Fragmenter and duplicate fragments.

I'm trying to use Fragmenter to produce an sdf table entry of every fragment for a given molecule and preserve the 3D coordinates for each. But when ever there are two duplicate fragments, they are merged into the same table entry (COUNT is increased) and subsequent 3D coordinates are lost. Is there a way to produce a unique table entry for each fragment, regardless of how many times it has appeared before?





Help is appreciated!

Fragmenter is a 2D tool that ignores conformation of the fragments created. In the present information the functionality you require is missing, I am afraid.





You can try to combine various ChemAxon components in your custom application/pipeline to generate the information you need. Use Fragmenter to generate your 2D fragment pool then apply MolSearch in your original 3D input to find the 3D fragments. It's not so straightforward, I admit, though all components needed are available. Does this help at all?





Regards,


Miklos