Brent Westbrook

@lucasfijen Thank you so much! I cloned the repo and can now reproduce!

Ah yes, I should have mentioned that in the issue! The root problem is indeed the Omega conformer generation. I also noticed that despite there being 52 records, there are...

I tried adjusting some of these settings to no avail. I tried slapping some zeros on things (`SetEnergyWindow(1500.0)`, `SetRMSThreshold(100.0)`), setting both of these options to zero, and even commenting out...

Here are the un-mapped SMILES. I'll try to reproduce with just OpenEye code. ```text [H]C1(C2=C(N=C(N2C([H])([H])[H])N3C(C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[N@](C([N@]1C([H])([H])[H])([H])[H])C([H])([H])[H])[H] [H]C1(C2=C(N=C(N2C([H])([H])[H])N3C(C(N(C(C3([H])[H])([H])[H])C([H])([H])[H])([H])[H])([H])[H])[N@](C(N1[H])([H])[H])C([H])([H])[H])[H] [H]c1c(nc(c(n1)[N@]2C([C@@]([C@](C2([H])[H])(C([H])([H])[H])O[H])([H])C([H])([H])[H])([H])[H])N(C([H])([H])[H])C([H])([H])[H])[H] [H]c1c(c(c(nc1C([H])([H])[H])[N@@]2C([C@@]3(C(=O)N(C(C(C3([H])[H])([H])[H])([H])[H])C([H])([H])C4(C(C4([H])[H])([H])[H])[H])C(C2([H])[H])([H])[H])([H])[H])C#N)C([H])([H])[H] [H]c1nc(c2c(n1)ON=C2C([H])([H])[H])[N@](C([H])([H])[H])C([H])([H])C3=C(ON=C3C([H])([H])[H])C([H])([H])[H] [H]c1c(c(nc(c1[H])[N@]2C([C@]3(C(=O)N(C(C(C3([H])[H])([H])[H])([H])[H])C([H])([H])[H])C(C2([H])[H])([H])[H])([H])[H])C(F)(F)F)[H] [H]c1c(c(nc(c1C([H])([H])[H])C([H])([H])[H])[N@@]2C([C@@]3(C(=O)N(C(C(C3([H])[H])([H])[H])([H])[H])C([H])([H])C4(C(C4([H])[H])([H])[H])[H])C(C2([H])[H])([H])[H])([H])[H])C#N [H]c1c(c(c(c(c1[H])[H])[N@@](C([H])([H])[H])C([H])([H])c2c(c(c(c(c2[H])[H])[C@]3([C@@](C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])([H])C(=O)O[H])[H])[H])[H])[H])[H] [H]c1c(c(c(c(c1[H])[H])[N@@](C([H])([H])[H])C([H])([H])c2c(c(c(c(c2[H])[H])[C@]3([C@@](C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])([H])C(=O)[O-])[H])[H])[H])[H])[H] [H]c1c(nc(c2c1OC(=C2[H])[H])[N@@](C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])N3C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])[H] [H]c1c(nc(c2c1OC(=C2[H])[H])[N@@](C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])[N+]3(C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])[H])[H] [H]c1c(c(nc(c1[H])[N@](C([H])([H])[H])C([H])([H])C([H])([H])[H])[H])[H] [H]c1c(c(c(c(c1[H])[H])C([H])([H])[N@](c2c(c(c(c(c2[H])[H])[H])[H])[H])C([H])([H])[H])[H])[H] ```

This fails with 2023.1.0 and works with 2022.1.1: ```python from openeye import oechem, oeomega smiles = "[H]C1(C2=C(N=C(N2C([H])([H])[H])N3C(C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[N@](C([N@]1C([H])([H])[H])([H])[H])C([H])([H])[H])[H]" # steps taken from # https://docs.eyesopen.com/toolkits/python/oechemtk/molctordtor.html#construction-from-smiles mol = oechem.OEMol() assert oechem.OESmilesToMol(mol, smiles) omega...

And checking all of them with the SMILES pasted into `smiles.dat`: ```python from openeye import oechem, oeomega win = 0 with open('smiles.dat') as inp: for smiles in inp: mol =...

I'm still running the benchmark to see if this is the root cause of the differences I've observed between the original Sage 2.1.0 fit and my attempt to reproduce it....

I'm not sure if I'm using the `Builder` correctly, but this does fail to run on 2022.1.1 for `AttributeError: 'OEMolBuilderOptions' object has no attribute 'SetIgnoreStereo'`, so that change must have...

I updated my last comment with some additional details and just sent an email to OpenEye support!

Should I close this? Based on the response from OpenEye support, it sounds like a known/expected change from their perspective. And unless we want to propagate the `OEMolBuilderOptions` or `OEOmegaOptions`...