/usr/share/RDKit/Data/SmartsLib/patty_rules.txt is in rdkit-data 201603.5-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 | # original source: http://tripod.nih.gov/files/patty.rules, copied July 2015
#
# CAT CATION, used for basic functionality; i.e., protonated
# ANI ANION, used for acidic functionality; i.e., de-protonated
#
# POL POLAR, atom is neither an ANION nor a CATION and has a LP
# and a polar H, or (due to tautomerization) can be a donor
# or an acceptor.
#
# DON DONOR, an atom that is none of the above and has a polar H.
# ACC ACCEPTOR, an atom that is none of the above and has an LP.
#
# HYD HYRDOPHOBIC, an atom that is none of the above and is an
# accessible atom that has hydrophobic functionality
#
# OTH OTHER, an atom that falls in none of the above classes.
* OTH # Default Rule
[#8] ACC # O
[#7] DON # N
[#6,#14] HYD # C, Si
[#16] HYD # S
[#34] HYD # Se
[#16] HYD # P
[#33] HYD # As
[#9D1,#17D1,#35D1,#53D1,#85D1] HYD # halogens
[#9D0,#17D0,#35D0,#53D0,#85D0] ANI
[OHD1] POL # hydroxide
[OH2] POL # water (NEW)
[#1] HYD # H
[#1][#7] DON
[NH0]#* ACC # :N# (sp)
[ND2](*)=* ACC # =N- (sp2)
[nH0] ACC # aomatic N - (sp2)
[NH;D1]=* POL # HN=X
[ND1]=* POL # N=N= (azide)
[#7,#15,#33;D4] CAT # quaternary N,P,As
# any nonconjugated sp3 N is a basic amine (except next
# to conjugated a N)
[#7D1]-* CAT
[#7D2](-*)-* CAT
[#7D3](-*)(-*)-* CAT
[#7v4] CAT
[#7D3]-N-*=* OTH
[#7D3](-*)(-*)-N-*#* OTH
# conjugated N's
[#7D1]-*=* DON
[#7D1]-*:* DON
[#7D1]-*#* DON
[#7H;D2]-*=* DON
[#7H;D2]-*:* DON
[#7H;D2]-*#* DON
[#7;D3]-*=* OTH # conj & buried
[#7;D3]-*:* OTH #
[#7;D3](*=*)(-&!@*)*:* OTH
[#7;D3]-*#* OTH
# amidine
#
# N+H2
# //
# CH3--C--:NH2
[#7D1]-C(-[#6])=[#7D1] CAT
[#7D1]=C(-[#6])-[#7D1] CAT
# changed to #7D1
[#7D1]-C(-S)=[#7D1] CAT
[#7D1]=C(-S)-[#7D1] CAT
# guanidinium
N-C(=N)-N CAT
N=C(-N)-N CAT
# nitro
[OD1]-N=[OD1] ACC
[OD1]=N-[OD1] ACC
# trisubstituted sp2 amines are cations with exceptions
[#7,#15,#33;D3]=* CAT
N([OD1])=[OD1] OTH
# disbustituted sp amines and exceptions
[N+;D2](=*)=* CAT # diazonium -[N+]#
[N+;D2]#* CAT # #N-
[N+;D2]#[CX1] OTH # isonitrile -N#C:
[CX1]#[N+;D2] ACC # isonitrile :C#N-
# trisubstituted oxygens, sulfurs and exceptions
[#8,#16;D3] CAT # -O(-*)(-*)
[#8,#16;D3](=*) CAT # =O-
S=[#8,#16;X1] OTH # dative sulfoxides
*-[#8,#16;X1] OTH # oxides,sulfides
# misc anions
[SD1]a ANI
# phosphate/arsenate monoanion and S equialents
#
# O O
# | |
# P--O (-) and --P--O (-)
# /
[#8,#16,#34;X1]~[#15,#33;D3]~[#8,#16,#34;D1] ANI
[#8,#16,#34;D1]~[#15,#33;D3]~[#8,#16,#34;X1] ANI
[#8,#16,#34;X1]~[#15,#33;D4]~[#8,#16,#34;D1] ANI
