/usr/share/pyshared/chemfp/rdmaccs.patterns is in python-chemfp 1.1p1-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 | # The contents of this file are derived from RDKit's Chem/MACCSkeys.py
# and translated by hand to the chemfp pattern format.
# The RDKit code is distributed with the following license:
# Copyright (c) 2006-2010
# Rational Discovery LLC, Greg Landrum, and Julie Penzotti
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Rational Discovery nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
#
# SMARTS definitions for the publically available MACCS keys
# and a MACCS fingerprinter
#
# I compared the MACCS fingerprints generated here with those from two
# other packages (not MDL, unfortunately). Of course there are
# disagreements between the various fingerprints still, but I think
# these definitions work pretty well. Some notes:
#
# 1) most of the differences have to do with aromaticity
# 2) there's a discrepancy sometimes because the current RDKit
# definitions do not require multiple matches to be distinct. e.g. the
# SMILES C(=O)CC(=O) can match the (hypothetical) key O=CC twice in my
# definition. It's not clear to me what the correct behavior is.
# 3) Some keys are not fully defined in the MDL documentation
# 4) Two keys, 125 and 166, have to be done outside of SMARTS.
# (Note: in chemfp those are bits 123 and 165)
# 5) Key 1 (ISOTOPE) isn't defined
0 1 <0> Isotope
#1 [#103,#104,#105,#106,#107,#106,#109,#110,#111,#112] 1 Isotope (Not complete)
1 1 [#103,#104] Isotope (Not complete)
# *NOTE* spec wrong
2 1 [Ge,#33,#34,Sn,Sb,#52,Tl,Pb,Bi] Group IVa,Va,VIa Periods 4-6 (Ge...)
3 1 [Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr] actinide
# *NOTE* spec wrong
4 1 [Sc,Ti,Y,Zr,Hf] Group IIIB,IVB (Sc...)
5 1 [La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu] Lanthanide
# *NOTE* spec wrong
6 1 [V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re] Group VB,VIB,VIIB (V...)
7 1 [!#6;!#1]~1~*~*~*~1 QAAA@1
8 1 [Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt] Group VIII (Fe...)
9 1 [Be,Mg,Ca,Sr,Ba,Ra] Group IIa (Alkaline earth)
10 1 *~1~*~*~*~1 4-member Ring
11 1 [Cu,Zn,Ag,Cd,Au,Hg] Group IB,IIB (Cu..)
12 1 [#8]~[#7](~[#6])~[#6] ON(C)C
13 1 [#16]-[#16] S-S
14 1 [#8]~[#6](~[#8])~[#8] OC(O)O
15 1 [!#6;!#1]~1~*~*~1 QAA@1
16 1 [#6]#[#6] CTC
# *NOTE* spec wrong
17 1 [#5,Al,Ga,In,Tl] Group IIIA (B...)
18 1 *~1~*~*~*~*~*~*~1 7-member Ring
19 1 [#14] Si
20 1 [#6]=[#6](~[!#6;!#1])~[!#6;!#1] C=C(Q)Q
21 1 *~1~*~*~1 3-member Ring
22 1 [#7]~[#6](~[#8])~[#8] NC(O)O
23 1 [#7]-[#8] N-O
24 1 [#7]~[#6](~[#7])~[#7] NC(N)N
25 1 [#6]=;@[#6](@*)@* C$=C($A)$A
26 1 [I] I
27 1 [!#6;!#1]~[CH2]~[!#6;!#1] QCH2Q
28 1 [#15] P
29 1 [#6]~[!#6;!#1](~[#6])(~[#6])~[!#1] CQ(C)(C)A
30 1 [!#6;!#1]~[F,Cl,Br,I] QX
31 1 [#6]~[#16]~[#7] CSN
32 1 [#7]~[#16] NS
33 1 [CH2]=* CH2=A
34 1 [Li,Na,K,Rb,Cs,Fr] Group IA (Alkali Metal)
35 1 [#16R] S Heterocycle
36 1 [#7]~[#6](~[#8])~[#7] NC(O)N
37 1 [#7]~[#6](~[#6])~[#7] NC(C)N
