Methods
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__init__
__str__
gen_CIP_sequence
get_neighbors_CIP_sorted
is_chiral
matches
raise_valency
raise_valency_to_senseful_value
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__init__
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__init__ (
self,
symbol='C',
charge=0,
coords=None,
)
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__str__
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__str__ ( self )
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gen_CIP_sequence
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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
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get_neighbors_CIP_sorted
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get_neighbors_CIP_sorted ( self )
return neighbors sorted according to the CIP rules
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is_chiral
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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
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matches
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matches ( self, other )
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raise_valency
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raise_valency ( self )
used in case where valency < occupied_valency to try to find a higher one
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raise_valency_to_senseful_value
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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
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