Molecules that break common workflows

[ChayaSt]

This issue is to keep track of chemistries that break common workflows, what their failures are, and if they were resolved.

Segfaults

Failure at oequacpac.OEEnumerateFormalCharges() (used to expand protonation states)

• CSSCCN=C=S
• CCN=C=S

Omega Failures

Force field setup failed due to missing parameters

These molecules were generated from oequacpac.OEEnumerateFormalCharges()

• C(N)[PH2+](=O)O
• [CH3-]
• [C@@H-](C#N)N=[N+]=[N-]
• [C@H-](C#N)N=[N+]=[N-]
• CO/N=[N+](\[C-](Br)Br)/[O-]
• CO/N=[N+](/[C-](Br)Br)\[O-]
• c1ccc(cc1)S(F)(F)(F)(F)F
• F[PH2+](F)(F)(F)(F)F
• F[P-](F)(F)(F)(F)F
• C[C-](C)S(=O)(=O)Br

RDKit failures

Explicit valence is greater than permitted

These molecules were generated from oequacpac.OEEnumerateFormalCharges()

• COc1ccc(cc1OC)C2=Oc3ccccc3C=C2
• c1cc(nc(c1[NH2+](=O)O)N)Cl
• c1cc(nc(c1N(=O)O)N)Cl
• c1cc(nc(c1[NH2+](=O)O)[NH-])Cl
• c1cc(nc(c1[NH2+](=O)O)N)Cl
• c1cc(nc(c1[NH2+](=O)O)[NH-])Cl