pKaTool/pKa_system_help.py
def single_parameter_analysis(self):
        """Vary every single parameter and record changes in the protonation states"""
        #
        # Store a copy of the wild type state
        #
        self.WT=self.update_pkasystem_curves()
        self.wt_state=self.pack_configuration()
        #
        # Start looping for all intrinsic pKa values
        #
        num_groups=len(self.groups.keys())
        self.tot_perms=2*num_groups+num_groups*(num_groups-1)
        self.do_states=self.tot_perms
        self.stab_test_on=1
        #
        self.curv_diffs=[]
        self.counter=0
        import time
        self.starttime=time.time()
        for group in self.groups.keys():
            #
            # Explore the difference in the intrinsic pKa
            #
            if self.has_modelpKs:
                #
                # Vary as fraction of desolv+backgr (=intpka-modelpk)
                #
                intpka_var=self.intpka_var.get()/100.0
                this_var=(self.groups[group].intpka.get()-self.groups[group].modelpK)*intpka_var
            else:
                this_var=self.intpka_var.get()
            #
            for diff in [-this_var,this_var]:
                self.unpack_configuration(self.wt_state) # Restore the wt state
                old_intpka=self.groups[group].intpka.get()
                self.groups[group].intpka.set(old_intpka+float(diff))
                self.measure_change()
            #
            # Now change the interaction energies for this group
            #
            intene_var=self.intene_var.get()/100.0
            groups2=self.groups[group].intenes.keys()
            groups2.sort()
            for igroup in groups2:
                for factor in [1.00-intene_var,1.00+intene_var]:
                    self.unpack_configuration(self.wt_state) # Restore the wt state
                    ene=self.groups[group].intenes[igroup].get()
                    self.groups[group].intenes[igroup].set(factor*ene)
                    self.measure_change()
        #
        # normal mode
        #
        self.stab_test_on=1
        return
Vary every single parameter and record changes in the protonation states
Vary every single parameter and record changes in the protonation states
Vary every single parameter and record changes in the protonation states
def single_parameter_analysis(self):
         Store a copy of the wild type state
        self.WT=self.update_pkasystem_curves()
        self.wt_state=self.pack_configuration()
         Start looping for all intrinsic pKa values
        num_groups=len(self.groups.keys())
        self.tot_perms=2*num_groups+num_groups*(num_groups-1)
        self.do_states=self.tot_perms
        self.stab_test_on=1
        self.curv_diffs=[]
        self.counter=0
        import time
        self.starttime=time.time()
        for group in self.groups.keys():
             Explore the difference in the intrinsic pKa
            if self.has_modelpKs:
                 Vary as fraction of desolv+backgr (=intpka-modelpk)
                intpka_var=self.intpka_var.get()/100.0
                this_var=(self.groups[group].intpka.get()-self.groups[group].modelpK)*intpka_var
            else:
                this_var=self.intpka_var.get()
            for diff in [-this_var,this_var]:
                self.unpack_configuration(self.wt_state)  Restore the wt state
                old_intpka=self.groups[group].intpka.get()
                self.groups[group].intpka.set(old_intpka+float(diff))
                self.measure_change()
             Now change the interaction energies for this group
            intene_var=self.intene_var.get()/100.0
            groups2=self.groups[group].intenes.keys()
            groups2.sort()
            for igroup in groups2:
                for factor in [1.00-intene_var,1.00+intene_var]:
                    self.unpack_configuration(self.wt_state)  Restore the wt state
                    ene=self.groups[group].intenes[igroup].get()
                    self.groups[group].intenes[igroup].set(factor*ene)
                    self.measure_change()
         normal mode
        self.stab_test_on=1
        return
def single_parameter_analysis ( self ) : self . WT = self . update_pkasystem_curves ( ) self . wt_state = self . pack_configuration ( ) num_groups = len ( self . groups . keys ( ) ) self . tot_perms = 2 * num_groups + num_groups * ( num_groups - 1 ) self . do_states = self . tot_perms self . stab_test_on = 1 self . curv_diffs = [ ] self . counter = 0 import time self . starttime = time . time ( ) for group in self . groups . keys ( ) : if self . has_modelpKs : intpka_var = self . intpka_var . get ( ) / 100.0 this_var = ( self . groups [ group ] . intpka . get ( ) - self . groups [ group ] . modelpK ) * intpka_var else : this_var = self . intpka_var . get ( ) for diff in [ - this_var , this_var ] : self . unpack_configuration ( self . wt_state ) old_intpka = self . groups [ group ] . intpka . get ( ) self . groups [ group ] . intpka . set ( old_intpka + float ( diff ) ) self . measure_change ( ) intene_var = self . intene_var . get ( ) / 100.0 groups2 = self . groups [ group ] . intenes . keys ( ) groups2 . sort ( ) for igroup in groups2 : for factor in [ 1.00 - intene_var , 1.00 + intene_var ] : self . unpack_configuration ( self . wt_state ) ene = self . groups [ group ] . intenes [ igroup ] . get ( ) self . groups [ group ] . intenes [ igroup ] . set ( factor * ene ) self . measure_change ( ) self . stab_test_on = 1 return
Vary every single parameter and record changes in the protonation states
Vary every single parameter and record changes in the protonation states
"""Vary every single parameter and record changes in the protonation states""" # # Store a copy of the wild type state # # # Start looping for all intrinsic pKa values # # # # Explore the difference in the intrinsic pKa # # # Vary as fraction of desolv+backgr (=intpka-modelpk) # # # Restore the wt state # # Now change the interaction energies for this group # # Restore the wt state # # normal mode #
self