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rdkit/Data/Functional_Group_Hierarchy.txt

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// $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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//
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