public class SubstructureFingerprinter extends AbstractFingerprinter implements IFingerprinter
IFingerprinter
that gives a bit set which has a size equal to the number
of substructures it was constructed from. A set bit indicates that that
substructure was found at least once in the molecule for which the
fingerprint was calculated. The fingerprint currently supports 307
substructures, listed below:
Bit position | Description | Pattern |
0 | Primary carbon | [CX4H3][#6] |
1 | Secondary carbon | [CX4H2]([#6])[#6] |
2 | Tertiary carbon | [CX4H1]([#6])([#6])[#6] |
3 | Quaternary carbon | [CX4]([#6])([#6])([#6])[#6] |
4 | Alkene | [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] |
5 | Alkyne | [CX2]#[CX2] |
6 | Allene | [CX3]=[CX2]=[CX3] |
7 | Alkylchloride | [ClX1][CX4] |
8 | Alkylfluoride | [FX1][CX4] |
9 | Alkylbromide | [BrX1][CX4] |
10 | Alkyliodide | [IX1][CX4] |
11 | Alcohol | [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] |
12 | Primary alcohol | [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])] |
13 | Secondary alcohol | [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])] |
14 | Tertiary alcohol | [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])] |
15 | Dialkylether | [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] |
16 | Dialkylthioether | [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] |
17 | Alkylarylether | [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] |
18 | Diarylether | [c][OX2][c] |
19 | Alkylarylthioether | [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] |
20 | Diarylthioether | [c][SX2][c] |
21 | Oxonium | [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])] |
22 | Amine | [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])] |
23 | Primary aliph amine | [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] |
24 | Secondary aliph amine | [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] |
25 | Tertiary aliph amine | [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] |
26 | Quaternary aliph ammonium | [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] |
27 | Primary arom amine | [NX3H2+0,NX4H3+]c |
28 | Secondary arom amine | [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] |
29 | Tertiary arom amine | [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] |
30 | Quaternary arom ammonium | [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] |
31 | Secondary mixed amine | [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])] |
32 | Tertiary mixed amine | [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])] |
33 | Quaternary mixed ammonium | [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])] |
34 | Ammonium | [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])] |
35 | Alkylthiol | [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])] |
36 | Dialkylthioether | [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])] |
37 | Alkylarylthioether | [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])] |
38 | Disulfide | [SX2D2][SX2D2] |
39 | 1,2-Aminoalcohol | [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])] |
40 | 1,2-Diol | [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H] |
41 | 1,1-Diol | [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H] |
42 | Hydroperoxide | [OX2H][OX2] |
43 | Peroxo | [OX2D2][OX2D2] |
44 | Organolithium compounds | [LiX1][#6,#14] |
45 | Organomagnesium compounds | [MgX2][#6,#14] |
46 | Organometallic compounds | [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-] |
47 | Aldehyde | [$([CX3H][#6]),$([CX3H2])]=[OX1] |
48 | Ketone | [#6][CX3](=[OX1])[#6] |
49 | Thioaldehyde | [$([CX3H][#6]),$([CX3H2])]=[SX1] |
50 | Thioketone | [#6][CX3](=[SX1])[#6] |
51 | Imine | [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])] |
52 | Immonium | [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])] |
53 | Oxime | [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H] |
54 | Oximether | [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])] |
55 | Acetal | [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] |
56 | Hemiacetal | [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] |
57 | Aminal | [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] |
58 | Hemiaminal | [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H] |
59 | Thioacetal | [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])] |
60 | Thiohemiacetal | [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H] |
61 | Halogen acetal like | [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] |
62 | Acetal like | [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] |
63 | Halogenmethylen ester and similar | [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] |
64 | NOS methylen ester and similar | [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] |
65 | Hetero methylen ester and similar | [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] |
66 | Cyanhydrine | [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H] |
67 | Chloroalkene | [ClX1][CX3]=[CX3] |
68 | Fluoroalkene | [FX1][CX3]=[CX3] |
69 | Bromoalkene | [BrX1][CX3]=[CX3] |
70 | Iodoalkene | [IX1][CX3]=[CX3] |
71 | Enol | [OX2H][CX3;$([H1]),$(C[#6])]=[CX3] |
72 | Endiol | [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H] |
73 | Enolether | [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3] |
74 | Enolester | [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])] |
75 | Enamine | [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3] |
76 | Thioenol | [SX2H][CX3;$([H1]),$(C[#6])]=[CX3] |
77 | Thioenolether | [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3] |
78 | Acylchloride | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] |
79 | Acylfluoride | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] |
80 | Acylbromide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] |
81 | Acyliodide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1] |
82 | Acylhalide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1] |
83 | Carboxylic acid | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])] |
