[Zinc-fans] SMILES?

[John J. Irwin]

Hi Reddy

When you ask "what kind of SMILES", I take it you are asking about the 
canonicalization scheme, since all SMILES should conform to the rules 
outlined in the Daylight Theory Manual.  
http://www.daylight.com/dayhtml/doc/theory/index.html

The SMILES you see in ZINC are mainly manipulated using OEChem, with 
some fine tuning to cope with some of the ambiguities of equivalent 3D 
structures.  For example, we take a 3D model and use OEChem to convert 
it to isomeric SMILES. However, a tertiary ammonium with all three 
substituents distinct is rendered as [N@@H+] or [N at H+], even though 
inversion is fast under assay conditions. Thus we remove the chiral 
specification at this N atom. There are dozens of other idiosyncratic 
examples, which I hope to get into a paper one of these days. It turns 
out, we still get (lots of) things wrong. But we are working on it, and 
we are slowly getting better.

ZINC SMILES are standard enough that they should be readable and 
interpretable by any program that expects SMILES.

I hope this is helpful.

Cheers

John


Reddy Tummala wrote:
>
> Hai,
> You have given SMILES format as an option to down load the molecules 
> from ZINC DATABASE
>
> May I ask you what types of smiles are these: original smiles? or Day 
> light smiles? or Conversational smiles?
>
>
> Thanks
>
> Dr.T.R.K.Reddy
>
>
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