// $Id: Functional_Group_Hierarchy.txt 10346 2013-07-04 14:53:03Z landrgr1 $
// Created by Greg Landrum, October 2006
//  Format: Name\tSmarts\tLabel\tRemovalReaction (optional)
//
//  NOTES:
//     1) be sure to make the distinguishing feature of the functional group
//        the first atom in the pattern
//     2) the RemovalReaction (if present) is used to remove the functional
//        group from the molecule. This is necessary for cases like boronic
//        ethers where the full functional group cannot be specified in SMARTS.
//
AcidChloride	C(=O)Cl	Acid Chloride
  AcidChloride.Aromatic	[$(C-!@[a])](=O)(Cl)	Aromatic
  AcidChloride.Aliphatic	[$(C-!@[A;!Cl])](=O)(Cl)	Aliphatic

CarboxylicAcid	C(=O)[O;H,-]	Carboxylic acid
  CarboxylicAcid.Aromatic	[$(C-!@[a])](=O)([O;H,-])	Aromatic
  CarboxylicAcid.Aliphatic	[$(C-!@[A;!O])](=O)([O;H,-])	Aliphatic
  CarboxylicAcid.AlphaAmino	[$(C-[C;!$(C=[!#6])]-[N;!H0;!$(N-[!#6;!#1]);!$(N-C=[O,N,S])])](=O)([O;H,-])	alpha Amino Acid

SulfonylChloride	[$(S-!@[#6])](=O)(=O)(Cl)	Sulfonyl Chloride
  SulfonylChloride.Aromatic	[$(S-!@c)](=O)(=O)(Cl)	 Aromatic
  SulfonylChloride.Aliphatic	[$(S-!@C)](=O)(=O)(Cl)	 Aliphatic

Amine				[N;$(N-[#6]);!$(N-[!#6;!#1]);!$(N-C=[O,N,S])]	Amine
  Amine.Primary			[N;H2;D1;$(N-!@[#6]);!$(N-C=[O,N,S])]		Primary
  Amine.Primary.Aromatic		[N;H2;D1;$(N-!@c);!$(N-C=[O,N,S])]		Primary aromatic
  Amine.Primary.Aliphatic	[N;H2;D1;$(N-!@C);!$(N-C=[O,N,S])]		Primary aliphatic
  Amine.Secondary		[N;H1;D2;$(N(-[#6])-[#6]);!$(N-C=[O,N,S])]	Secondary
  Amine.Secondary.Aromatic	[N;H1;D2;$(N(-[c])-[#6]);!$(N-C=[O,N,S])]	Secondary aromatic
  Amine.Secondary.Aliphatic	[N;H1;D2;$(N(-C)-C);!$(N-C=[O,N,S])]	Secondary aliphatic
  Amine.Tertiary		[N;H0;D3;$(N(-[#6])(-[#6])-[#6]);!$(N-C=[O,N,S])]	Tertiary
  Amine.Tertiary.Aromatic	[N;H0;D3;$(N(-[c])(-[#6])-[#6]);$(N-C=[O,N,S])]	Tertiary aromatic
  Amine.Tertiary.Aliphatic	[N;H0;D3;$(N(-C)(-C)-C);!$(N-C=[O,N,S])]	Tertiary aliphatic
  Amine.Aromatic		[N;$(N-c);!$(N-[!#6;!#1]);!$(N-C=[O,N,S])]		Aromatic
  Amine.Aliphatic		[N;!$(N-c);$(N-C);!$(N-[!#6;!#1]);!$(N-C=[O,N,S])]		Aliphatic
  Amine.Cyclic			[N;R;$(N-[#6]);!$(N-[!#6;!#1]);!$(N-C=[O,N,S])]	Cyclic