84 | Carboxylic ester | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])] |
85 | Lactone | [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])] |
86 | Carboxylic anhydride | [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1]) |
87 | Carboxylic acid derivative | [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6] |
88 | Carbothioic acid | [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])] |
89 | Carbothioic S ester | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])] |
90 | Carbothioic S lactone | [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])] |
91 | Carbothioic O ester | [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])] |
92 | Carbothioic O lactone | [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])] |
93 | Carbothioic halide | [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1] |
94 | Carbodithioic acid | [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])] |
95 | Carbodithioic ester | [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])] |
96 | Carbodithiolactone | [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])] |
97 | Amide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
98 | Primary amide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2] |
99 | Secondary amide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])] |
100 | Tertiary amide | [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])] |
101 | Lactam | [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
102 | Alkyl imide | [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) |
103 | N hetero imide | [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) |
104 | Imide acidic | [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1]) |
105 | Thioamide | [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
106 | Thiolactam | [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
107 | Oximester | [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])] |
108 | Amidine | [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])] |
109 | Hydroxamic acid | [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])] |
110 | Hydroxamic acid ester | [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])] |
111 | Imidoacid | [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] |
112 | Imidoacid cyclic | [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] |
113 | Imidoester | [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] |
114 | Imidolactone | [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] |
115 | Imidothioacid | [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] |
116 | Imidothioacid cyclic | [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] |
117 | Imidothioester | [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] |
118 | Imidothiolactone | [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] |
119 | Amidine | [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])] |
120 | Imidolactam | [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])] |
121 | Imidoylhalide | [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] |
122 | Imidoylhalide cyclic | [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] |
123 | Amidrazone | [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])] |
124 | Alpha aminoacid | [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-] |
125 | Alpha hydroxyacid | [OX2H][C][CX3](=[OX1])[OX2H,OX1-] |
126 | Peptide middle | [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] |
127 | Peptide C term | [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-] |
128 | Peptide N term | [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] |
129 | Carboxylic orthoester | [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] |
130 | Ketene | [CX3]=[CX2]=[OX1] |
131 | Ketenacetal | [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3] |
132 | Nitrile | [NX1]#[CX2] |
133 | Isonitrile | [CX1-]#[NX2+] |
134 | Vinylogous carbonyl or carboxyl derivative | [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I] |
135 | Vinylogous acid | [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])] |
136 | Vinylogous ester | [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])] |
137 | Vinylogous amide | [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
138 | Vinylogous halide | [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1] |
139 | Carbonic acid dieester | [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])] |
140 | Carbonic acid esterhalide | [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1] |
141 | Carbonic acid monoester | [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])] |
142 | Carbonic acid derivatives | [!#6][#6X3](=[!#6])[!#6] |
143 | Thiocarbonic acid dieester | [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])] |
144 | Thiocarbonic acid esterhalide | [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1] |
145 | Thiocarbonic acid monoester | [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])] |
146 | Urea | [#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])] |
147 | Thiourea | [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])] |
148 | Isourea | [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])] |
149 | Isothiourea | [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])] |
150 | Guanidine | [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+] |
151 | Carbaminic acid | [NX3]C(=[OX1])[O;X2H,X1-] |
152 | Urethan | [#7X3][#6](=[OX1])[#8X2][#6] |
153 | Biuret | [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3] |
154 | Semicarbazide | [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] |
155 | Carbazide | [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1] |
156 | Semicarbazone | [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] |
157 | Carbazone | [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1] |
158 | Thiosemicarbazide | [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] |
159 | Thiocarbazide | [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1] |
160 | Thiosemicarbazone | [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] |
