Protool/electrostatics.py
def calculate_desolvation(self,filename=None,updater=None):
        """Calculate the desolvation energies for all titratable groups"""
        if not getattr(self,'atom_close',None):
            self.get_atoms_around()
        #
        #
        titgrps=self.titratable_groups
        residues=titgrps.keys()
        residues.sort()
        self.desolv={}
        for residue in residues:
            if updater:
                updater('Calculating for %s' %residue)
            for group in titgrps[residue]:
                name1=self.get_titgroup_name(residue,group)
                #
                # Calculate the desolvation
                #
                self.desolv[name1]=12.5*math.pow(self.atom_close[name1],1.7)
        #
        # Write the file
        #
        if filename:
            import pKaIO
            X=pKaIO.pKaIO()
            X.desolv=self.desolv
            X.write_desolv(filename+'.DESOLV.DAT')
        return self.desolv
Calculate the desolvation energies for all titratable groups
Calculate the desolvation energies for all titratable groups
Calculate the desolvation energies for all titratable groups
def calculate_desolvation(self,filename=None,updater=None):
        if not getattr(self,'atom_close',None):
            self.get_atoms_around()
        titgrps=self.titratable_groups
        residues=titgrps.keys()
        residues.sort()
        self.desolv={}
        for residue in residues:
            if updater:
                updater('Calculating for %s' %residue)
            for group in titgrps[residue]:
                name1=self.get_titgroup_name(residue,group)
                 Calculate the desolvation
                self.desolv[name1]=12.5*math.pow(self.atom_close[name1],1.7)
         Write the file
        if filename:
            import pKaIO
            X=pKaIO.pKaIO()
            X.desolv=self.desolv
            X.write_desolv(filename+'.DESOLV.DAT')
        return self.desolv
def calculate_desolvation ( self , filename = None , updater = None ) : if not getattr ( self , 'atom_close' , None ) : self . get_atoms_around ( ) titgrps = self . titratable_groups residues = titgrps . keys ( ) residues . sort ( ) self . desolv = { } for residue in residues : if updater : updater ( 'Calculating for %s' % residue ) for group in titgrps [ residue ] : name1 = self . get_titgroup_name ( residue , group ) self . desolv [ name1 ] = 12.5 * math . pow ( self . atom_close [ name1 ] , 1.7 ) if filename : import pKaIO X = pKaIO . pKaIO ( ) X . desolv = self . desolv X . write_desolv ( filename + '.DESOLV.DAT' ) return self . desolv
Calculate the desolvation energies for all titratable groups
Calculate the desolvation energies for all titratable groups
"""Calculate the desolvation energies for all titratable groups""" # # # # Calculate the desolvation # # # Write the file #
self
filename
updater