/usr/share/RDKit/Data/FragmentDescriptors.csv is in rdkit-data 201503-3.
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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 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 | # Copyright (C) 2002 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.
#Code Description SMARTS MOE_SMARTS Notes
##########
# Oxygens
##########
fr_C=O "Number of carbonyl O" [CX3]=[OX1] C=O "Includes carboxylic acids, esters, amides, etc."
fr_C=O_noCOO "Number of carbonyl O, excluding COOH" [C!$(C-[OH])]=O [C!$(C-[OH])]=O "Excludes COOH but not COO- (assumes no formal charge) hydroxyls. Includes esters, amides, etc."
fr_Al_OH "Number of aliphatic hydroxyl groups" [C!$(C=O)]-[OH] [C!$(C=O)]-[OH] "Excludes COOH but not COO- (assumes no formal charge) hydroxyls"
fr_Ar_OH "Number of aromatic hydroxyl groups" c[OH1] c[OH1]
fr_methoxy "Number of methoxy groups -OCH3" [OX2](-[#6])-[CH3] O(-[#6])-CH3 "Aliphatic. Includes esters. Includes OMe groups on aromatic rings."
fr_oxime "Number of oxime groups" [CX3]=[NX2]-[OX2] C=N-O
fr_ester "Number of esters" [#6][CX3](=O)[OX2H0][#6] C(=O)O-C
fr_Al_COO "Number of aliphatic carboxylic acids" C-C(=O)[O;H1,-] "C-C(=O)[OH] or C-C(=O)[O-]"
fr_Ar_COO "Number of Aromatic carboxylic acide" c-C(=O)[O;H1,-] "c-C(=O)[OH] or c-C(=O)[O-]"
fr_COO "Number of carboxylic acids" [#6]C(=O)[O;H,-1] "[#6]C(=O)[OH] or [#6]C(=O)[O-]"
fr_COO2 "Number of carboxylic acids" [CX3](=O)[OX1H0-,OX2H1] "[#6]C(=O)[OH] or [#6]C(=O)[O-]"
fr_ketone "Number of ketones" [#6][CX3](=O)[#6]
fr_ether "Number of ether oxygens (including phenoxy)" [OD2]([#6])[#6]
fr_phenol "Number of phenols" [OX2H]-c1ccccc1
fr_aldehyde "Number of aldehydes" [CX3H1](=O)[#6]
############
# Nitrogens
############
fr_quatN "Number of quarternary nitrogens" [$([NX4+]),$([NX4]=*)] [NX4]
fr_NH2 "Number of Primary amines" [NH2,nH2] [NH2] "Include aromatic Ns"
fr_NH1 "Number of Secondary amines" [NH1,nH1] "[NH1] or [nH1]"
fr_NH0 "Number of Tertiary amines" [NH0,nH0] "[NH0] or [nH0]"
fr_Ar_N "Number of aromatic nitrogens" n n
fr_Ar_NH "Number of aromatic amines" [nH]
fr_aniline "Number of anilines" c-[NX3;!$(N=*)]
fr_Imine "Number of Imines" [Nv3](=C)-[#6] [Nv3](=C)-[#6] "Aliphatic. Excludes aromatic sp2 nitrogens."
fr_nitrile "Number of nitriles" [NX1]#[CX2] C#N
fr_hdrzine "Number of hydrazine groups" [NX3]-[NX3] [NX3]-[NX3] "Includes primary, secondary hydrazines, carbazides, cyclic hydrazines. Excludes hydrazones"
fr_hdrzone "Number of hydrazone groups" C=N-[NX3] C=N-[NX3] "Includes cyclic hydrazones"
fr_nitroso "Number of nitroso groups, excluding NO2" [N!$(N-O)]=O [N!$(N-O)]=O "Includes N-N=O"
fr_N-O "Number of hydroxylamine groups" [N!$(N=O)](-O)-C [N!$(N=O)](-O)-C
fr_nitro "Number of nitro groups" [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] N(=O)(O)[#6]
#fr_nitro "Number of nitro groups" N(=O)(O)[#6] N(=O)(O)[#6]
fr_azo "Number of azo groups" [#6]-N=N-[#6] [#6]-N=N-[#6] "Both nitrogens must be attached to a C. Excludes azides."
