Is there a easier way to clean all structures

Hi,

I imported structures from sd file., but the structures do not look nice. I am cleaning the structure one by one now.  Is there an easier way to clean all structures at once?

Thanks

Probably the easiest way is to clean the structures before importing. You can do this by applying a standardizer  to your file. This will generate a new file of "corrected" structures. You could apply any standardizer rules, but the relevent one would be the clean2d action. See here for details of how to do this:
http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/standardizing_structure_files.html />Once you have corrected the structures you would import as normal. You would need a standardizer license to do this.

Alternatively, if you had to do this on structures that had already been imported then it would be possible to write a script that iterated through all the structures and applied a clean2D on them, and saved the cleaned structure back to the database. You would of course need to write the script that does this. If you need any help with this then let us know.

Tim

Thanks Tim. I followed the procedure you showed me to apply a standardizer, but it seems it did not work. The 1st pic is 'after standardize', the 2nd pic is 'standardizing', the 3rd pic is 'before standardizing'. Can you give me more suggestion?

Hi,

First the obvious question - you did re-import the standardized SD file after you had applied the standardizer to it (the file that was output, not the input file)?

Assuming so, what part is not working for you? Are you saying that none of the standardizer actions have been applied, or is it just a question of the clean2D not working to your satisfaction?

Tim

Tim,

I re-imported the standardized sd file after I applied the standardizer. The reason I am saying it is working is because the structure 198 before standardzied in pic 3 and the structure 198 after standardized in pic 1 are almost same.

Could you send that structure (as molfile or mrv format). It certainly looks a mess, and clean2D would be expected to improve it, but its not clear form the picture exactly what the structure is.

Tim 

Tim,

Thanks for your help. Most structures in database are good, I will clean the structrue manually.