`coordgen!()` changes chirality from unspecified to specified

[hhaensel]

Here's a demo with the demo molecule from tests

julia> txt = read("MolecularGraph/assets/test/demo.mol", String);

julia> mol = sdftomol(IOBuffer(txt));

julia> i1 = inchi(mol);

julia> coordgen!(mol);

julia> i2 = inchi(mol);

julia> compare_inchi(i1, i2)
Comparing InChI layers:
[6][b] ✗ different:
    1: b7-5+,8-6+,11-9?;
    2: b7-5+,8-6+,11-9+;
false

I tried to track it down to libcoordgen.setStereoCenter() and libcoordgen.setStereoBond(), but I couldn't find the definition in the coordgenlibs repo.
@mojaie Could you help me where that is defined? I already tried passing in 2 (unspecified) for undefined parity, but that didn't help.
Here's the helper function that I used above, we might add this to repo as well?

# utility function to compare inchi strings
function compare_inchi(i1::String, i2::String; verbose::Union{Symbol, Bool} = :fail)
    identical = true
    # strip "InChI=1S/" prefix if present
    strip_prefix(s) = startswith(s, "InChI=") ? split(s, "/", limit=2)[2] : s
    s1 = strip_prefix(i1)
    s2 = strip_prefix(i2)

    # split into layers
    layers1 = split(s1, "/")
    layers2 = split(s2, "/")

    maxlen = max(length(layers1), length(layers2))
    (verbose == false) || println("Comparing InChI layers:")
    for i in 1:maxlen
        l1 = i <= length(layers1) ? layers1[i] : "(none)"
        l2 = i <= length(layers2) ? layers2[i] : "(none)"
        tag = first(l1, 1)
        if l1 == l2
            (verbose == true || verbose == :all) && println("[$i][$tag] ✓ identical: $l1")
        else
            identical = false
            verbose == false || begin
                println("[$i][$tag] ✗ different:")
                println("    1: $l1")
                println("    2: $l2")
            end
        end
    end
    return identical
end

[mojaie]

I just forked and added minimizerInterfaceC.h and minimizerInterfaceC.cpp to coordgenlibs.
https://github.com/mojaie/coordgenlibs/blob/cinterface/minimizerInterfaceC.cpp

I’m not sure, but I found some cases that coordgenlibs cannot parse wedges correctly (or I may not fully understand coordgenlibs' stereo features correctly.). And InChI may also have similar issues.