fr_diazo "Number of diazo groups" [N+]#N [N+]#N
fr_azide "Number of azide groups" [$(*-[NX2-]-[NX2+]#[NX1]),$(*-[NX2]=[NX2+]=[NX1-])] [#6]-N=[N+]=[N-]
fr_amide "Number of amides" C(=O)-N C(=O)-N "Any amide"
fr_priamide "Number of primary amides" C(=O)-[NH2] C(=O)-[NH2]
fr_amidine "Number of amidine groups" C(=N)(-N)-[!#7] C(=N)(-N)-[!#7] "Excludes guanidine"
fr_guanido "Number of guanidine groups" C(=N)(N)N C(=N)(N)N
fr_Nhpyrrole "Number of H-pyrrole nitrogens" [nH] [nH]
fr_imide "Number of imide groups" N(-C(=O))-C=O N(-C(=O))-C=O
fr_isocyan "Number of isocyanates" N=C=O N=C=O
fr_isothiocyan "Number of isothiocyanates" N=C=S N=C=S
fr_thiocyan "Number of thiocyanates" S-C#N S-C#N
###########
# Halogens
###########
fr_halogen "Number of halogens" [#9,#17,#35,#53] "F or I or Cl or Br"
fr_alkyl_halide "Number of alkyl halides" [CX4]-[Cl,Br,I,F]
##########
# Sulfurs
##########
fr_sulfide "Number of thioether" [SX2](-[#6])-C [SLp2](-[#6])-C "Aliphatic. Excludes sulfones, etc. Includes SMe groups on aromatic rings."
fr_SH "Number of thiol groups" [SH] [SH]
fr_C=S "Number of thiocarbonyl" C=[SX1] C=S "Includes thioamides, thioureas, etc."
fr_sulfone "Number of sulfone groups" S(=,-[OX1;+0,-1])(=,-[OX1;+0,-1])(-[#6])-[#6] "S(=O)(=O)(-[#6])-[#6] or S(-[O-])(-[O-])(-[#6])-[#6]" "Or charged form. Excludes sulfonamides, sulfonyl Cl, etc.."
fr_sulfone "Number of sulfone groups" S(=,-[OX1;+0,-1])(=,-[OX1;+0,-1])(-[#6])-[#6] "S(=O)(=O)(-[#6])-[#6] or S(-[O-])(-[O-])(-[#6])-[#6]" "Or charged form. Excludes sulfonamides, sulfonyl Cl, etc.."
fr_sulfonamd "Number of sulfonamides" N-S(=,-[OX1;+0,-1])(=,-[OX1;+0,-1])-[#6] "N-S(=O)(=O)-[#6] or N-S(-[O-])(-[O-])-[#6]" "Any sulfonamide"
fr_prisulfonamd "Number of primary sulfonamides" [NH2]-S(=,-[OX1;+0;-1])(=,-[OX1;+0;-1])-[#6] "[NH2]-S(=O)(=O)-[#6] or [NH2]-S(-[O-])(-[O-])-[#6]"
##################################
# Miscellaneous Functional Groups
##################################
fr_barbitur "Number of barbiturate groups" C1C(=O)NC(=O)NC1=O C1C(=O)NC(=O)NC1=O
fr_urea "Number of urea groups" C(=O)(-N)-N C(=O)(-N)-N "Includes cyclic ureas, hydroxyureas, barbiturates, etc."
fr_term_acetylene "Number of terminal acetylenes" C#[CH] C#[CH]
fr_imidazole "Number of imidazole rings" n1cncc1 n1cncc1 "Includes bicyclics"
fr_furan "Number of furan rings" o1cccc1 o1cccc1 "Includes bicyclics"
fr_thiophene "Number of thiophene rings" s1cccc1 s1cccc1 "Includes bicyclics"
fr_thiazole "Number of thiazole rings" c1scnc1 c1scnc1 "Includes bicyclics"
fr_oxazole "Number of oxazole rings" c1ocnc1 c1ocnc1 "Includes bicyclics"
fr_pyridine "Number of pyridine rings" n1ccccc1 n1ccccc1 "Includes bicyclics"
fr_piperdine "Number of piperdine rings" N1CCCCC1 N1CCCCC1
fr_piperzine "Number of piperzine rings" N1CCNCC1 N1CCNCC1
fr_morpholine "Number of morpholine rings" O1CCNCC1 O1CCNCC1
fr_lactam "Number of beta lactams" N1C(=O)CC1 N1C(=O)CC1
fr_lactone "Number of cyclic esters (lactones)" [C&R1](=O)[O&R1][C&R1]
#fr_intrahbonds "Number of intramolecular H-bonds (o-OH and -C=O) + (o-NH2 and -COOH) + 8-OH/NH2 in quinolones" "c1([OH])c(C(=O))aaaa1 or c1([OH])c([NH2])aaaa1 or c1([NH2])c(C(=O)[OH])aaaa1 or n1c2c([OH])cccc2ccc1 or n1c2c([NH2])cccc2ccc1" "This is just a guess and may be missing other possible examples"
fr_tetrazole "Number of tetrazole rings" c1nnnn1 c1nnnn1
fr_epoxide "Number of epoxide rings" O1CC1 O1CC1
