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MathGroup Archive 2009

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ChemicalData[], SMILES, EdgeRules

  • To: mathgroup at smc.vnet.net
  • Subject: [mg103990] ChemicalData[], SMILES, EdgeRules
  • From: "Scot T. Martin" <smartin at seas.harvard.edu>
  • Date: Wed, 14 Oct 2009 07:58:59 -0400 (EDT)
  • References: <hb1ntf$son$1@smc.vnet.net> <200910140319.XAA22431@smc.vnet.net>

I have used ImportString[%,"SMILES"] to obtain the following from 
Mathematica:

{"EdgeRules" -> {{1 -> 2, 2 -> 3, 2 -> 4, 4 -> 5, 4 -> 7, 5 -> 6}},
  "EdgeTypes" -> {{"Single", "Double", "Single", "Single", "Single",
     "Single"}}, "FormalCharges" -> {{0, 0, 0, 0, 0, 0, 0}},
  "VertexTypes" -> {{"C", "C", "O", "C", "C", "O", "O"}}}

My question is: how do I next use this information? I would like to have 
access to all of the ChemicalData[] functionality, such as drawing a three 
dimesional structure, molecular weight calculation, "ElementTally", and so 
forth.

However, I cannot find any way that Mathematica will recognize the Rules 
list produced as output from ImportString as an input for chemical 
structure for use by ChemicalData[].

Anyone have hints?





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