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Monster entrypoints

Previously merging in Monster was overly complicated and an add-on, now it is cleaner as the initialisation of the object does not do a placement. To do that one has to do:

monster = Monster(hits)
monster.place(mol)
monster.positioned_mol

or place_smiles for a SMILES.

While to do a merger

monster = Monster(hits)
monster.combine()
monster.positioned_mol

Additionally, the attribute modifications was added/expanded, so that intermediate steps are stored for potential inspection. It is a dictionary, but since 3.6 dict is ordered and .keep_copy(mol, label) prevents over-writes. This includes scaffold (the template) and chimera (the template with the atom symbols adapted), which are no longer attributes.

Equally viable alternatives are stored in a list

monster.mol_options

combine still calls simply_merge_hits, which is used by placement too and merges by fragmentation —unlike atom-ring absorption events. The fact that two different approaches are present is just historical.

If one wanted to merge two or more hits, independently of those in .hits attribute and without ring collapsing and rectification etc. simply_merge_hits is still the method to use:

monster = Monster([])
monster.simply_merge_hits([molA, molB])

The place method accepts the argument merging_mode, by default it is "permissive_none", which calls .no_blending(broad=True), but "off" (nothing), "full" (.full_blending()), "partial" (.partial_blending()) and "none" (.no_blending()) are accepted.

Names

The names "merge" and "place" were ultra-confusingly ambiguous when it comes to the other methods, especially those of "place".

  • Now all the cases where hits are partially combined for placement purposes are called "blending" The placement of the (distorted) 3D final monster compound Victor is called "plonk".

  • place and position are used synonymously

  • combine and merge are used synonymously

Future

Victor however still has the merger as a side route.

Overlapping rings

There was a bug in the code for Monster that meant that if two rings from different origins that were not bonded —i.e. without side atoms that were absorbed they were not assessed for merging. This has been corrected.

Namely, what happens to rings is controlled in expand_ring method, which calls _add_novel_bonding, where "novel" means that does not share the same "origin" (original molecule). The latter method calls in turn _get_novel_ringcore_pairs, which now get ring marking atoms that are close or bonded. Closeness is determined by ring atoms (not ring core markers) within 1.5 Å cutoff (viz. _get_close_nonorigin_ringcores)

The test case was the merger of a phenylacetic acid and phenylacetamide which overlap in two ring carbons and a terminal oxygen, resulting in a phenylene-like ring (where one ring is an oxazine). See tests.

phenylene