fr_unbrch_alkane "Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes)" [R0;D2][R0;D2][R0;D2][R0;D2]
fr_bicyclic "Bicyclic" [R2][R2]
fr_benzene "Number of benzene rings" c1ccccc1
#############
# Phosphates
#############
fr_phos_acid "Number of phosphoric acid groups" [$(P(=[OX1])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)]),$([P+]([OX1-])([$([OX2H]),$([OX1-]),$([OX2]P)])([$([OX2H]),$([OX1-]),$([OX2]P)])[$([OX2H]),$([OX1-]),$([OX2]P)])]
fr_phos_ester "Number of phosphoric ester groups" [$(P(=[OX1])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)]),$([P+]([OX1-])([OX2][#6])([$([OX2H]),$([OX1-]),$([OX2][#6])])[$([OX2H]),$([OX1-]),$([OX2][#6]),$([OX2]P)])]
#####################
# Topliss Metabolism
#####################
fr_nitro_arom "Number of nitro benzene ring substituents" [$(c1(-[$([NX3](=O)=O),$([NX3+](=O)[O-])])ccccc1)]
#fr_nitro_arom "Number of nitro aromatic ring substituents" c-[$([NX3](=O)=O),$([NX3+](=O)[O-])]
fr_nitro_arom_nonortho "Number of non-ortho nitro benzene ring substituents" [$(c1(-[$([NX3](=O)=O),$([NX3+](=O)[O-])])ccccc1);!$(cc-!:*)]
fr_dihydropyridine "Number of dihydropyridines" [$([NX3H1]1-C=C-C-C=C1),$([Nv3]1=C-C-C=C-C1),$([Nv3]1=C-C=C-C-C1),$([NX3H1]1-C-C=C-C=C1)]
#fr_readily_oxidized "Number of readily oxidized moieties: thiols+dihydropyridines"
fr_phenol_noOrthoHbond "Number of phenolic OH excluding ortho intramolecular Hbond substituents" [$(c1(-[OX2H])ccccc1);!$(cc-!:[CH2]-[OX2H]);!$(cc-!:C(=O)[O;H1,-]);!$(cc-!:C(=O)-[NH2])]
fr_Al_OH_noTert "Number of aliphatic hydroxyl groups excluding tert-OH" [$(C-[OX2H]);!$([CX3](-[OX2H])=[OX1]);!$([CD4]-[OX2H])]
fr_benzodiazepine "Number of benzodiazepines with no additional fused rings" [c&R2]12[c&R1][c&R1][c&R1][c&R1][c&R2]1[N&R1][C&R1][C&R1][N&R1]=[C&R1]2
fr_para_hydroxylation "Number of para-hydroxylation sites" [$([cH]1[cH]cc(c[cH]1)~[$([#8,$([#8]~[H,c,C])])]),$([cH]1[cH]cc(c[cH]1)~[$([#7X3,$([#7](~[H,c,C])~[H,c,C])])]),$([cH]1[cH]cc(c[cH]1)-!:[$([NX3H,$(NC(=O)[H,c,C])])])] na "Includes benzofuran and benzimidazole"
#fr_para_hydroxylation "Number of para-hydroxylation sites" [$([cH]1[cH]cc(c[cH]1)-!:[$([OX2,$(O-[H,c,C])])]),$([cH]1[cH]cc(c[cH]1)-!:[$([NX3,$(N([H,c,C])-[H,c,C])])]),$([cH]1[cH]cc(c[cH]1)-!:[$([NX3H,$(NC(=O)[H,c,C])])])]
fr_allylic_oxid "Number of allylic oxidation sites excluding steroid dienone" [$(C=C-C);!$(C=C-C-[N,O,S]);!$(C=C-C-C-[N,O]);!$(C12=CC(=O)CCC1C3C(C4C(CCC4)CC3)CC2)]
fr_aryl_methyl "Number of aryl methyl sites for hydroxylation" [$(a-[CH3]),$(a-[CH2]-[CH3]),$(a-[CH2]-[CH2]~[!N;!O]);!$(a(:a!:*):a!:*)]
fr_Ndealkylation1 "Number of XCCNR groups" [$(N(-[CH3])-C-[$(C~O),$(C-a),$(C-N),$(C=C)]),$(N(-[CH2][CH3])-C-[$(C~O),$(C-a),$(C-N),$(C=C)])]
fr_Ndealkylation2 "Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)" [$([N&R1]1(-C)CCC1),$([N&R1]1(-C)CCCC1),$([N&R1]1(-C)CCCCC1),$([N&R1]1(-C)CCCCCC1),$([N&R1]1(-C)CCCCCCC1)]
fr_alkyl_carbamate "Number of alkyl carbamates (subject to hydrolysis)" C[NH1]C(=O)OC
fr_ketone_Topliss "Number of ketones excluding diaryl, a,b-unsat. dienones, heteroatom on Calpha" [$([CX3](=[OX1])(C)([c,C]));!$([CX3](=[OX1])([CH1]=C)[c,C])]
fr_ArN "Number of N functional groups attached to aromatics" [$(a-[NX3H2]),$(a-[NH1][NH2]),$(a-C(=[OX1])[NH1][NH2]),$(a-C(=[NH])[NH2])]
fr_HOCCN "Number of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic" [$([OX2H1][CX4][CX4H2][NX3&R1]),$([OH1][CX4][CX4H2][NX3][CX4](C)(C)C)]
###############
# Toxicophores
###############
|