To-Do List

FragmentRetro

• Finish Retrosynthesis class
• Create a Solution class to visualize retrosynthesis "solutions".
• Rewrite is_substructure_BBs such that BBs change at every stage (take out unnecessary BBs).
• Write tests for the CompoundFilter class (with or without filter should work the same for substructure matcher)
• Write tests for the RetrosynthesisSolution class
• Write tests for the parallelization of substructure matcher
• Write tests for BRICSFragmenter.
• Write tests for get_combination_smiles.
• Ignore chirality at the neighbor of dummy atoms for is_strict_substructure.
• Confirm that SubstructureMatcher.addH_to_wildcard_neighbors is the most efficient way to do is_strict_substructure.
• Write tests for the Retrosynthesis class

New Fragmentation Rules

• Come up with ring fragmentation rules that covers enough common types of rings in drug-like compounds.