def getlssparameters(self, trtab, tg, init_B, final_B, alpha):
self.trtab = trtab
self.tg = tg
self.init_B = init_B
self.final_B = final_B
alphainit = []
asides = []
for i in range(len(alpha)):
alphainit.append(1.0)
asides.append(0.1)
self.alpha = fmin(self.iterfunalpha, alphainit, side=asides, tol=1e-10)
for i in range(len(self.trtab)):
self.tr = trtab[i]
lssinit = [0.1, 0.1]
logkw, s = fmin(self.iterfun, lssinit, side=[0.1, 0.1], tol=1e-3)
self.logkw.append(logkw)
self.s.append(s)
return self.logkw, self.s, self.alpha
def getlssparameters(self, trtab, tg, init_B, final_B, alpha):
self.trtab = trtab
self.tg = tg
self.init_B = init_B
self.final_B = final_B
alphainit = []
asides = []
for i in range(len(alpha)):
alphainit.append(1.0)
asides.append(0.1)
self.alpha = fmin(self.iterfunalpha, alphainit, side=asides, tol=1e-10)
for i in range(len(self.trtab)):
self.tr = trtab[i]
lssinit = [0.1, 0.1]
logkw, s = fmin(self.iterfun, lssinit, side=[0.1, 0.1], tol=1e-3)
self.logkw.append(logkw)
self.s.append(s)
return self.logkw, self.s, self.alpha
def getlogssparameters(self, tr, tg, init_B, final_B):
""" Return the logKw and S parameters for logarithmic gradient conditions"""
self.tr = tr
self.tg = tg
self.init_B = init_B
self.final_B = final_B
lssinit = [0.1, 0.1]
#simplex optimization
self.lss_logkw, self.lss_s = fmin(self.logiterfun, lssinit, side=[0.1, 0.1], tol=1e-10)
return self.lss_logkw, self.lss_s
def getloggradientconditions(self, tr_min, tr_max):
"""
Optimize the logarithmic gradient conditions
finding different value of flow rate,
initial and final organic solvent and time gradient.
The equation to be used are these and the equation for the resolution
it is the same of the isocratic conditions.
"""
self.maxtg = tr_max
self.tr_min = tr_min
self.tr_max = tr_max
best_ss = None
best_gcond = None
for init_b in drange(0.00, 1.0, 0.1):
for final_b in drange(init_b+0.1, 1.0, 0.1):
for tg in drange(1, self.maxtg, 1):
gcond = [init_b, final_b, tg]
tmp_bestgcond = fmin(self.optloggradfun, gcond, side=[0.05, 0.05, 1], tol=1e-10)
tmp_ssmax = self.optloggradfun(tmp_bestgcond)
if best_ss != None:
if tmp_ssmax < best_ss:
best_ss = tmp_ssmax
best_gcond = tmp_bestgcond
else:
continue
else:
best_gcond = tmp_bestgcond
best_ss = tmp_ssmax
"""
self.maxtg = 15
gcond = [0.05, 1., 15]
best_gcond = fmin(self.optloggradfun, gcond, side=[0.05, 0.05, 1], tol=1e-10)
best_ss = self.optloggradfun(best_gcond)
"""
init_b = best_gcond[0]
final_b = best_gcond[1]
tg = best_gcond[2]
# Function calculation
t0 = self.v_m/self.flow
td = self.v_d/self.flow
logssmol = SSGenerator(None, None, None, t0, self.v_d, self.flow)
tr = []
for i in range(len(self.logkw_s_tab)):
logkw = self.logkw_s_tab[i][0]
s = self.logkw_s_tab[i][1]
tr.append(logssmol.logrtpred(logkw, s, tg, init_b, final_b, t0, td))
# return the best condition, the retention times and the best rs average
return best_gcond, tr, 1/best_ss
def getloggradientconditions(self, tr_min, tr_max):
"""
Optimize the logarithmic gradient conditions
finding different value of flow rate,
initial and final organic solvent and time gradient.
The equation to be used are these and the equation for the resolution
it is the same of the isocratic conditions.