BoronicAcid			[$(B-!@[#6])](O)(O)		Boronic Acid		[#6:1]-!@[B:2]([O:3])[O:4]>>[#6:1][X].[B:2]([O:3])[O:4]
  BoronicAcid.Aromatic		[$(B-!@c)](O)(O)	Aromatic	[c:1]-!@[B:2]([O:3])[O:4]>>[c:1][X].[B:2]([O:3])[O:4]
  BoronicAcid.Aliphatic		[$(B-!@C)](O)(O)		Aliphatic	[C:1]-!@[B:2]([O:3])[O:4]>>[C:1][X].[B:2]([O:3])[O:4]

Isocyanate			[$(N-!@[#6])](=!@C=!@O)	Isocyanate
  Isocyanate.Aromatic		[$(N-!@c)](=!@C=!@O)	Aromatic
  Isocyanate.Aliphatic		[$(N-!@C)](=!@C=!@O)	Aliphatic

Alcohol				[O;H1;$(O-!@[#6;!$(C=!@[O,N,S])])]	Alcohol
  Alcohol.Aromatic		[O;H1;$(O-!@c)]	Aromatic
  Alcohol.Aliphatic		[O;H1;$(O-!@[C;!$(C=!@[O,N,S])])]	Aliphatic

Aldehyde			[CH;D2;!$(C-[!#6;!#1])]=O	Aldehyde
  Aldehyde.Aromatic		[CH;D2;$(C-!@[a])](=O)	Aromatic
  Aldehyde.Aliphatic		[CH;D2;$(C-!@C)](=O)	Aliphatic

Halogen				[$([F,Cl,Br,I]-!@[#6]);!$([F,Cl,Br,I]-!@C-!@[F,Cl,Br,I]);!$([F,Cl,Br,I]-[C,S](=[O,S,N]))]	Halogen
  Halogen.Aromatic		[F,Cl,Br,I;$(*-!@c)]	Aromatic
  Halogen.Aliphatic		[$([F,Cl,Br,I]-!@C);!$([F,Cl,Br,I]-!@C-!@[F,Cl,Br,I])]	Aliphatic
  Halogen.NotFluorine		[$([Cl,Br,I]-!@[#6]);!$([Cl,Br,I]-!@C-!@[F,Cl,Br,I]);!$([Cl,Br,I]-[C,S](=[O,S,N]))]	Not Fluorine
  Halogen.NotFluorine.Aliphatic		[$([Cl,Br,I]-!@C);!$([Cl,Br,I]-!@C-!@[F,Cl,Br,I]);!$([Cl,Br,I]-[C,S](=[O,S,N]))]	Aliphatic Not Fluorine
  Halogen.NotFluorine.Aromatic		[$([Cl,Br,I]-!@c)]	Aromatic Not Fluorine
  Halogen.Bromine	[Br;$([Br]-!@[#6]);!$([Br]-!@C-!@[F,Cl,Br,I]);!$([Br]-[C,S](=[O,S,N]))]	Bromine
  Halogen.Bromine.Aliphatic	[Br;$(Br-!@C);!$(Br-!@C-!@[F,Cl,Br,I]);!$(Br-[C,S](=[O,S,N]))]	Aliphatic Bromine
  Halogen.Bromine.Aromatic	[Br;$(Br-!@c)]	Aromatic Bromine
  Halogen.Bromine.BromoKetone	[Br;$(Br-[CH2]-C(=O)-[#6])]	Bromoketone
  
Azide				[N;H0;$(N-[#6]);D2]=[N;D2]=[N;D1]	Azide
  Azide.Aromatic		[N;H0;$(N-c);D2]=[N;D2]=[N;D1]	Aromatic Azide
  Azide.Aliphatic		[N;H0;$(N-C);D2]=[N;D2]=[N;D1]	Aliphatic Azide

Nitro				[N;H0;$(N-[#6]);D3](=[O;D1])~[O;D1]	Nitro
  Nitro.Aromatic		[N;H0;$(N-c);D3](=[O;D1])~[O;D1]	Aromatic Nitro
  Nitro.Aliphatic		[N;H0;$(N-C);D3](=[O;D1])~[O;D1]	Aliphatic Nitro

TerminalAlkyne			[C;$(C#[CH])]			Terminal Alkyne
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