I recently generated some libraries with the Reactor and I found some badly generated structures. Is there any function in IJC or among Chemaxon's product which can do the structure check for a whole database. I know that for single compounds I can do it in the Marvin's Structure menu. But what if I want to do it for the whole database?
By checking, you presumably refer to cleaning structures so that they display nicely?
If so then Marvin does indeed have a function for doing this type of operation, and probably the most useful is to do a 2D cleaning. There are several approaches that could probably be used, but one that might be useful can be done inside IJC is described here:
1. create new standardizer file. (File -> New File...).
2. choose the new empty standardizer and it will be added to your project
3. the editor for the standardizer will open in the main window
4. add the Clean2D action to teh set of actions (plus any others you might want)
5. close the editor
6. r-click the standardizer file int he projects window and choose 'Standardize...'
7. specify you input file (the output from reactor) and perform the standardization
8. import the standardized file into IJC as usual.
If this doesn't help then there are probably alternative ways of doing this outside IJC.
No. My problem is not to see nice molecules, but to see chemically correct entities. I mean no 5 valence carbon and 4 valence nitrogen. In Marvin's structure menu there's an option: check structure which investigates if there are problems with valency, charge etc.. This concerns the rude chemical structure. I'm interested in that if this option of Marvin can be extended to whole databases and not just for solo compounds. If there's something that for exemple during import signs if it found a record with chemically irrelevant structure. So to simplify my question: Is there any mean to launch Marvin's check structure function for more than one compound the same time?
I'd like to be sure that the 23k compounds generated in Reactor is at least chemically correct, if we can synthetize them it's an other question.
No. My problem is not to see nice molecules, but to see chemically correct entities. I mean no 5 valence carbon and 4 valence nitrogen.
First check your reaction definitions. Reactor allows you to generate 5 valence carbons, but with a proper reaction schema it can be avoided.
Is there any mean to launch Marvin's check structure function for more than one compound the same time?
Marvin 5.4 will contain Structure Checker application; it will be similar to Standardizer, and will check/fix structures in batch mode.
Until 5.4 is released you can use hasValenceError() Chemical Terms function to filter out structures with valence errors. Let us know if you need more help on this.
Thank You Guys!
This is exactly what I was intersted in!