Pysmiles does not allow partial aromatic fragments (for good reason) yet we still want to do them. Thus here we have a workaround. If two atoms are marked as aromatic we simply convert them to regular elements and later change it back. It's stupid but works.
Pysmiles does not allow partial aromatic fragments (for good reason) yet we still want to do them. Thus here we have a workaround. If two atoms are marked as aromatic we simply convert them to regular elements and later change it back. It's stupid but works.
Example Case Martini3 p-cresol:
The aromatic ring is fragmented into four fragments.