/usr/share/RDKit/Data/FunctionalGroups.txt is in rdkit-data 201403-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 | // Copyright (C) 2003 Rational Discovery LLC
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
// NOTES:
// - larger functional groups should come before smaller ones involving
// the same core atom
// - the first atom in the SMARTS query is not part of the group itself
// - it is essential that the fields in this file be separated by tabs
// (not spaces).
//
// Label SMARTS Notes
//--------------------------------------------------
-NC(=O)CH3 *-[N;D2]-[C;D3](=O)-[C;D1;H3] methyl amide
-C(=O)O *-C(=O)[O;D1] carboxylic acids
-C(=O)OMe *-C(=O)[O;D2]-[C;D1;H3] carbonyl methyl ester
-C(=O)H *-C(=O)-[C;D1] terminal aldehyde
-C(=O)N *-C(=O)-[N;D1] amide
-C(=O)CH3 *-C(=O)-[C;D1;H3] carbonyl methyl
-N=C=O *-[N;D2]=[C;D2]=[O;D1] isocyanate
-N=C=S *-[N;D2]=[C;D2]=[S;D1] isothiocyanate
//--------------------------------------------------
// Nitrogen containing
-NO2 *-[N;D3](=[O;D1])[O;D1] nitro
-N=O *-[N;R0]=[O;D1] nitroso
=N-O *=[N;R0]-[O;D1] oximes
=NCH3 *=[N;R0]-[C;D1;H3] Imines
-N=CH2 *-[N;R0]=[C;D1;H2] Imines
-N=NCH3 *-[N;D2]=[N;D2]-[C;D1;H3] terminal azo
-N=N *-[N;D2]=[N;D1] hydrazines
-N#N *-[N;D2]#[N;D1] diazo
-C#N *-[C;D2]#[N;D1] cyano
//--------------------------------------------------
// S containing
-SO2NH2 *-[S;D4](=[O;D1])(=[O;D1])-[N;D1] primary sulfonamide
-NHSO2CH3 *-[N;D2]-[S;D4](=[O;D1])(=[O;D1])-[C;D1;H3] methyl sulfonamide
-SO3H *-[S;D4](=O)(=O)-[O;D1] sulfonic acid
-SO3CH3 *-[S;D4](=O)(=O)-[O;D2]-[C;D1;H3] methyl ester sulfonyl
-SO2CH3 *-[S;D4](=O)(=O)-[C;D1;H3] methyl sulfonyl
-SO2Cl *-[S;D4](=O)(=O)-[Cl] sulfonyl chloride
-SOCH3 *-[S;D3](=O)-[C;D1] methyl sulfinyl
-SCH3 *-[S;D2]-[C;D1;H3] methylthio
-S *-[S;D1] thiols
=S *=[S;D1] thiocarbonyls
//--------------------------------------------------
//Miscellaneous fragments:
-X *-[#9,#17,#35,#53] halogens
-tBu *-[C;D4]([C;D1])([C;D1])-[C;D1] t-butyl
-CF3 *-[C;D4](F)(F)F trifluoromethyl
-C#CH *-[C;D2]#[C;D1;H] acetylenes
-cPropyl *-[C;D3]1-[C;D2]-[C;D2]1 cyclopropyl
//--------------------------------------------------
//Really teeny stuff:
-OEt *-[O;D2]-[C;D2]-[C;D1;H3] ethoxy
-OMe *-[O;D2]-[C;D1;H3] methoxy
-O *-[O;D1] side-chain hydroxyls
=O *=[O;D1] side-chain aldehydes or ketones
-N *-[N;D1] primary amines
=N *=[N;D1] ???
#N *#[N;D1] nitriles
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