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Documenting a subset of the SMILES language.
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Delocalization Subgraph Section
#8
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rapodaca
closed
2 years ago
rapodaca
commented
3 years ago
VB model makes graphs unequal even though they should be treated as equal
DIME
the DS solution
encodes alternating single-double bond pattern as a perfect matching
maximum, maximal, perfect matching
a node-induced subgraph over VB graph
unlabeled
possibly empty
encodes and therefore guarantees a perfect matching
corollary: every atom will be assigned a double bond
only node membership is specified
edge membership is deduced
composition
atoms
C, N, O, P, S, unknown
selection
adding an atom to the DS
"selected atom", "selected atoms"
"induced bond", "induced bonds"
bonds
by definition (node-induced) both terminals are members
literature refers to "aromaticity"
not using that term because of its (imprecise) meaning in chemistry
algorithmic fill/empty
every molecule expressed with a DS can also be expressed without it
in other words, 1:1 translation
fill algorithm
empty algorithm
aka "kekulization"
examples
invent a notation for node/edge membership (color?, weight?)
graphics only
error states
no perfect matching possible
to re-iterate: DS is just another way to express single/double bond layout