java.lang.Object
- org.openscience.cdk.fingerprint.AbstractFingerprinter
- - org.openscience.cdk.fingerprint.SubstructureFingerprinter

All Implemented Interfaces:: IFingerprinter

Direct Known Subclasses:: KlekotaRothFingerprinter

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:

Table: 1: Default substructure patterns (SMARTS) for each bit position
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	`&#47[D2]=[D2]/`
289	Trans double bond	`&#47[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](~)~)]`

Author:: egonw
Source code:: main
Belongs to CDK module:: fingerprint
Keywords:: fingerprint, similarity
Created on:: 2005-12-30

Constructor Summary

Constructors
Constructor	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.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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.

Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter
getFingerprint, getParameters, getVersionDescription

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter
getFingerprint, getVersionDescription

- Constructor Detail
  - SubstructureFingerprinter
```
public SubstructureFingerprinter(String[] smarts)
```
    Set up the fingerprinter to use a user-defined set of fragments.
    
    Parameters:
    
    smarts - The collection of fragments to look for
  - SubstructureFingerprinter
```
public SubstructureFingerprinter()
```
    Set up the fingerprinter to use the fragments from StandardSubstructureSets.
- Method Detail
  - getBitFingerprint
```
public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer)
                                  throws CDKException
```
    Returns the bit fingerprint for the given IAtomContainer.
    
    Specified by:
    
    getBitFingerprint in interface IFingerprinter
    
    Parameters:
    
    atomContainer - IAtomContainer for which the fingerprint should be calculated.
    
    Returns:
    
    the bit fingerprint
    
    Throws:
    
    CDKException - may be thrown if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error
  - getCountFingerprint
```
public ICountFingerprint getCountFingerprint(IAtomContainer atomContainer)
                                      throws CDKException
```
    Returns the count fingerprint for the given IAtomContainer.
    
    Specified by:
    
    getCountFingerprint in interface IFingerprinter
    
    Parameters:
    
    atomContainer - IAtomContainer for which the fingerprint should be calculated.
    
    Returns:
    
    the count fingerprint
    
    Throws:
    
    CDKException - if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error.
  - getRawFingerprint
```
public Map<String,Integer> getRawFingerprint(IAtomContainer iAtomContainer)
                                            throws CDKException
```
    Returns the raw representation of the fingerprint for the given IAtomContainer. The raw representation contains counts as well as the key strings.
    
    Specified by:
    
    getRawFingerprint in interface IFingerprinter
    
    Parameters:
    
    iAtomContainer - IAtomContainer for which the fingerprint should be calculated.
    
    Returns:
    
    the raw fingerprint
    
    Throws:
    
    CDKException
  - getSize
```
public int getSize()
```
    Returns the size (or length) of the fingerprint.
    
    Specified by:
    
    getSize in interface IFingerprinter
    
    Returns:
    
    the size of the fingerprint
  - getSubstructure
```
public String getSubstructure(int bitIndex)
```
    Retrieves the SMARTS representation of a substructure for a given bit in the fingerprint.
    
    Parameters:
    
    bitIndex -
    
    Returns:
    
    SMARTS representation of substructure at index bitIndex.

Class SubstructureFingerprinter

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter

Methods inherited from class java.lang.Object

Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter

Constructor Detail

SubstructureFingerprinter

SubstructureFingerprinter

Method Detail

getBitFingerprint

getCountFingerprint

getRawFingerprint

getSize

getSubstructure