It's great to see these files in place (syn7287882). Thanks @tim.james!
Is it possible for you to upload them to a Synapse Table? It would be great to be able to query them more robustly without downloading them. You can do this through the web interface by navigating to the 'tables' tab and click 'upload table'.
thanks,
sara
Created by Sara Gosline sgosline I've just uploaded an updated set of files where I've corrected the entries for a number of small molecules that were being inappropriately matched in the public databases because they're common counterions/salts. I've also converted the more important files to Synapse tables - please let me know how you get on with them. As mentioned in my previous post, a small number of entries in the the "unique structures" table contain nonstandard SMILES. This extension is necessary to allow the specification of relative stereochemistry in a 2D format - standard SMILES does not allow for this. I've used the ChemAxon extended SMILES only for this small subset of molecules, but I suspect that they may not be parsed correctly by chemoinformatics software from other software suppliers. Sure, I have just uploaded a new version of the files with some extra duplicates removed. I will have a look at the table functionality - I guess that we will need to adjust the SD files by switching the structures to SMILES format, which may create some issues with extended stereochemistry notation as this tends to be somewhat proprietary to different cheminformatics software vendors.