Enhancements to reaction templates and assemblers

[timbernat]

Numerous feature expansion are planned for rdutils.reactions and the related rdutils.bonding, including:

• reaction.reactions :
  • make labels for functional groups in AnnotatedReaction more specific (viz wild-type R-group atoms)
  • Reimplement R-group labelling to not require edit to MolFileBlock (can label linker sites simply with rdmol.GetAtom().SetProp(“dummyLabel”, “R”)
• reactions.assembly : Implementing JSONification of reaction assemblers. This would involved implementing JOSNSerializers for RDKit Mols to SMILES and SMARTS
• reactions.assembly : implementing product stereoisomer enumeration and probabilistic reaction pathways. Would require, as a subgoal, detailed option passing for rdChemReactions.ChemicalReaction sanitization flags (which are separate to the default SANITIZE_FLAGS)
• reactions.fragment : implementing an IntermonomerBondIdentificationStrategy which supports ringed molecule cleavage via search for bridge edges coinciding with newly-formed bonds