same structure different smiles code

JChem4Excel: 5.11.2.820

MarvinSketch: 5.11.2

Dear Sir,

I have a
problem with smiles codes from the same structures. The structures in the file
were differently generated with MarvinSketch. If I change the ortho fluoro atom
in the difluorophenyl substituent into the other ortho position the smiles code
is also changing.

With kind
regards,

Peter
Schneider

Hi Peter,

You can find a detailed description of different types of SMILES strings we are generating here:

http://www.chemaxon.com/marvin/help/formats/smiles-doc.html

In JChem for Excel we are generating the so called "generic SMILES", which takes into account only the order of the atoms in molecules, this way for your orto substituted derivatives it is possible that different SMILES strings will be generated.

Hope this helps, but let me know if you have further questions.

Regards,

Anna

Hi Anna,

how can I make a unique smiles. If I change the phenyl to an aromatized phenyl, then both smiles are the same!

Kind regards,

Peter

Hi Peter,

You can use a JChem for Excel function (JCMolFormat) to specify the type of SMILES to be generated, please check in the attached file. In "Generic SMILES" column you can find the ones generated with the default algorithm, in "Unique SMILES" column the ones, which have been generated with :u option. If you would need more information about JC4XL functions, you can find it here:

http://www.chemaxon.com/jchem4excel/userguide/jchemexcelfunctions.html

Regards,

Anna

Hallo Anna,

thank you for the helpful help and the demonstration file.

Is it also possible to use "smiles:u" also in a VBA environment? and how?

many thanks,

Peter

If you hit Alt(left)+F11 you will go to the VBA environment.

If you use Ctrl+G then the Immediate window is available for you.

Please type:

?Application.Evaluate("JCMolFormat(A2,""smiles:u"")") and then press Enter.

The expression will be evaluated. The result printed out there: Fc1ccc(OCC(=O)N2CCC(C2)c2ccccc2F)c(F)c1

Code:

if you add a module and type a new global function in this way:

Public Function Test(ByVal cCell As Range)
      Test = Application.Evaluate("JCMolFormat(" & cCell.Address & ",""smiles:u"")")
End Function

And call it from immediate window:

?Test(ActiveCell)
Fc1ccc(OCC(=O)N2CCC(C2)c2ccccc2F)c(F)c1

 

I hope this helps,

Viktor 

Dear Viktor, dear Anna,

your explanations and examples were of big help, thank you very much.

With kind regards,

Peter

schnpete wrote:

Dear Viktor, dear Anna, your explanations and examples were of big help, thank you very much. With kind regards, Peter