38 1 [#8]~[#16](~[#8])~[#8] OS(O)O
39 1 [#16]-[#8] S-O
40 1 [#6]#[#7] CTN
41 1 F F
42 1 [!C;!c;!#1;!H0]~*~[!C;!c;!#1;!H0] QHAQH
# I have no idea (APD)
#43 1 <rdmaccs-bit-43> OTHER
43 1 <0> OTHER
44 1 [#6]=[#6]~[#7] C=CN
45 1 Br BR
46 1 [#16]~*~[#7] SAN
47 1 [#8]~[!#6;!#1](~[#8])(~[#8]) OQ(O)O
48 1 [!+0] CHARGE
49 1 [#6]=[#6](~[#6])~[#6] C=C(C)C
50 1 [#6]~[#16]~[#8] CSO
51 1 [#7]~[#7] NN
52 1 [!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0] QHAAAQH
53 1 [!#6;!#1;!H0]~*~*~[!#6;!#1;!H0] QHAAQH
54 1 [#8]~[#16]~[#8] OSO
55 1 [#8]~[#7](~[#8])~[#6] ON(O)C
56 1 [#8R] O Heterocycle
57 1 [!#6;!#1]~[#16]~[!#6;!#1] QSQ
58 1 [#16]!:*:* Snot%A%A
59 1 [#16]=[#8] S=O
60 1 [!#1]~[#16](~[!#1])~[!#1] AS(A)A
61 1 *@*!@*@* A$!A$A
62 1 [#7]=[#8] N=O
63 1 *@*!@[#16] A$A!S
64 1 c:n C%N
65 1 [#6]~[#6](~[#6])(~[#6])~[!#1] CC(C)(C)A
66 1 [!#6;!#1]~[#16] QS
67 1 [!#6;!#1;!H0]~[!#6;!#1;!H0] QHQH (&...) FIX: incomplete definition
68 1 [!#6;!#1]~[!#6;!#1;!H0] QQH
69 1 [!#6;!#1]~[#7]~[!#6;!#1] QNQ
70 1 [#7]~[#8] NO
71 1 [#8]~*~*~[#8] OAAO
72 1 [#16]=* S=A
73 1 [CH3]~*~[CH3] CH3ACH3
74 1 [!#1]!@[#7]@[!#1] A!N$A
75 1 [#6]=[#6](~[!#1])~[!#1] C=C(A)A
76 1 [#7]~*~[#7] NAN
77 1 [#6]=[#7] C=N
78 1 [#7]~*~*~[#7] NAAN
79 1 [#7]~*~*~*~[#7] NAAAN
80 1 [#16]~*(~[!#1])~[!#1] SA(A)A
81 1 [!#1]~[CH2]~[!#6;!#1;!H0] ACH2QH
82 1 [!#6;!#1]~1~*~*~*~*~1 QAAAA@1
83 1 [NH2] NH2
84 1 [#6]~[#7](~[#6])~[#6] CN(C)C
85 1 [C;H2,H3][!#6;!#1][C;H2,H3] CH2QCH2
86 1 [F,Cl,Br,I]!@*@* X!A$A
87 1 [#16] S
88 1 [#8]~*~*~*~[#8] OAAAO
#89 1 [$([!#6;!#1;!H0]~*~*~[CH2]~[!#1]),$([!#6;!#1;!H0;R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[CH2;R]1)] QHAACH2A
89 1 [$([!#6;!#1;!H0]~*~*~[CH2]~[!#1]),$([!#6;!#1;!H0;R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[CH2;R]1)] QHAACH2A
90 1 [$([!#6;!#1;!H0]~*~*~*~[CH2]~[!#1]),$([!#6;!#1;!H0;R]1@[R]@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~*~[R]1@[R]@[CH2;R]1)] QHAAACH2A
91 1 [#8]~[#6](~[#7])~[#6] OC(N)C
92 1 [!#6;!#1]~[CH3] QCH3
93 1 [!#6;!#1]~[#7] QN
94 1 [#7]~*~*~[#8] NAAO
95 1 *~1~*~*~*~*~1 5 M ring
96 1 [#7]~*~*~*~[#8] NAAAO
97 1 [!#6;!#1]~1~*~*~*~*~*~1 QAAAAA@1
98 1 [#6]=[#6] C=C
99 1 [!#1]~[CH2]~[#7] ACH2N
100 1 [$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1)] 8M Ring or larger. This only handles up to ring sizes of 14
101 1 [!#6;!#1]~[#8] QO
102 1 Cl CL
103 1 [!#6;!#1;!H0]~*~[CH2]~[!#1] QHACH2A
104 1 *@*(@*)@* A$A($A)$A
105 1 [!#6;!#1]~*(~[!#6;!#1])~[!#6;!#1] QA(Q)Q
106 1 [F,Cl,Br,I]~*(~[!#1])~[!#1] XA(A)A
107 1 [CH3]~*~*~*~[CH2]~[!#1] CH3AAACH2A
108 1 [!#1]~[CH2]~[#8] ACH2O
109 1 [#7]~[#6]~[#8] NCO
110 1 [#7]~*~[CH2]~[!#1] NACH2A
111 1 [!#1]~*(~[!#1])(~[!#1])~[!#1] AA(A)(A)A
112 1 [#8]!:*:* Onot%A%A
113 1 [CH3]~[CH2]~[!#1] CH3CH2A
114 1 [CH3]~*~[CH2]~[!#1] CH3ACH2A
115 1 [$([CH3]~*~*~[CH2]~[!#1]),$([CH3]~*1~*~[CH2]1)] CH3AACH2A
116 1 [#7]~*~[#8] NAO
117 2 [$([!#1]~[CH2]~[CH2]~[!#1]),$(*1~[CH2]~[CH2]1)] ACH2CH2A > 1
118 1 [#7]=* N=A
# FIX: incomplete definition
119 2 [!#6;R] Heterocyclic atom > 1 (&...)
