Re: ChemicalData[], SMILES, EdgeRules

*To*: mathgroup at smc.vnet.net*Subject*: [mg104062] Re: ChemicalData[], SMILES, EdgeRules*From*: "Scot Martin" <smartin at seas.harvard.edu>*Date*: Sat, 17 Oct 2009 07:04:15 -0400 (EDT)*Organization*: Harvard University*References*: <hb1ntf$son$1@smc.vnet.net> <200910140319.XAA22431@smc.vnet.net> <200910151118.HAA09216@smc.vnet.net>*Reply-to*: <scot_martin at harvard.edu>

Mike, Thank you for your input on this. Here's the further information you asked about, most grateful if you can be helpful. First, what I am trying to do essentially? I have about 500 SMILES strings in a text file and I want to get the element count in each (i.e., number of carbon, oxygen, etc.). So, my plan was, "ImportString[] with SMILES and then use 'ElementTally' of ChemicalData[]." I was surprised, however, that I couldn't convert the SMILES data from ImportString[] into a format for ChemicalData[ ]. Here is some more specific information: In[1]:= ImportString["CC1=CCC2CC1C2(C)C", "SMILES"] Out[1]= {"EdgeRules" -> {{1 -> 2, 2 -> 3, 2 -> 7, 3 -> 4, 4 -> 5, 5 -> 6, 5 -> 8, 6 -> 7, 7 -> 8, 8 -> 9, 8 -> 10}}, "EdgeTypes" -> {{"Single", "Double", "Single", "Single", "Single", "Single", "Single", "Single", "Single", "Single", "Single"}}, "FormalCharges" -> {{0, 0, 0, 0, 0, 0, 0, 0, 0, 0}}, "VertexTypes" -> {{"C", "C", "C", "C", "C", "C", "C", "C", "C", "C"}}} In[2]:= GraphPlot[First["EdgeRules" /. %]] Out[2]:= :: graphics :: For comparison, this molecule is alpha-pinene: In[3]:= ChemicalData["AlphaPinene"] Out[3]:= :: graphics :: In[4]:= ChemicalData["AlphaPinene", "ElementTally"] Out[4]= {{"C", 10}, {"H", 16}} In[5]:= ChemicalData["AlphaPinene", "SMILES"] Out[5]= "CC1=CCC2CC1C2(C)C" But how to get ImportString to communicate to ChemicalData[] that I mean "AlphaPinene"? Scot -----Original Message----- From: Armand Tamzarian [mailto:mike.honeychurch at gmail.com] Sent: Thursday, October 15, 2009 07:19 To: mathgroup at smc.vnet.net Subject: [mg104062] [mg104012] Re: ChemicalData[], SMILES, EdgeRules 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:*Carl Woll <carlw@wolfram.com>

**Re: ChemicalData[], SMILES, EdgeRules***From:*Carl Woll <carlw@wolfram.com>

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

**Re: ChemicalData[], SMILES, EdgeRules***From:*Armand Tamzarian <mike.honeychurch@gmail.com>