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

**Follow-Ups**:**Re: ChemicalData[], SMILES, EdgeRules***From:*"Scot Martin" <smartin@seas.harvard.edu>

**References**:**Re: Mathematica 7.01 and Mac OS 10.6 (Snow Leopard)***From:*Joel Reymont <joelr1@gmail.com>