The oxygen atom bonded to the benzene in PEEK didn't have a hydrogen, meaning it was forming a double bond with the aromatic carbon. This is only an issue at the terminal monomer since the monomer-monomer bonds occurred at this oxygen. Quick change for now is to change the 'o' to 'O' at the beginning of the completed SMILES string. Maybe a future fix will be expanding the .json compound files with SMILES strings for terminal monomers.
I also added parameters to the System class that allow us to set assert_dihedrals to False when using foyer's apply() function.
The oxygen atom bonded to the benzene in PEEK didn't have a hydrogen, meaning it was forming a double bond with the aromatic carbon. This is only an issue at the terminal monomer since the monomer-monomer bonds occurred at this oxygen. Quick change for now is to change the 'o' to 'O' at the beginning of the completed SMILES string. Maybe a future fix will be expanding the .json compound files with SMILES strings for terminal monomers.
I also added parameters to the System class that allow us to set assert_dihedrals to False when using foyer's apply() function.