--- a/CADDSuite-1.6/data/fragments/functionalGroups.smarts	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,133 +0,0 @@
-C[*X1](C)([*X1])[*X1]	terminal primary C(sp3)
-[C,c]([C,c])([C,c])(*)*	 total secondary C(sp3)
-[C,c]([C,c])([C,c])([C,c])*	total tertiary C(sp3)
-[C,c]([C,c])([C,c])([C,c])[C,c]	total quaternary C(sp3)
-[$([Cr,cr]([Cr,cr])([Cr,cr])(*)*),$([Cr,cr]([Cr,cr])([C,c])([*r])*)]		ring secondary C(sp3)
-[$([Cr,cr]([Cr,cr])([Cr,cr])([C,c])*),$([Cr,cr]([Cr,cr])([C,c])([C,c])[*r])]	ring tertiary C(sp3)
-[Cr,cr]([Cr,cr])([Cr,cr])([C,c])[C,c]	ring quaternary C(sp3)
-[cX3]		aromatic C(sp2)
-[Ch1,ch1]1[C,c][C,c][C,c][C,c][C,c]1	unsubstituted benzene C(sp2)
-[Ch0,ch0]1[C,c][C,c][C,c][C,c][C,c]1	substituted benzene C(sp2)
-O=CC1=CCCC=C1		non-aromatic conjugated C(sp2)
-[C,c]=[C,c](*)(*)		terminal primary C(sp2)
-C=C(C)(*)	aliphatic secondary C(sp2)
-C=C(C)(C)	aliphatic tertiary C(sp2)
-[C,c]=[C,c]=[C,c]		allenes groups
-[*X1][C,c]#C	terminal C(sp)
-**[C,c]#C	non-terminal C(sp)
-OC#N		cyanates
-O=C=N	isocyanates
-SC#N		thiocyanates
-N=C=S	isothiocyanates
-[OH,Oh]C=O	carboxylic acids
-[*;!H]OC=O	 esters
-[NH2,Nh2]C=O		primary amides
-[*;!H][NH,Nh]C=O		secondary amides
-[*;!H]N([*;!H])C=O	tertiary amides
-*N(*)C([O,S]*)=[O,S]		(thio-)carbamates
-[F,Cl,Br,I,At]C(*)=O		acyl halogenides
-[$([OH,Oh]C(*)=S),$([SH,Sh]C(*)=O)]		thioacids
-[SH,Sh]C(*)=S		dithioacids
-[$([*;!H]OC(*)=S),$([*;!H]SC(*)=O)]		thioesters
-[*;!H]SC(*)=S		dithioesters
-[CH,Ch](*)=O	aldehydes
-*C(*)=O		ketones
-[NX3]C([NX3])=[O,S]		urea (-thio) derivatives
-[OX2,SX2]C([OX2,SX2])=[O,S]	carbonate (-thio) derivatives
-[NX2]C([C,H])[NX3]	amidine derivatives
-[NX3]C(=[NX2])[NX3]	guanidine derivatives
-*C(*)=N[N,C,H]		imines
-*C(*)=NO*	oximes
-[NH2X3,Nh2X3]		primary amines
-[NH1X3,Nh1X3]		secondary amines
-[NH0X3;Nh0X3]	 tertiary amines
-[C,H][NX3][NX3][C,H]		N hydrazines
-[C,H][NX2]=[NX2][C,H]	N azo-derivatives
-N#C*	nitriles
-[N+n]	positive charged N
-[NX4]	quaternary N
-*N(*)O*	hydroxylamines
-*N(*)N=O		nitrosamine
-*N=O	nitroso groups
-*N(O)=O		nitro groups
-[CX3](=[O,S])[NX3]([H,C])[CX3]=[O,S]	imides
-[C,H]C([C,H])=NN([C,H])[C,H]	hydrazones
-A[OX2h1,OX2H1]		hydroxyl groups
-a[OX2h1,OX2H1]		aromatic hydroxyls
-C[CH2,Ch2][OH,Oh]		primary alcohols
-C[CH,Ch](C)[OH,Oh]	secondary alcohols
-CC(C)(C)[OH,Oh]	tertiary alcohols
-*O*	 ethers
-*O[F,Cl,Br,I,At]	hypohalogenides
-[CX3](=[O,S])O[CX3][O,S]	anhydrides
-[OH2,Oh2]	water
-C[SH,Sh]	thiols
-S=C(C)C	thioketones
-C[SX2]C	sulfides
-C[SX2][SX2]C	disulfides
-[$(CS(C)=O),$(C=S=O),$(S=S=O)]	sulfoxides
-[$(O=[SX4]=O),$(O=S(=[C,S])=O)]	sulfones
-[SX2][Oh1,OH1,Sh1,SH1]		sulfenic acids
-[SX3](=[O,S])[Oh1,OH1,Sh1,SH1]		sulfinic acids
-[SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1]		sulfonic acids
-[OX2,SX2][SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1]		sulfuric acids
-[SX3](=[O,S])[OX2,SX2]		sulfites
-[SX4](=[O,S])(=[O,S])[OX2,SX2]	sulfonates
-[OX2,SX2][SX4](=[O,S])(=[O,S])[OX2,SX2]	sulfates
