[Zinc-fans] Comparison mol2 and smiles files

[John J. Irwin]

Hi Emanuele

I am finally getting back to your question. You are quite correct. I
just did:


>  zmore sial_p0.smi.gz | awk '{print $2}' | sort -u > smiles_codes  
>  zcat sial_p0.?.mol2.gz | grep ZINC | sort -u > mol2_p0_codes
>  wc -l smiles_codes mol2_p0_codes
 114763 smiles_codes
 112069 mol2_p0_codes
> diff smiles_codes  mol2_p0_codes  |wc -l
4265

I agree that there are a little over 2,500 differences in the mol2 and
SMILES of Sigma Aldrich in ZINC version 7, a little over 2% of the
library. This is of course wrong, and we will attempt to do better in
future versions.

Thank you for reporting this. I have put it on the ZINC errata page,
which I am finally getting around to updating.
http://wiki.compbio.ucsf.edu/wiki/index.php/ZINC:Errata

John



emanuele wrote:
> Dear all ZINC-fans,
>
> I downloaded the databases Asinex and Sigma-aldrich from the version 7 
> of ZINC in both the formats SMILES and MOL2.  For both the databases I 
> found a difference in the molecules present in the archives, that means 
> some molecules present in the multi-mol2 file and not in the SMILES and 
> vice versa.
>
> Is it possible or I did some errors in the comparison?
>
> Thanks in advance
> Regards,
>
> Emanuele
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