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Re: ChemicalData[], SMILES, EdgeRules

  • To: mathgroup at smc.vnet.net
  • Subject: [mg104012] Re: ChemicalData[], SMILES, EdgeRules
  • From: Armand Tamzarian <mike.honeychurch at gmail.com>
  • Date: Thu, 15 Oct 2009 07:18:46 -0400 (EDT)
  • References: <hb1ntf$son$1@smc.vnet.net> <200910140319.XAA22431@smc.vnet.net>

On Oct 14, 6:59 am, "Scot T. Martin" <smar... at seas.harvard.edu> wrote:
> 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 thre=
e
> dimesional structure, molecular weight calculation, "ElementTally", and s=
o
> 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?

Can you provide more details? For started when you use GraphPlot with
those rules you don't get a molecular structure you get 4 unconnected
lines so I think the file you imported to generate those rules is
unusual.

ref/format/SMILES

ChemicalData[] can be used to produce SMILES information but it
doesn't follow -- at least as far as I know -- that given the SMILES
information you can then identify the molecule in ChemicalData[] which
is what you appear to be wanting to do (???)

Mike


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