161 | Thiocarbazone | [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1] |
162 | Isocyanate | [NX2]=[CX2]=[OX1] |
163 | Cyanate | [OX2][CX2]#[NX1] |
164 | Isothiocyanate | [NX2]=[CX2]=[SX1] |
165 | Thiocyanate | [SX2][CX2]#[NX1] |
166 | Carbodiimide | [NX2]=[CX2]=[NX2] |
167 | Orthocarbonic derivatives | [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I] |
168 | Phenol | [OX2H][c] |
169 | 1,2-Diphenol | [OX2H][c][c][OX2H] |
170 | Arylchloride | [Cl][c] |
171 | Arylfluoride | [F][c] |
172 | Arylbromide | [Br][c] |
173 | Aryliodide | [I][c] |
174 | Arylthiol | [SX2H][c] |
175 | Iminoarene | [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])] |
176 | Oxoarene | [c]=[OX1] |
177 | Thioarene | [c]=[SX1] |
178 | Hetero N basic H | [nX3H1+0] |
179 | Hetero N basic no H | [nX3H0+0] |
180 | Hetero N nonbasic | [nX2,nX3+] |
181 | Hetero O | [o] |
182 | Hetero S | [sX2] |
183 | Heteroaromatic | [a;!c] |
184 | Nitrite | [NX2](=[OX1])[O;$([X2]),$([X1-])] |
185 | Thionitrite | [SX2][NX2]=[OX1] |
186 | Nitrate | [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] |
187 | Nitro | [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] |
188 | Nitroso | [NX2](=[OX1])[!#7;!#8] |
189 | Azide | [NX1]~[NX2]~[NX2,NX1] |
190 | Acylazide | [CX3](=[OX1])[NX2]~[NX2]~[NX1] |
191 | Diazo | [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] |
192 | Diazonium | [#6][NX2+]#[NX1] |
193 | Nitrosamine | [#7;!$(N*=O)][NX2]=[OX1] |
194 | Nitrosamide | [NX2](=[OX1])N-*=O |
195 | N-Oxide | [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] |
196 | Hydrazine | [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])] |
197 | Hydrazone | [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6] |
198 | Hydroxylamine | [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])] |
199 | Sulfon | [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])] |
200 | Sulfoxide | [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])] |
201 | Sulfonium | [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])] |
202 | Sulfuric acid | [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] |
203 | Sulfuric monoester | [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] |
204 | Sulfuric diester | [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] |
205 | Sulfuric monoamide | [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] |
206 | Sulfuric diamide | [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
207 | Sulfuric esteramide | [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] |
208 | Sulfuric derivative | [SX4D4](=[!#6])(=[!#6])([!#6])[!#6] |
209 | Sulfonic acid | [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])] |
210 | Sulfonamide | [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
211 | Sulfonic ester | [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])] |
212 | Sulfonic halide | [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1] |
213 | Sulfonic derivative | [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6] |
214 | Sulfinic acid | [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])] |
215 | Sulfinic amide | [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
216 | Sulfinic ester | [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] |
217 | Sulfinic halide | [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1] |
218 | Sulfinic derivative | [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6] |
219 | Sulfenic acid | [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])] |
220 | Sulfenic amide | [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
221 | Sulfenic ester | [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])] |
222 | Sulfenic halide | [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1] |
223 | Sulfenic derivative | [SX2;$([H1]),$([H0][#6])][!#6] |
224 | Phosphine | [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])] |
225 | Phosphine oxide | [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])] |
226 | Phosphonium | [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])] |
227 | Phosphorylen | [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])] |
228 | Phosphonic acid | [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] |
229 | Phosphonic monoester | [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] |
230 | Phosphonic diester | [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] |
231 | Phosphonic monoamide | [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
232 | Phosphonic diamide | [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
233 | Phosphonic esteramide | [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
234 | Phosphonic acid derivative | [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6] |
235 | Phosphoric acid | [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] |
236 | Phosphoric monoester | [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] |
237 | Phosphoric diester | [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] |
238 | Phosphoric triester | [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] |
239 | Phosphoric monoamide | [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
240 | Phosphoric diamide | [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
241 | Phosphoric triamide | [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
242 | Phosphoric monoestermonoamide | [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
243 | Phosphoric diestermonoamide | [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
244 | Phosphoric monoesterdiamide | [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
245 | Phosphoric acid derivative | [PX4D4](=[!#6])([!#6])([!#6])[!#6] |
246 | Phosphinic acid | [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])] |
247 | Phosphinic ester | [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] |
248 | Phosphinic amide | [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
249 | Phosphinic acid derivative | [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6] |
250 | Phosphonous acid | [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] |
