pKa/Design_pKa.py
def find_reporter_groups(self,mutations,check_groups=False):
        """Find all the reporter groups that are valid with this set of mutations

        If check_groups is True then check that the pKa values of the groups are
        inside pH_start and pH_stop

        """
        if not check_groups:
            reporter_groups=self.desired_pKa_changes.keys()
        else:
            #
            # If so requested get dpKa values for all wild type residues
            #
            reporter_groups=[]
            groups=self.wt_pKas.keys()
            groups.sort()
            for group in groups:
                if self.params['use_titration_curves']:
                    reporter_groups.append(group)
                else:
                    if self.wt_pKas[group]>self.params['pHstart'] and self.wt_pKas[group]<self.params['pHstop']:
                        reporter_groups.append(group)
        #
        # Make sure that we remove the groups that are included in the mutation
        #
        delete=[]
        for mutation in mutations:
            if mutation:
                import pKD_tools
                orgres=pKD_tools.get_oldres_from_mut(mutation)
                if orgres in reporter_groups:
                    delete.append(orgres)
        #
        rep_tmp=[]
        for group in reporter_groups:
            if group in delete:
                pass
            else:
                rep_tmp.append(group)
        reporter_groups=rep_tmp
        return reporter_groups
Find all the reporter groups that are valid with this set of mutations

        If check_groups is True then check that the pKa values of the groups are
        inside pH_start and pH_stop

        
Find all the reporter groups that are valid with this set of mutations
If check_groups is True then check that the pKa values of the groups are
inside pH_start and pH_stop
Find all the reporter groups that are valid with this set of mutations If check_groups is True then check that the pKa values of the groups are inside pH_start and pH_stop
def find_reporter_groups(self,mutations,check_groups=False):
        if not check_groups:
            reporter_groups=self.desired_pKa_changes.keys()
        else:
             If so requested get dpKa values for all wild type residues
            reporter_groups=[]
            groups=self.wt_pKas.keys()
            groups.sort()
            for group in groups:
                if self.params['use_titration_curves']:
                    reporter_groups.append(group)
                else:
                    if self.wt_pKas[group]>self.params['pHstart'] and self.wt_pKas[group]<self.params['pHstop']:
                        reporter_groups.append(group)
         Make sure that we remove the groups that are included in the mutation
        delete=[]
        for mutation in mutations:
            if mutation:
                import pKD_tools
                orgres=pKD_tools.get_oldres_from_mut(mutation)
                if orgres in reporter_groups:
                    delete.append(orgres)
        rep_tmp=[]
        for group in reporter_groups:
            if group in delete:
                pass
            else:
                rep_tmp.append(group)
        reporter_groups=rep_tmp
        return reporter_groups
def find_reporter_groups ( self , mutations , check_groups = False ) : if not check_groups : reporter_groups = self . desired_pKa_changes . keys ( ) else : reporter_groups = [ ] groups = self . wt_pKas . keys ( ) groups . sort ( ) for group in groups : if self . params [ 'use_titration_curves' ] : reporter_groups . append ( group ) else : if self . wt_pKas [ group ] > self . params [ 'pHstart' ] and self . wt_pKas [ group ] < self . params [ 'pHstop' ] : reporter_groups . append ( group ) delete = [ ] for mutation in mutations : if mutation : import pKD_tools orgres = pKD_tools . get_oldres_from_mut ( mutation ) if orgres in reporter_groups : delete . append ( orgres ) rep_tmp = [ ] for group in reporter_groups : if group in delete : pass else : rep_tmp . append ( group ) reporter_groups = rep_tmp return reporter_groups
Find all the reporter groups that are valid with this set of mutations
If check_groups is True then check that the pKa values of the groups are
inside pH_start and pH_stop
Find all the reporter groups that are valid with this set of mutations If check_groups is True then check that the pKa values of the groups are inside pH_start and pH_stop
"""Find all the reporter groups that are valid with this set of mutations

        If check_groups is True then check that the pKa values of the groups are
        inside pH_start and pH_stop

        """ # # If so requested get dpKa values for all wild type residues # # # Make sure that we remove the groups that are included in the mutation # #
self
mutations
check_groups