# name; SMILES; optional indexes of atoms to be ignored (they just define the surrounding)

# carboxyles and carbonyles
aldehyde; carbonyl group; HC=O
ketone; carbonyl group; CC(=O)C; 1,4
carboxylic acid; carboxyl group; HOC=O
carboxylate anion; carboxyl group; [O-]C=O
ester; carboxyl group; COC=O; 1
anhydride; ; O=COC=O
acyl chloride; ; O=CCl
acyl flouride; ; O=CF
acyl bromide; ; O=CBr
acyl iodide; ; O=CI
nitrile; ; C#N
amide; ; C(=O)N

# simple one-atom groups
alkyl chloride; ; C-Cl; 1
alkyl bromide; ; C-Br; 1
alkyl fluoride; ; C-F; 1
alkyl iodide; ; C-I; 1
alcohol; hydroxy group; C-[OH]; 1
alcoxide anion; alkoxide; C-[O-]; 1
ether; ; C-O-C; 1,3
thiol; ; C-[SH]; 1
thiolate anion; thiolate; C-[S-]; 1
thioether; ; C-S-C; 1,3
primary amine; amino group; C-[NH2]; 1
secondary amine; amino group; C-[NH]-C; 1,3
tertiary amine; amino group; CN(C)C; 1,3,4
quarternary ammonium salt; amino group; C[N+](C)(C)C; 1,3,4,5
borane; ; C-[BH2]; 1
borane; ; C-[BH]-C; 1,3
borane; ; C-B(C)C; 1,3,4

# more complex hetero functional groups
nitro compound; nitro group; C-N(=O)=O; 1
sulfonic acid; sulfonyl group; C-S(=O)(=O)O; 1
sulfate anion; sulfate; C-S(=O)(=O)[O-]; 1

# rings
#benzene; ; c1ccccc1
#pyridine; ; c1ccncc1
#thiophene; ; c1cscc1
#pyrrole; ; c1cncc1
#furane; ; c1cocc1


# what about formic acid??