251 | Phosphonous monoester | [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] |
252 | Phosphonous diester | [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] |
253 | Phosphonous monoamide | [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
254 | Phosphonous diamide | [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
255 | Phosphonous esteramide | [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
256 | Phosphonous derivatives | [PX3;$([D2]),$([D3][#6])]([!#6])[!#6] |
257 | Phosphinous acid | [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])] |
258 | Phosphinous ester | [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])] |
259 | Phosphinous amide | [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
260 | Phosphinous derivatives | [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6] |
261 | Quart silane | [SiX4]([#6])([#6])([#6])[#6] |
262 | Non-quart silane | [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])] |
263 | Silylmonohalide | [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6] |
264 | Het trialkylsilane | [SiX4]([!#6])([#6])([#6])[#6] |
265 | Dihet dialkylsilane | [SiX4]([!#6])([!#6])([#6])[#6] |
266 | Trihet alkylsilane | [SiX4]([!#6])([!#6])([!#6])[#6] |
267 | Silicic acid derivative | [SiX4]([!#6])([!#6])([!#6])[!#6] |
268 | Trialkylborane | [BX3]([#6])([#6])[#6] |
269 | Boric acid derivatives | [BX3]([!#6])([!#6])[!#6] |
270 | Boronic acid derivative | [BX3]([!#6])([!#6])[!#6] |
271 | Borohydride | [BH1,BH2,BH3,BH4] |
272 | Quaternary boron | [BX4] |
273 | Aromatic | a |
274 | Heterocyclic | [!#6;!R0] |
275 | Epoxide | [OX2r3]1[#6r3][#6r3]1 |
276 | NH aziridine | [NX3H1r3]1[#6r3][#6r3]1 |
277 | Spiro | [D4R;$(*(@*)(@*)(@*)@*)] |
278 | Annelated rings | [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])] |
279 | Bridged rings | [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])] |
280 | Sugar pattern 1 | [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)] |
281 | Sugar pattern 2 | [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] |
282 | Sugar pattern combi | [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)] |
283 | Sugar pattern 2 reducing | [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)] |
284 | Sugar pattern 2 alpha | [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] |
285 | Sugar pattern 2 beta | [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] |
286 | Conjugated double bond | *=*[*]=,#,:[*] |
287 | Conjugated tripple bond | *#*[*]=,#,:[*] |
288 | Cis double bond | */[D2]=[D2]/* |
289 | Trans double bond | */[D2]=[D2]/* |
290 | Mixed anhydrides | [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))] |
291 | Halogen on hetero | [FX1,ClX1,BrX1,IX1][!#6] |
292 | Halogen multi subst | [F,Cl,Br,I;!$([X1]);!$([X0-])] |
293 | Trifluoromethyl | [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1]) |
294 | C ONS bond | [#6]~[#7,#8,#16] |
295 | Charged | [!+0] |
296 | Anion | [-1,-2,-3,-4,-5,-6,-7] |
297 | Kation | [+1,+2,+3,+4,+5,+6,+7] |
298 | Salt | ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7]) |
299 | 1,3-Tautomerizable | [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)] |
300 | 1,5-Tautomerizable | [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)] |
301 | Rotatable bond | [!$(*#*)&!D1]-!@[!$(*#*)&!D1] |
302 | Michael acceptor | [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])] |
303 | Dicarbodiazene | [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1]) |
304 | CH-acidic | [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)] |
305 | CH-acidic strong | [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])] |
306 | Chiral center specified | [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)] |
Constructor and Description |
---|
SubstructureFingerprinter()
Set up the fingerprinter to use the fragments from
StandardSubstructureSets . |
SubstructureFingerprinter(String[] smarts)
Set up the fingerprinter to use a user-defined set of fragments.
|
Modifier and Type | Method and Description |
---|---|
IBitFingerprint |
getBitFingerprint(IAtomContainer atomContainer)
Returns the bit fingerprint for the given
IAtomContainer . |
ICountFingerprint |
getCountFingerprint(IAtomContainer atomContainer)
Returns the count fingerprint for the given
IAtomContainer . |
Map<String,Integer> |
getRawFingerprint(IAtomContainer iAtomContainer)
Returns the raw representation of the fingerprint for the given IAtomContainer.
|
int |
getSize()
Returns the size (or length) of the fingerprint.
|
String |
getSubstructure(int bitIndex)
Retrieves the SMARTS representation of a substructure for a given
bit in the fingerprint.
|
getFingerprint, getParameters, getVersionDescription
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFingerprint, getVersionDescription
public SubstructureFingerprinter(String[] smarts)
smarts
- The collection of fragments to look forpublic SubstructureFingerprinter()
StandardSubstructureSets
.public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer) throws CDKException
IAtomContainer
.getBitFingerprint
in interface IFingerprinter
atomContainer
- IAtomContainer
for which the fingerprint should be calculated.CDKException
- may be thrown if there is an error during aromaticity detection
or (for key based fingerprints) if there is a SMARTS parsing errorpublic ICountFingerprint getCountFingerprint(IAtomContainer atomContainer) throws CDKException
IAtomContainer
.getCountFingerprint
in interface IFingerprinter
atomContainer
- IAtomContainer
for which the fingerprint should be calculated.CDKException
- if there is an error during aromaticity detection
or (for key based fingerprints) if there is a SMARTS parsing error.public Map<String,Integer> getRawFingerprint(IAtomContainer iAtomContainer) throws CDKException
getRawFingerprint
in interface IFingerprinter
iAtomContainer
- IAtomContainer for which the fingerprint should be calculated.CDKException
public int getSize()
getSize
in interface IFingerprinter
public String getSubstructure(int bitIndex)
bitIndex
- bitIndex
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