| 
        
            | Methods |  |  
        | __init__ apply_gen_to_atoms
 calculate_coords
 process_all_anelated_rings
 process_atom_neigbors
 process_one_anelated_ring
 
 |  
            |  | __init__ |  
        | 
__init__ ( self,  bond_length=1 )
 |  
            |  | apply_gen_to_atoms |  
        | 
apply_gen_to_atoms (
        self,
        gen,
        atoms,
        start,
        bond_length=None,
        )
 |  
            |  | calculate_coords |  
        | 
calculate_coords (
        self,
        mol,
        bond_length=0,
        force=0,
        )
the bond_length (when given) sets the self.bond_length,
    if bond_length == -1 we suppose that there is already part of the molecule containing
    coords and we calculate the bond_length from it;
    force says if we should recalc all coords |  
            |  | process_all_anelated_rings |  
        | 
process_all_anelated_rings ( self,  base )
 |  
            |  | process_atom_neigbors |  
        | 
process_atom_neigbors ( self,  v )
 |  
            |  | process_one_anelated_ring |  
        | 
process_one_anelated_ring ( self,  base )
 |  |