option for checking duplicates
I wanted to know is there any option for checking duplicates in instant Jchem
I checked the « duplicates removal » option when importing sd files into a JChem table. However, I would like to remove duplicates without taking stereochemistry into account (I attached some examples). Is there any way to perform this operation?
Many thanks in advance.
Yes, you can do this, but you need a Standardizer to do it.
You should define a standardizer for your JChem table and include the clear stereo action in its definition (you should also have aromatize and Remove Explicit Hydrogens - see the screen shot).
Then when you import into that table the stereo duplicates are detected and not imported (see screen shot).
This way you end up with just the non-duplicate structures. The one you have is the first one that was found, which may be chiral (see screen shot).
If you want all structures to have the stereochemistry removed prior to import then you should create a standardizer file that includes the clear stereo option and process your file with that prior to importing. See:
If you do this I have found a small bug with the JChem version that is used with IJC1.0.7 - you need to first aromatize the structures before you can clear the stereo (and then you can de-aromatize afterwards). This bug seems to be fixed in the development version of JChem so this work around will not be needed in future.
Note: to do any of this you will need a Standardizer license.
Thanks a lot. It works perfectly. Still one problem: when I cut and paste from structure column to do a substructure search on the whole table, I have the message "Quey returned no hits", even when I "standardize" the query!
What do you think about this?
Not sure. It seems to be working for me with IJC1.0.7 and the small file you provided. I can paste a structure from the grid view to the query and it runs correctly when I do a substructure search.
Which IJC version are you using (what does it say at the top of the Welcome screen)?
The query structure will be standardized automatically. So if you have standardized your JChem table so as to remove the stereochemistry the same will be done to your query.
I am using the 2.0.0 version. Hereafter some screenshots ...
This seems to be working for me in 2.0.
Did you remember to add the standardizer actions for aromatize and remove explicit hydrogens, as well as the clear stereo action?
The aromatize and remove explicit hydrogens actions are the default standardization, and without these searches for aromatic structures (such as the one in your screen shot) will give inconsistent results (depending on how the query is drawn).
Tim, I found the error when taking a screenshot of the standardization I applied. I was adding the explicit H instead of removing them!! :-\ SSS is now working and this did not change the number of removed molecules.
Thank you very much for your precious help.
I was just in the process of writing a response to say that I was baffled because it seemed to be working for me.