Table of Contents

Class: coords_generator bkchem/oasa/oasa/coords_generator.py
Methods   
__init__
_continue_with_the_coords
_process_multi_anelated_ring
_process_simply_anelated_ring
apply_gen_to_atoms
calculate_coords
process_all_anelated_rings
process_atom_neigbors
process_one_anelated_ring
  __init__ 
__init__ ( self,  bond_length=1 )

  _continue_with_the_coords 
_continue_with_the_coords (
        self,
        mol,
        processed=[],
        )

processes the atoms in circles around the backbone (processed) until all is done

  _process_multi_anelated_ring 
_process_multi_anelated_ring (
        self,
        ring,
        angle_shift=0,
        )

Exceptions   
( "i am not able to handle this, it should normaly not happen. please send me the input." )
  _process_simply_anelated_ring 
_process_simply_anelated_ring (
        self,
        ring,
        base,
        )

Exceptions   
"this should not happen"
  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 )


Table of Contents

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