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MathGroup Archive 2009

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Re: ChemicalData[], SMILES, EdgeRules


If you can convert the SMILES string to a molecular formula in Hill 
display order (I think), then you can use ChemicalData on this string. 
For example:

In[19]:= Pick[ChemicalData["C10H16"], ChemicalData["C10H16", "SMILES"], 
"CC1=CCC2CC1C2(C)C"]

Out[19]= {"PlusMinusAlphaPinene", "AlphaPinene", "PlusAlphaPinene", 
"MinusAlphaPinene"}

Carl Woll
Wolfram Research

Scot Martin wrote:
> 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
>
>
>
>   



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