Table of Contents

Class: atom ../bkchem/oasa/oasa/atom.py
Base Classes   
chem_vertex
Methods   
__init__
__str__
gen_CIP_sequence
get_neighbors_CIP_sorted
is_chiral
matches
raise_valency
raise_valency_to_senseful_value
  __init__ 
__init__ (
        self,
        symbol='C',
        charge=0,
        coords=None,
        )

  __str__ 
__str__ ( self )

  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
  get_neighbors_CIP_sorted 
get_neighbors_CIP_sorted ( self )

return neighbors sorted according to the CIP rules

  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

  matches 
matches ( self,  other )

  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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