After updating to 5.7 we cannot do substructure searches!!!

User 40fe9b3632

28-11-2011 15:47:19

Is this a general bug?


We can draw and run the searches, but the answers are wrong. Eg if we draw a methyl group (no explict hydrogens) we do not find eg acids or alcohols, but we do find CF3


Thanks,


Thomas


 


 


Details from About Instant Jchem below:


Instant JChem Version: 5.7.0 (build: 201111280314-159231)
JChem Version: 5.7.0
JChem Table Version: 5070000
Marvin Version: 5.7.0 (build date: 2011-11-07)
Java: 1.6.0_18; Java HotSpot(TM) Client VM 16.0-b13
System: Windows 7 version 6.1 running on x86; Cp1252; da_DK (instantjchem)
NetBeans build: 110214-aec102d89c78
Userdir: C:\Users\tb\AppData\Roaming\.instantjchem\ijc_5_4
Java Web Start: No
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ChemAxon 60ee1f1328

28-11-2011 17:48:31

Hi Thomas,


I think we need some further information to resolve your issues please.


Using the 5.7 IJC release, for example:


Running such a query as below, in a test set I have accessed, will give a terminal methyl found and highlighted in each case as expected.


"[H]C([H])[H]"


Running such a query as below in the same set will return the whole set as is probably expected for such a broad query. In that set I can see examples of OH, COOH and CF3 as well as many other functionalities.


"C"


(The highlighhted Carbon (blue) can be found in various places (not terminal) depending upon the record) 


I did my simple tests using Derby. Did you use Oracle?


Is it possible to share the data set you used so we can see examples of what you are expecting to find in your table?


Thanks,


Daniel. 


 

User 40fe9b3632

29-11-2011 08:07:15

Hi Daniel,


We are using a MySql database. I have looked into the problem a little bit more this morning, and I think I havce solved the problem for now, but I still think there's a bug, although I am not sure I have understood completely.


Because we had the experience that stereo centers were not displayed correct, we spoke to Tim about it and he suggested to remove the "clean 2D" function from our standadizer. I did that yesterday, and also removed the Aromatize function, so the only thing in the standardizer was "no-explicit hydrogens".


This morning I have added the "Aromatize" again, and now I can do substructure searches again. Also stereocenters are displayed correct.


Thanks,


 


Thomas

ChemAxon 60ee1f1328

29-11-2011 09:59:25

Hi Thomas,


Thanks for the information on the resolution & of course glad to hear it solved for you.


I will leave this open for a while longer in case your issue re-emerges in any sense.


Daniel.