120 1 [#7;R] N Heterocycle
121 1 [!#1]~[#7](~[!#1])~[!#1] AN(A)A
122 1 [#8]~[#6]~[#8] OCO
123 1 [!#6;!#1]~[!#6;!#1] QQ
124 2 <aromatic-rings> Aromatic Ring > 1
125 1 [!#1]!@[#8]!@[!#1] A!O!A
# FIX: incomplete definition
126 2 *@*!@[#8] A$A!O > 1 (&...)
127 1 [$([!#1]~[CH2]~*~*~*~[CH2]~[!#1]),$([R]1@[CH2;R]@[R]@[R]@[R]@[CH2;R]1),$([!#1]~[CH2]~[R]1@[R]@[R]@[CH2;R]1),$([!#1]~[CH2]~*~[R]1@[R]@[CH2;R]1)] ACH2AAACH2A
128 1 [$([!#1]~[CH2]~*~*~[CH2]~[!#1]),$([R]1@[CH2]@[R]@[R]@[CH2;R]1),$([!#1]~[CH2]~[R]1@[R]@[CH2;R]1)] ACH2AACH2A
# FIX: incomplete definition
129 2 [!#6;!#1]~[!#6;!#1] QQ > 1 (&...)
130 2 [!#6;!#1;!H0] QH > 1
131 1 [#8]~*~[CH2]~[!#1] OACH2A
132 1 *@*!@[#7] A$A!N
133 1 [F,Cl,Br,I] X (HALOGEN)
134 1 [#7]!:*:* Nnot%A%A
135 2 [#8]=* O=A > 1
136 1 [!#6;R] Heterocycle
# FIX: incomplete definition
137 2 [!#6;!#1]~[CH2]~[!#1] QCH2A > 1 (&...)
138 1 [O;!H0] OH
# FIX: incomplete definition
139 4 [#8] O > 3 (&...)
# FIX: incomplete definition
140 3 [CH3] CH3 > 2 (&...)
141 2 [#7] N > 1
142 1 *@*!@[#8] A$A!O
143 1 [!#1]!:*:*!:[!#1] Anot%A%Anot%A
144 2 *~1~*~*~*~*~*~1 6-member ring > 1
145 3 [#8] O > 2
146 1 [$([!#1]~[CH2]~[CH2]~[!#1]),$([R]1@[CH2;R]@[CH2;R]1)] ACH2CH2A
147 1 [!#1]~[!#6;!#1](~[!#1])~[!#1] AQ(A)A
148 2 [C;H3,H4] CH3 > 1
149 1 [!#1]!@*@*!@[!#1] A!A$A!A
150 1 [#7;!H0] NH
151 1 [#8]~[#6](~[#6])~[#6] OC(C)C
152 1 [!#6;!#1]~[CH2]~[!#1] QCH2A
153 1 [#6]=[#8] C=O
154 1 [!#1]!@[CH2]!@[!#1] A!CH2!A
155 1 [#7]~[!#1](~[!#1])~[!#1] NA(A)A
156 1 [#6]-[#8] C-O
157 1 [#6]-[#7] C-N
158 2 [#8] O>1
159 1 [C;H3,H4] CH3
160 1 [#7] N
161 1 a Aromatic
162 1 *~1~*~*~*~*~*~1 6-member Ring
163 1 [#8] O
164 1 [R] Ring
# this can't be done in SMARTS
165 2 <fragments> more than one fragment
|