Table of Contents

Class: atom bkchem/oasa/oasa/atom.py
Base Classes   
graph.vertex
Methods   
__init__
__str__
_get_charge
_get_coords
_get_free_valency
_get_multiplicity
_get_occupied_valency
_get_symbol
_get_valency
_set_charge
_set_coords
_set_multiplicity
_set_symbol
_set_valency
gen_CIP_sequence
gen_CIP_sequence_does_something_else
get_free_valency
get_neighbors_CIP_sorted
get_x
get_y
get_z
has_aromatic_bonds
is_chiral
raise_valency
raise_valency_to_senseful_value
  __init__ 
__init__ (
        self,
        symbol='C',
        charge=0,
        coords=None,
        )

  __str__ 
__str__ ( self )

  _get_charge 
_get_charge ( self )

  _get_coords 
_get_coords ( self )

  _get_free_valency 
_get_free_valency ( self )

free_valency

  _get_multiplicity 
_get_multiplicity ( self )

  _get_occupied_valency 
_get_occupied_valency ( self )

occupied_valency

  _get_symbol 
_get_symbol ( self )

  _get_valency 
_get_valency ( self )

  _set_charge 
_set_charge ( self,  charge )

charge

  _set_coords 
_set_coords ( self,  coords )

coords

Exceptions   
"wrong number of coordinates"
  _set_multiplicity 
_set_multiplicity ( self,  multiplicity )

multiplicity

  _set_symbol 
_set_symbol ( self,  symbol )

symbol

Exceptions   
ValueError, "wrong atom symbol %s" % symbol
  _set_valency 
_set_valency ( self,  valency )

valency

  gen_CIP_sequence 
gen_CIP_sequence (
        self,
        iter_over=None,
        came_from=None,
        )

generates the CIP (Cahn-Ingold-Prelog) stream of atoms suitable for comparison in searches for chiral centres, their configuration etc., the values in different layers (with raising distance from self) are separated by Nones

Exceptions   
StopIteration
  gen_CIP_sequence_does_something_else 
gen_CIP_sequence_does_something_else (
        self,
        iter_over=None,
        came_from=None,
        )

Exceptions   
StopIteration
  get_free_valency 
get_free_valency ( self )

returns free valency of atom. Aromatic bonds should be localized, otherwise they are counted as simple

  get_neighbors_CIP_sorted 
get_neighbors_CIP_sorted ( self )

return neighbors sorted according to the CIP rules

  get_x 
get_x ( self )

  get_y 
get_y ( self )

  get_z 
get_z ( self )

  has_aromatic_bonds 
has_aromatic_bonds ( self )

  is_chiral 
is_chiral ( self )

this code is CIP (Cahn-Ingold-Prelog) based and therefore not necessarily the fastest for this job, however in newer versions it will be able to take care of the chirality of other centres and therefor will be universal, for now it takes only care of the connectivity

  raise_valency 
raise_valency ( self )

used in case where valency < occupied_valency to try to find a higher one

  raise_valency_to_senseful_value 
raise_valency_to_senseful_value ( self )

set atoms valency to the lowest possible, so that free_valency if non-negative (when possible) or highest possible, does not lower valency when set to higher then necessary value


Table of Contents

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