Place reactants instead of products

[kate-fie]

As of now, Fragmenstein places products in the pocket which are then fed into HIPPO. Those that cannot be minimized within the time constraint or have an RMSD over the set threshold are thrown out. This is the bottleneck of the pipeline, placing all the chosen reactant combinations.

What if I placed the reactants instead of the full products?

• If the reactant clashes, then the product won't fit
• Atom mapping from reactant to fragment should not be too difficult -> would have to determine which fragment the reactant corresponds to. Could do reactant to fragment labelling from base compound.

[kate-fie]

I don't think this is enough of a bottleneck to add. I think there is a significant benefit to placing the full compound instead of the reactants.

1. Dependable way to find 'reaction atoms' to restrict movement for.
2. The restriction of the 'reaction atoms' might not accurately match the full compounds accessible angle and bond distances.