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Standardizer Stripping Stereochemistry
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Scott

Joined: 25 Nov 2012
Posts: 4

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Link to postPosted: Fri Aug 22, 2014 5:37 pmPost subject: Standardizer Stripping Stereochemistry Reply with quote

Hi,

It appears that standardizer is stripping stereochemistry from CHEMBL100.

Attached is the standardizer config we used and the original CHEMBL100 in sdf format ("chembl100_original.sdf")

chemaxon/jchem/bin/standardize -c standardizer.xml -f smiles:un -o cheml100.smi chembl100.sdf
The output is the following without stereochemistry information
CC1(C)Oc2ccc(cc2C(C1O)N1CCCC1=O)C#N
It should output
CC1(C)Oc2ccc(cc2[C@H]([C@@H]1O)N1CCCC1=O)C#N
We have attached a working sdf that does render the correct smiles after standardization.( chembl100_working.sdf)
Is there something wrong with the chembl mol format?



 Filename: standardizer_chembl100.zip    Filesize: 1.95 KB    Downloaded: 39 Time(s)
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Peter
ChemAxon personnel
Joined: 28 Feb 2008
Posts: 310

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Link to postPosted: Mon Aug 25, 2014 1:52 pmPost subject: Reply with quote

Hi Scott,

I think you've mixed up the original and the working files.

The problem is in the header line of  the file:

SciTegic01161211223D

This tells our importer to interpret the file as a 3D molecule, but the coordinates are missing for the third dimension, therefore the parity information is missing.

If you change this line to

SciTegic01161211222D

then the stereo information is preserved.

I could not find this sdf file in ChemBl, all the downloaded files had the correct header line. Could you let us know how you've downloaded this file?

Best regards,

Peter

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