Partial parity

When inserting a structure I 've got sometime the following message : Warning : Partial parity information is applied





What does it mean ? what are concequences ? how can I catch this warning ?





Thanks

I suppose you are inserting a SMILES string.


In this case 2D coordinates are generated, and the parity specified in the SMILES string should appear as up/down wedges in the molecule. You get this warning because it was not possible to arrange the wedges to get the same parities specified in the SMILES string.


As a consequence the molecule you have in the viewer has less parity information than in the SMILES string.


Actually you cannot catch this warning.

Could you write me the problematic SMILES if possible, to examine the problem more deeply.

Sorry but I don't try to insert any smile ... it is a molfile and I as I can't catch this warning I can not say which of my 47000 moecules is concerned ...

To detect the problem I need your help. Where from and where to have you inserted this molfile.


A Molfile usually has the 2D coordinates already, so I have to find out why your program gets into the 2D cleaning process (where this warning is originated from).


Don't you use somewhere in your code molecule cleaning:

Code:

molecule.clean(2,...);

Hello,





i have a similar problem. The warning:


Warning: Partial parity information is applied.


appears when applying the pKaPlugin to mol-Files.


An example for an affected file is attached.





sincerely seb

Seb,


What do you do exactly when you get this message? I cannot reproduce the error.


Anyway, you can neglect the warning, because the problem will not have any influence on the prediction.