Tautermization strips stereo information

Hi,

I am running a basic standardization to return the canonical tautomer.

However, in this sample case the tautemerization is removing the stereo information.

Is this the expected behavior. Is there a way to preserve the stereo information after applying the tautomerize rule?

 

Running version 5.3.1.

 

Cheers,

Guy

Hi,

I am running a basic standardization to return

 the canonical tautomer.


However, in this sample case the tautemerization is removing the 

stereo information.


Is this the expected behavior. Is there a way to preserve the 

stereo information after applying the tautomerize rule?

This is  a bug of the canonical tautomer generation. It was fixed. Now we test the fixed 5.3.2 version.

What kind of command line do you use for generating the canonical tautomer?

 

Jozsi

Great.

When is the release date for 5.3.2?

For the sample tautomer I used the standardizer gui.

In real life, I access the standardizer through java.

Do I get different behavior if I access it through the command line?

Hi,

When is the release date for 5.3.2?

It will available in a couple of days. We test the beta version now.

Do I get different behavior if I access it 

through the command line?

No, you will get the same result. 

I just thinking  about the "standardization".  Whether the "tautomerization" should be part of the "standardization" or not.

As you know the "tautomterization" is an indepndent tool of Marvin.

The "standardization" invokes the "tautomterization" tool through the "canonical tautomer" option.  I sketched  the 4 alternative ionic forms of your simple example in Marvin's canvas and I generated the "canonical tautomers". 

Is it not a better way for you to use this independent "tautomerization" tool and subsequently apply the "standardization" (if neccessary at all)?

 

I  wonder what do you mean on  the "standard tautomeric" form: what is it?

 

 

Jozsi

Hi,

I'm using the Standardizer (5.3.0.2) to help identify duplicates.  (I'm working with Guy on this.)  The picture attached here shows the input files (three structures on the top line), output file (after running through the Standardizer using Tautomerize to generate the canonical tautomer) and the output I had expected to get (bottom three structures).  

The point here is that the first two input structures are the same and the third input structure is different;  thus I would expect the output to show two identical structures and one that is different.  But instead, the output shows three identical structures and both the up/down bonds and the Absolute flags have been removed.  

Is there a way to generate the correct output?

Hi,

I fixed this bug. The fix will be available in the 5.3.3 version.

Thanks for the bug report.

 

 

Jozsi