#
# Now get the titration curves
#
# pMC returns a specification of how many values it returns
#
pH_start = pKa_values[count]
pH_step = pKa_values[count + 1]
pH_num = pKa_values[count + 2]
count = count + 3
#
#
#
self.pHvalues = []
self.prot_states = {}
for residue in residues:
self.prot_states[residue] = {}
while 1:
pH = float(pKa_values[count])
count = count + 1
charge = float(pKa_values[count])
count = count + 1
#
# If we find the terminator value
#
if pKa_values[count] == 999.0:
if pKa_values[count + 1] == -999.0:
count = count + 2
break
self.prot_states[residue][pH] = charge
#
#
if self.pHvalues == []:
self.pHvalues = self.prot_states[residue].keys()
self.pHvalues.sort()
#
# prot_states also contain the pKa value
#
self.prot_states[residue]['pKa'] = pkavalues[residue]
#
# Construct the proper pKa array
#
self.pka = {}
for group in pkavalues.keys():
self.pka[group] = {'pKa': pkavalues[group]}
if complete_pka:
self.complete_pka()
#
# Construct the pHvalues array
#
#
# All done
#
loadtid = (loadtime - starttime) / 60.0
tid = time.time() - starttime
tid = tid / 60.0
#print 'CPP calculations took %.4f minutes' %tid
#print 'setup time %.4f minutes' %loadtid
#import sys
#sys.stdout.flush()
return pkavalues