File: query_file1.txt

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