Protool/mutate.py
def find_debump_atoms(self,residue,radius):
        """Get atoms close to the residue"""
        #close_atoms=[]
        #for atom in self.PI.residues[residue]:
        #    for catom in self.PI.get_neighbour_atoms(atom):
        #        if not catom in close_atoms:
        #            close_atoms.append(catom)
        #return close_atoms
        close_atoms=[]
        if self.PI.resname(residue)!='GLY':
            CB=residue+':CB'
        else:
            # Use CA instead
            CB=residue+':CA'
        for atom in self.PI.atoms.keys():
            if self.PI.dist(CB,atom)<radius:
                if not atom in self.PI.residues[residue]:
                    close_atoms.append(atom)
        #print 'I am using %d debump atoms' %(len(close_atoms))
        return close_atoms
Get atoms close to the residue
Get atoms close to the residue
Get atoms close to the residue
def find_debump_atoms(self,residue,radius):
        close_atoms=[]
        if self.PI.resname(residue)!='GLY':
            CB=residue+':CB'
        else:
            CB=residue+':CA'
        for atom in self.PI.atoms.keys():
            if self.PI.dist(CB,atom)<radius:
                if not atom in self.PI.residues[residue]:
                    close_atoms.append(atom)
        return close_atoms
def find_debump_atoms ( self , residue , radius ) : close_atoms = [ ] if self . PI . resname ( residue ) != 'GLY' : CB = residue + ':CB' else : CB = residue + ':CA' for atom in self . PI . atoms . keys ( ) : if self . PI . dist ( CB , atom ) < radius : if not atom in self . PI . residues [ residue ] : close_atoms . append ( atom ) return close_atoms
Get atoms close to the residue
Get atoms close to the residue
"""Get atoms close to the residue""" #close_atoms=[] #for atom in self.PI.residues[residue]: #    for catom in self.PI.get_neighbour_atoms(atom): #        if not catom in close_atoms: #            close_atoms.append(catom) #return close_atoms # Use CA instead #print 'I am using %d debump atoms' %(len(close_atoms))
self
residue
radius