-[$(C[SX4](=O)(=O)[NX3]),$(C[SX4](=S)(=O)[NX3]),$(C[SX3](=O)[NX3]),$(C[SX3](=S)[NX3]),$(CS[NX3])]	sulfonamides/sulfinamides/sulfenamides
-[O,S]P([O,S])[O,S]	phosphites/thiophosphites
-[O,S]P(=[O,S])([O,S])[O,S]		phosphates/thiophosphates
-[O,S]P([O,S])[O,S]	phosphanes
-[H,S,F,Cl,Br,I,At][PX4](=[S,O])([SX2,OX2])[SX2,OX2]	phosphonates/thiophosphonates
-[$([H,S,F,Cl,Br,I,At][PX4](=[S,O])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At]),$([H,S,F,Cl,Br,I,At][PX5]([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At])]		phosphoranes/thiophosphoranes
-[F,Cl,Br,I,At][CX4h2,CX4H2,cx4h2,cx4H2][C,c]		CH2RX
-[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[C,c]	CHR2X
-[F,Cl,Br,I,At][C,c]([C,c])([C,c])[C,c]		CR3X
-[C,c]=[CX3h1,cX3h1,CX3H1,cX3H1][F,Cl,Br,I,At]	R=CHX
-[C,c]=[C,c]([C,c])[F,Cl,Br,I,At]		R=CRX
-[F,Cl,Br,I,At]C#C		R#CX
-[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[F,Cl,Br,I,At]	 CHRX2
-[F,Cl,Br,I,At][C,c]([C,c])([C,c])[F,Cl,Br,I,At]	CR2X2
-[C,c]=[C,c]([F,Cl,Br,I,At])[F,Cl,Br,I,At]	 R=CX2
-[F,Cl,Br,I,At][C,c]([C,c])([F,Cl,Br,I,At])[F,Cl,Br,I,At]	CRX3
-[F,Cl,Br,I,At][ar]	halogene on aromatic ring
-[CrX4,crX4][F,Cl,Br,I,At]	X on ring C(sp3)
-[CrX3,crX3][F,Cl,Br,I,At]	X on ring C(sp2)
-[C,c]=[C,c]([F,Cl,Br,I,At])[C,c]=[C,c]	 halogene on exo-conjugated C
-[N,n]1@[C,c]@[C,c]1	Aziridines
-[O,o]1@[C,c]@[C,c]1	Oxiranes
-[S,s]1@[C,c]@[C,c]1	Thiranes
-[N,n]1@[C,c]@[C,c]@[C,c]1	Azetidines
-[O,o]1@[C,c]@[C,c]@[C,c]1	Oxetanes
-[S,s]1@[C,c]@[C,c]@[C,c]1	Thioethanes
-[N,n]12@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1(@[C,c]@C2(=O))	Beta-Lactams
-[N,n]1@[C,c]@[C,c]@[C,c]1		Pyrrolidines
-[O,o]1[C,c][C,c][C,c][C,c]1	Oxolanes
-[S,s]1[C,c][C,c][C,c][C,c]1	tetrahydro-Thiophenes
-[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]1	Pyrroles
-[N,n]1@[N,n]@[C,c]@[C,c]@[C,c]1	Pyrazoles
-[N,n]1@[C,c]@[N,n]@[C,c]@[C,c]1	Imidazoles
-[O,o]1[C,c]=[C,c][C,c]=[C,c]1	Furanes
-[S,s]1[C,c]=[C,c][C,c]=[C,c]1	Thiophenes
-[O,o]1@[C,c]@[N,n]@[C,c]@[C,c]1	Oxazoles
-[O,o]1@[N,n]@[C,c]@[C,c]@[C,c]1	Isoxazoles
-[S,s]1@[C,c]@[N,n]@[C,c]@[C,c]1	Thiazoles
-[S,s]1@[N,n]@[C,c]@[C,c]@[C,c]1	Isothiazoles
-[$([N,n]1@[N,n]@[C,c]@[N,n]@C1),$([N,n]1@[N,n]@[N,n]@[C,c]@[C,c]1)]	Triazoles
-[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1	Pyridines
-[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[N,n]1	Pyridazines
-[N,n]1@[C,c]@[C,c]@[C,c]@[N,n]@[C,c]1	Pyrimidines
-[N,n]1@[C,c]@[C,c]@[N,n]@[C,c]@[C,c]1	Pyrazines
-[N,n]1@[C,c]@[N,n]@[C,c]@[N,n]@[C,c]1	135-Triazines
-[N,n]1@[C,c]@[N,n]@[N,n]@[C,c]@[C,c]1	124-Triazines
-[C,c]1([Oh1,OH1])[C,c][C,c][C,c][C,c][C,c]1	Phenoles
-[C,c]1([C])[C,c][C,c][C,c][C,c][C,c]1	Phenyles
-[C,c]1([CH3,ch3])[C,c][C,c][C,c][C,c][C,c]1	Toluenes
-OC[C,c]1@[C,c](O)@[C,c](O)@[C,c](O)@[C,c](O)@[O,o]1	Glucose
-OC[C,c]1(O)@[C,c](O)@[C,c](O)@[C,c](CO)[O,o]1	Fructose
-[CH3,Ch3]	Methyl
-[F,Cl,Br,I,At]		Halogenides
-[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Propyl
-[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Butyl
-[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Pentyl
-CC=C([CH3,Ch3])([CH3,Ch3])	Prenyl