org.openscience.cdk.fingerprint

Class SubstructureFingerprinter

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:

master

Belongs to CDK module:

fingerprint

Keywords:

fingerprint, similarity

Created on:

2005-12-30

Constructor Summary

Constructors

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.

Method Summary

Methods

Modifier and Type	Method and Description
IBitFingerprint	getBitFingerprint(IAtomContainer atomContainer) Returns the bit fingerprint for the given IAtomContainer.
ICountFingerprint	getCountFingerprint(IAtomContainer container) 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()

Set up the fingerprinter to use the fragments from StandardSubstructureSets.

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

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

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.

getCountFingerprint

public ICountFingerprint getCountFingerprint(IAtomContainer container)
                                      throws CDKException

Returns the count fingerprint for the given IAtomContainer.

Specified by:

getCountFingerprint in interface IFingerprinter

Parameters:

container - 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.