2021-05-19 Reproducing Lim results with Season 1 components meeting notes

Use of <group>-<mol>-<conformer> in codebase

Lorenzo

• In the analysis module, for many analyses we rely on a clear separation by molecule, conformer. Need to be able to do this on the Lim set as well.

  • DD: Lim dataset has a clear pattern that is analogous to what we used for Season 1:

    • ['C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-0', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-1', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-2', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-3', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-4', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-5', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-6', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-7', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-8', 'C[NH2+]C[C@@H](c1ccc(c(c1)O)O)O-9', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-0', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-1', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-2', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-3', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-4', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-5', 'CO/N=C/1\\C[N@](C[C@H]1C[NH3+])c2c(cc3c(=O)c(cn(c3n2)C4CC4)C(=O)[O-])F-6', 'c1cc(ccc1[C@H]2C[NH2+]CCc3c2cc(c(c3Cl)O)O)O-0', 'c1cc(ccc1[C@H]2C[NH2+]CCc3c2cc(c(c3Cl)O)O)O-1', 'c1cc(ccc1[C@H]2C[NH2+]CCc3c2cc(c(c3Cl)O)O)O-2', 'c1cc(ccc1[C@H]2C[NH2+]CCc3c2cc(c(c3Cl)[O-])O)O-0', 'c1cc(ccc1[C@H]2C[NH2+]CCc3c2cc(c(c3Cl)[O-])O)O-1', 'c1cc(ccc1[C@H]2C[NH2+]CCc3c2cc(c(c3Cl)[O-])O)O-2',

       

  • This means that if the export component populates the SDF properties appropriately, all the downstream analysis code will work as is.

Export issues around 'OpenFF Full Optimization Benchmark 1'

David

• We are currently blocked by QCElemental model mismatch on public QCArchive; Ben is working on a migration that he intends to take place later this week

  • it’s a better use of our time at the moment to wait for this migration to unblock this work than trying to work entirely around it; hitting too many issues with parsing results