pKarun/pKarun_base.py
def autonomy (self):
        """
        # Calculate titration curves for the autonomy analysis
        """
        import os, string
        os.chdir(self.topdir)
        #
        # Right now we need a full pKa calculation to do the autonomy calcs
        #
        command=self.startcom+'\n pka \n autpka \n'
        command=command+'y \n'
        command=command+self.desolvfile+' \n'+self.backgrfile+' \n '+self.matrixfile+' \n '
        command=command+str(self.params['lowph'])+' \n '
        command=command+str(self.params['highph'])+' \n'
        command=command+str(self.params['phstep'])+'\n'
        if self.params['groups']:
            #
            # If we calculate only for specific groups then put them in
            # command file
            #
            command=command+' n \n'
            groups=string.split(self.params['groups'],',')
            for group in groups:
                command=command+str(group)+' \n'
            command=command+'0 \n'
        else:
            command=command+'y \n'
        command=self.flags+command
        import WHAT_IF
        x=WHAT_IF.Whatif()
        x.RedirectOutput('CLUSTER.log')
        x.Run(command,'C.log')
        return

        # Calculate titration curves for the autonomy analysis
        
Calculate titration curves for the autonomy analysis
Calculate titration curves for the autonomy analysis
def autonomy (self):
        import os, string
        os.chdir(self.topdir)
         Right now we need a full pKa calculation to do the autonomy calcs
        command=self.startcom+'\n pka \n autpka \n'
        command=command+'y \n'
        command=command+self.desolvfile+' \n'+self.backgrfile+' \n '+self.matrixfile+' \n '
        command=command+str(self.params['lowph'])+' \n '
        command=command+str(self.params['highph'])+' \n'
        command=command+str(self.params['phstep'])+'\n'
        if self.params['groups']:
             If we calculate only for specific groups then put them in
             command file
            command=command+' n \n'
            groups=string.split(self.params['groups'],',')
            for group in groups:
                command=command+str(group)+' \n'
            command=command+'0 \n'
        else:
            command=command+'y \n'
        command=self.flags+command
        import WHAT_IF
        x=WHAT_IF.Whatif()
        x.RedirectOutput('CLUSTER.log')
        x.Run(command,'C.log')
        return
def autonomy ( self ) : import os , string os . chdir ( self . topdir ) command = self . startcom + '\n pka \n autpka \n' command = command + 'y \n' command = command + self . desolvfile + ' \n' + self . backgrfile + ' \n ' + self . matrixfile + ' \n ' command = command + str ( self . params [ 'lowph' ] ) + ' \n ' command = command + str ( self . params [ 'highph' ] ) + ' \n' command = command + str ( self . params [ 'phstep' ] ) + '\n' if self . params [ 'groups' ] : command = command + ' n \n' groups = string . split ( self . params [ 'groups' ] , ',' ) for group in groups : command = command + str ( group ) + ' \n' command = command + '0 \n' else : command = command + 'y \n' command = self . flags + command import WHAT_IF x = WHAT_IF . Whatif ( ) x . RedirectOutput ( 'CLUSTER.log' ) x . Run ( command , 'C.log' ) return
Calculate titration curves for the autonomy analysis
Calculate titration curves for the autonomy analysis
"""
        # Calculate titration curves for the autonomy analysis
        """ # # Right now we need a full pKa calculation to do the autonomy calcs # # # If we calculate only for specific groups then put them in # command file #
self