"""
self.maxtg = tr_max
self.tr_min = tr_min
self.tr_max = tr_max
best_ss = None
best_gcond = None
for init_b in drange(0.00, 1.0, 0.1):
for final_b in drange(init_b+0.1, 1.0, 0.1):
for tg in drange(1, self.maxtg, 1):
gcond = [init_b, final_b, tg]
tmp_bestgcond = fmin(self.optloggradfun, gcond, side=[0.05, 0.05, 1], tol=1e-10)
tmp_ssmax = self.optloggradfun(tmp_bestgcond)
if best_ss != None:
if tmp_ssmax < best_ss:
best_ss = tmp_ssmax
best_gcond = tmp_bestgcond
else:
continue
else:
best_gcond = tmp_bestgcond
best_ss = tmp_ssmax
"""
self.maxtg = 15
gcond = [0.05, 1., 15]
best_gcond = fmin(self.optloggradfun, gcond, side=[0.05, 0.05, 1], tol=1e-10)
best_ss = self.optloggradfun(best_gcond)
"""
init_b = best_gcond[0]
final_b = best_gcond[1]
tg = best_gcond[2]
# Function calculation
t0 = self.v_m/self.flow
td = self.v_d/self.flow
logssmol = SSGenerator(None, None, None, t0, self.v_d, self.flow)
tr = []
for i in range(len(self.logkw_s_tab)):
logkw = self.logkw_s_tab[i][0]
s = self.logkw_s_tab[i][1]
tr.append(logssmol.logrtpred(logkw, s, tg, init_b, final_b, t0, td))
# return the best condition, the retention times and the best rs average
return best_gcond, tr, 1/best_ss
def getlogssparameters(self, tr, tg, init_B, final_B):
""" Return the logKw and S parameters for logarithmic gradient conditions"""
self.tr = tr
self.tg = tg
self.init_B = init_B
self.final_B = final_B
lssinit = [0.1, 0.1]
#simplex optimization
self.lss_logkw, self.lss_s = fmin(self.logiterfun,
lssinit,
side=[0.1, 0.1],
tol=1e-10)
return self.lss_logkw, self.lss_s
def getisoconditions(self):
""" Optimizer function starting
from the 10% of organic modifier"""
if len(self.temp) > 1: # Two temperature experiments according to de Vant Hoff
return 0
else: # one temperature experiment
phi = fmin(self.isocratic_iterfun, [0.2], side=[0.1], tol=1e-10)
tr = []
for row in self.logkw_s_tab:
logk = row[0] - row[1]*phi
k = pow(10, logk)
t0 = self.v_m/self.flow
tr.append((k * t0) + t0)
return phi*100, tr
def getisoconditions(self):
""" Optimizer function starting
from the 10% of organic modifier"""
if len(self.temp) > 1: # Two temperature experiments according to de Vant Hoff
return 0
else: # one temperature experiment
phi = fmin(self.isocratic_iterfun, [0.2], side=[0.1], tol=1e-10)
tr = []
for row in self.logkw_s_tab:
logk = row[0] - row[1]*phi
k = pow(10, logk)
t0 = self.v_m/self.flow
tr.append((k * t0) + t0)
return phi*100, tr
def getlssparameters(self, tr, tg, init_B, final_B):
""" Return the logKw and S parameters """
self.tr = tr
self.tg = tg
self.init_B = init_B
self.final_B = final_B
# fast static optimization
param_init = [1.0, 1.0, 1.0]
best_param = fmin(self.iterfun, param_init, side=[1.0, 1.0, 1.0], tol=1e-6, iterations=1000)
self.logkw = best_param[0]
self.S = best_param[1]
c = best_param[1]
return self.logkw, self.S, c
def getgradientconditions(self, tr_min, tr_max):
"""
Optimize the gradient conditions
finding different value of flow rate,
initial and final organic solvent and time gradient.
The equation to be used are these and the equation for the resolution
it is the same of the isocratic conditions.
"""
self.tr_min = tr_min
self.tr_max = tr_max
best_rsmax = None
best_gcond = None
for init_b in drange(0.00, 1.0, 0.1):
for final_b in drange(init_b+0.1, 1.0, 0.1):
for tg in drange(1, self.maxtg, 9):
gcond = [init_b, final_b, tg]
tmp_bestgcond = fmin(self.optgradfun, gcond, side=[0.05, 0.05, 1], tol=1e-10)
tmp_rsmax = self.optgradfun(tmp_bestgcond)
if best_rsmax != None:
if tmp_rsmax < best_rsmax:
best_rsmax = tmp_rsmax
best_gcond = tmp_bestgcond
else:
continue
else:
best_gcond = tmp_bestgcond
best_rsmax = tmp_rsmax
init_b = best_gcond[0]
final_b = best_gcond[1]
tg = best_gcond[2]
# Function calculation
deltafi = final_b - init_b
t0 = self.v_m/self.flow
td = self.v_d/self.flow
tr = []
for row in self.logkw_s_tab:
b = float((self.v_m * deltafi * row[1]) / (tg*self.flow))
k0 = pow(10, row[0] - (row[1] * init_b))
tr.append(((t0/b) * log10(2.3*k0*b)) + t0 + td)
# return the best condition, the retention times and the best rs average
return best_gcond, tr, 1/best_rsmax
def getgradientconditions(self, tr_min, tr_max):
"""
Optimize the gradient conditions
finding different value of flow rate,
initial and final organic solvent and time gradient.
