Filtering for nonhydrogen bonds and hydrogen bonds

[jeleclaire]

BiochemicalAlgorithms.jl/src/core/bond.jl

Line 269 in c7011f8

@inline non_hydrogen_bonds(ac) = filter(b -> !haskey(b.properties, :TYPE__HYDROGEN), bonds(ac))

• To do: It seems that test cases for these little helper functions are still missing.

• Consistency: I am wondering if TYPE__HYDROGEN should not better be a flag than a property. For instance, residues can be tagged with C-Terminal or 5-Prime as flags... what is again the definition for properties or flags?

[tkemmer]

what is again the definition for properties or flags?

Flags are just symbols associated with an entity. Properties can additionally be assigned values, e.g.:

BiochemicalAlgorithms.jl/src/fileformats/pubchem_json.jl

Line 120 in c7011f8

mol.properties[Symbol(d.urn.label)] = d

If we don't need to assign any additional information to :TYPE__HYDROGEN, this should indeed rather be a flag than a property.