Protool/electrostatics.py
def find_salt_bridges(self,cutoff=8.0):
        """Find all salt bridges in the protein
        """
        SBs=[]
        self.get_titratable_groups()
        for res1 in self.titratable_groups.keys():
            r1_cens=self.calculate_titgroup_center(res1)
            for group1 in r1_cens[res1].keys():
                group1_ID='%s:%s' %(res1,group1)
                for res2 in self.titratable_groups.keys():
                    r2_cens=self.calculate_titgroup_center(res2)
                    for group2 in r2_cens[res2].keys():
                        group2_ID='%s:%s' %(res2,group2)
                        if group1_ID!=group2_ID:
                            if self.titgroups[group1]['charge']*self.titgroups[group2]['charge']==-1:
                                import geometry
                                dist=geometry.length(r1_cens[res1][group1]-r2_cens[res2][group2])
                                if dist<=cutoff:
                                    SBs.append([group1_ID,group2_ID,dist])
        #
        # Done
        #
        return SBs
Find all salt bridges in the protein
        
Find all salt bridges in the protein
Find all salt bridges in the protein
def find_salt_bridges(self,cutoff=8.0):
        SBs=[]
        self.get_titratable_groups()
        for res1 in self.titratable_groups.keys():
            r1_cens=self.calculate_titgroup_center(res1)
            for group1 in r1_cens[res1].keys():
                group1_ID='%s:%s' %(res1,group1)
                for res2 in self.titratable_groups.keys():
                    r2_cens=self.calculate_titgroup_center(res2)
                    for group2 in r2_cens[res2].keys():
                        group2_ID='%s:%s' %(res2,group2)
                        if group1_ID!=group2_ID:
                            if self.titgroups[group1]['charge']*self.titgroups[group2]['charge']==-1:
                                import geometry
                                dist=geometry.length(r1_cens[res1][group1]-r2_cens[res2][group2])
                                if dist<=cutoff:
                                    SBs.append([group1_ID,group2_ID,dist])
         Done
        return SBs
def find_salt_bridges ( self , cutoff = 8.0 ) : SBs = [ ] self . get_titratable_groups ( ) for res1 in self . titratable_groups . keys ( ) : r1_cens = self . calculate_titgroup_center ( res1 ) for group1 in r1_cens [ res1 ] . keys ( ) : group1_ID = '%s:%s' % ( res1 , group1 ) for res2 in self . titratable_groups . keys ( ) : r2_cens = self . calculate_titgroup_center ( res2 ) for group2 in r2_cens [ res2 ] . keys ( ) : group2_ID = '%s:%s' % ( res2 , group2 ) if group1_ID != group2_ID : if self . titgroups [ group1 ] [ 'charge' ] * self . titgroups [ group2 ] [ 'charge' ] == - 1 : import geometry dist = geometry . length ( r1_cens [ res1 ] [ group1 ] - r2_cens [ res2 ] [ group2 ] ) if dist <= cutoff : SBs . append ( [ group1_ID , group2_ID , dist ] ) return SBs
Find all salt bridges in the protein
Find all salt bridges in the protein
"""Find all salt bridges in the protein
        """ # # Done #
self
cutoff