The equation to be used are these and the equation for the resolution
it is the same of the isocratic conditions.
"""
self.tr_min = tr_min
self.tr_max = tr_max
best_rsmax = None
best_gcond = None
for init_b in drange(0.0, 0.2, 0.05):
for final_b in drange(0.7, 1.0, 0.05):
for tg in drange(self.tr_min, self.tr_max, 2.):
gcond = [init_b, final_b, tg]
tmp_bestgcond = fmin(self.optgradfun, gcond, side=[0.05, 0.05, 1], tol=1e-2)
tmp_rsmax = self.optgradfun(tmp_bestgcond)
if best_rsmax != None:
if tmp_rsmax < best_rsmax:
best_rsmax = tmp_rsmax
best_gcond = tmp_bestgcond
else:
continue
else:
best_gcond = tmp_bestgcond
best_rsmax = tmp_rsmax
init_b = best_gcond[0]
final_b = best_gcond[1]
tg = best_gcond[2]
# Function calculation
deltafi = final_b - init_b
t0 = self.v_m/self.flow
td = self.v_d/self.flow
tr = []
for row in self.logkw_s_tab:
b = float((self.v_m * deltafi * row[1]) / (tg*self.flow))
k0 = pow(10, row[0] - (row[1] * init_b))
tr.append(((t0/b) * log10(2.3*k0*b)) + t0 + td)
# return the best condition, the retention times and the best rs average
return best_gcond, tr, 1/best_rsmax
def iterfunalpha(self, alpha):
""" Return the logKw and S parameters """
self.alpha = alpha
rmsd = 0.
for i in range(len(self.trtab)):
self.tr = self.trtab[i]
lssinit = [0.1, 0.1]
#simplex optimization
logkw, s = fmin(self.iterfun, lssinit, side=[0.1, 0.1], tol=1e-10)
#calcualte retention time of all compounds with this alpha
sz_grad = len(self.flow)
for j in range(len(self.trtab[i])):
trpred = self.rtpred(logkw, s, self.tg[j % sz_grad], self.init_B[j % sz_grad], self.final_B[j % sz_grad], self.alpha[j % sz_grad], self.t0[j % sz_grad], self.td[j % sz_grad])
rmsd += square(self.trtab[i][j] - trpred)
print("%.2f %.2f [%f %f]") % (self.trtab[i][j], trpred, self.t0[j % sz_grad], self.td[j % sz_grad])
#print alpha
print ("-"*20)
sleep(1)
rmsd /= float(len(self.trtab))
rmsd = sqrt(rmsd)
return rmsd
def iterfunalpha(self, alpha):
""" Return the logKw and S parameters """
self.alpha = alpha
rmsd = 0.
for i in range(len(self.trtab)):
self.tr = self.trtab[i]
lssinit = [0.1, 0.1]
#simplex optimization
logkw, s = fmin(self.iterfun, lssinit, side=[0.1, 0.1], tol=1e-10)
#calcualte retention time of all compounds with this alpha
sz_grad = len(self.flow)
for j in range(len(self.trtab[i])):
trpred = self.rtpred(logkw, s, self.tg[j % sz_grad], self.init_B[j % sz_grad], self.final_B[j % sz_grad], self.alpha[j % sz_grad], self.t0[j % sz_grad], self.td[j % sz_grad])
rmsd += square(self.trtab[i][j] - trpred)
print("%.2f %.2f [%f %f]") % (self.trtab[i][j], trpred, self.t0[j % sz_grad], self.td[j % sz_grad])
#print alpha
print ("-"*20)
sleep(1)
rmsd /= float(len(self.trtab))
rmsd = sqrt(rmsd)
return rmsd