Rattler-build recipe, geometry alignment, intramolecular beta scissions #493
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Type inconsistency between set and list.
Gearing up to implement central geometry alignment, to avoid bugs.
Next step is to route all `geo_idx_dct` handling through this function. It works as follows. Given a graph, a geometry, a `geo_idx_dct`, and some set of graph key arguments, the alignment function is called like so: ``` gra, geo, args, idx_dct = graph.align_with_geometry(gra, geo, args, geo_idx_dct) ``` This puts the graph keys in consecutive order and reorders the geometry atoms to match the graph. It also remaps the graph keys in `args` onto the new (consecutive) graph keys. The `idx_dct` returned can be used to undo the reordering of atoms in the geometry: ``` geo = geom.reorder(geo, idx_dct) # restore the original order ```
I'm switching over in stages to check for bugs
Simplifies confusing geometry embedding code and brings some sanity to the handling of mis-aligned graphs and geometries with `geo_idx_dct`s
If marked as stereogenic rather than excluded, these are ring-opening TS
graphs and the bond has ambiguous stereochemistry
O O
\ / \ \ /
C---C* -> C===C
/ \ / \
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