Protool/mutate.py
def find_bumps(self,residue,close_atoms,use_backbone=1):
        """Find bumps between the residue and the close atoms

        If use_backbone is 1, then also count the bumps that the backbone atoms of residue make.
        If use_backbone is None then only debump the side chain
        """
        bump_val=0.0
        for atom1 in self.PI.residues[residue]:
            if not use_backbone:
                if self.PI.is_backbone(atom1):
                    continue
            bound_atoms=self.getbound(atom1)
            #print 'Bound to',atom1,bound_atoms
            for atom2 in close_atoms:
                if not atom2 in bound_atoms:
                    bump_val=bump_val+self.get_overlap(atom1,atom2)
                    #print 'Overlap',atom1,atom2,self.get_overlap(atom1,atom2)
                else:
                    bump_val=bump_val
            if bump_val>self.max_tolerated_bump:
                return None
        return bump_val
Find bumps between the residue and the close atoms

        If use_backbone is 1, then also count the bumps that the backbone atoms of residue make.
        If use_backbone is None then only debump the side chain
        
Find bumps between the residue and the close atoms
If use_backbone is 1, then also count the bumps that the backbone atoms of residue make.
If use_backbone is None then only debump the side chain
Find bumps between the residue and the close atoms If use_backbone is 1 then also count the bumps that the backbone atoms of residue make . If use_backbone is None then only debump the side chain
def find_bumps(self,residue,close_atoms,use_backbone=1):
        bump_val=0.0
        for atom1 in self.PI.residues[residue]:
            if not use_backbone:
                if self.PI.is_backbone(atom1):
                    continue
            bound_atoms=self.getbound(atom1)
            for atom2 in close_atoms:
                if not atom2 in bound_atoms:
                    bump_val=bump_val+self.get_overlap(atom1,atom2)
                else:
                    bump_val=bump_val
            if bump_val>self.max_tolerated_bump:
                return None
        return bump_val
def find_bumps ( self , residue , close_atoms , use_backbone = 1 ) : bump_val = 0.0 for atom1 in self . PI . residues [ residue ] : if not use_backbone : if self . PI . is_backbone ( atom1 ) : continue bound_atoms = self . getbound ( atom1 ) for atom2 in close_atoms : if not atom2 in bound_atoms : bump_val = bump_val + self . get_overlap ( atom1 , atom2 ) else : bump_val = bump_val if bump_val > self . max_tolerated_bump : return None return bump_val
Find bumps between the residue and the close atoms
If use_backbone is 1, then also count the bumps that the backbone atoms of residue make.
Find bumps between the residue and the close atoms If use_backbone is 1 then also count the bumps that the backbone atoms of residue make .
"""Find bumps between the residue and the close atoms

        If use_backbone is 1, then also count the bumps that the backbone atoms of residue make.
        If use_backbone is None then only debump the side chain
        """ #print 'Bound to',atom1,bound_atoms #print 'Overlap',atom1,atom2,self.get_overlap(atom1,atom2)
self
residue
close_atoms
use_backbone