Missing SMARTS strings

[Aariq]

We are currently missing SMARTS strings to search for the following functional groups used in the SIMPOL.1 algorithm:

• Carbons on the acid-side of an amide
• C=C-C=O in a non-aromatic ring
• Alicyclic ethers
• Aromatic ethers
• Aromatic amines
• carbonylperoxynitrate
• hydroperoxide
• carbonylperoxyacid
• nitrophenol
• nitroester

[Aariq]

Needs testing, but I think these will work:

• peroxides (ROOR only, not ROOH): "[OX2D2][OX2D2]"
• hydroperoxides (ROOH): "[OX2][OX2H,OX1-]"
• nitrophenols (would also capture di- and tri-nitrophenols, I think, but might double or triple count? Are these really functional groups though?):
  • ortho-: "Oc1ccccc1[N+]([O-])=O"
  • meta-: "Oc1cccc(c1)[N+]([O-])=O"
  • para-: "c1cc(ccc1[N+](=O)[O-])O"
• nitroester (R-ONO₂): "[OX2][N+]([O-])=O"
• ether_alkyl: "[OD2]([CR0])[CR0]" (CR0 means a aliphatic carbon in zero rings)
• ether_aromatic: "[OX2](c)[c,CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]" modified from SMARTS in openbabel repo

[Aariq]

Possibly useful list here: https://github.com/openbabel/openbabel/blob/master/data/SMARTS_InteLigand.txt