[#8,#16,#34;D1]~[#15,#33;D4]~[#8,#16,#34;X1] ANI
[#15,#33;D3]([#8,#16,#34;X1])~[#8,#16,#34;D1] OTH
[#15,#33;D3]([#8,#16,#34;D1])~[#8,#16,#34;X1] OTH
[#15,#33;D4]([#8,#16,#34;X1])~[#8,#16,#34;D1] OTH
[#15,#33;D4]([#8,#16,#34;D1])~[#8,#16,#34;X1] OTH
# sulfite and selenite anion and S equivalents
#
# O O
# | |
# S--O (-) and O--S--O (-)
# / |
[#8,#16,#34;X1]~[#8,#16,#34;D3]~[#8,#16,#34;D1] ANI
[#8,#16,#34;D1]~[#8,#16,#34;D3]~[#8,#16,#34;X1] ANI
[#8,#16,#34;X1]~[#8,#16,#34;D4](~[#8,#16,#34;D1])~[#8,#16,#34;X1] ANI
[#8,#16,#34;D1]~[#8,#16,#34;D4](~[#8,#16,#34;X1])~[#8,#16,#34;X1] ANI
# muscimol anion (first O is ANI, N is ACC)
#
# *--* *--*
# / | / |
# (-) O-C O or O=C O
# \\ / \ /
# N: :N (-)
[#8D1][#6]1=[#7][#8]**1 ANI
[#7]1=[#6]([#8D1])**[#8]1 ANI
[#8]=[#6]1[#7][#8]**1 ANI
[#7]1[#6](=O)**[#8]1 ANI
# tetrazole anion (all Ns are ANI)
#
# :N--N: (-) :N--N:
# # || / ||
# :N C or :N C (aromatic)
# \ / \\ /
# N: (-) N:
[nD2]1[nD2][nD2][nD2]c1 ANI
[nD2]1[nD2][nD2]c[nD2]1 ANI
[nD2]1[nD2]c[nD2][nD2]1 ANI
[nD2]1c[nD2][nD2][nD2]1 ANI
# diaminopyrimidine (ring Ns are POL)
#
# *==*
# / \
# :N C--NH2 (aromatic)
# \\ #
# C--N:
# /
# NH2
[nD2]1c(N)[nD2]c(N)aa1 POL
[nD2]1c(N)aa[nD2]c1(N) POL
# make imidazole Ns both POL
#
# C==C C==C
# / | / |
# :N NH or HN N: (aromatic)
# \\ / \ #
# C C
#
#
n1cncc1 POL
# stabilized sulfonamides and phosphonamides
#
# O
# |
# a--S--NH2
# |
# O
[ND1]~[SD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) POL
[ND1]~[PD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) POL
[#8,#16,#34;D1]~[SD4](a)(~[#8,#16,#34;D1])~[ND1] ACC
[#8,#16,#34;D1]~[PD4](a)(~[#8,#16,#34;D1])~[ND1] ACC
[#8,#16,#34;D1]~[SD4](a)(~[#8,#16,#34;D1])~[ND2] ANI
[#8,#16,#34;D1]~[PD4](a)(~[#8,#16,#34;D1])~[ND2] ANI
[ND2]~[SD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) ANI
# carbonyl-hydroxide tautaumers
#
# !O !O
# | |
# C C
# / \\/ \\
# OH X O
[OH]C(*)=*C=O POL
O=C*=C(*)[OH] POL
O=C-*:[#6](*)[OH] POL
# carboxylates and S equivalents
#
# O
# #
# -C
# \
# O (-)
[#8,#16,#34;D1]C=[#8,#16,#34] ANI
[#8,#16,#34]=C[#8,#16,#34;D1] ANI
# *==*
# / \
# * C==O (aromatic)
# \\ /
# C--C And 4 Cs away
# /
# OH
[OH]c1cc(=O)aaa1 POL
O=c1cc([OH])aaa1 POL
[OH]c1ccc(=O)aa1 POL
O=c1ccc([OH])aa1 POL
# special ionizations of adjacent keto/enols
[OD1]C=CC(=O)[O]* ANI
[OD1]C=CC(=O)[N]* ANI
O=C-CC(=O)[O]* ANI
O=C-CC(=O)[N]* ANI
OC=C-C(=O)C=CO ANI
OC-C=C(-O)C=CO ANI
# planar buried C bonded to electronegative atom
[#6D3](=*)-[#7,#8] OTH
[#6D3](:*)(:*)[#7,#8] OTH
[#6D3](-*)(:*):[#7,#8] OTH
[#6D3]=[#7,#8] OTH
[#6D2](#*)-[#7,#8] OTH
[#6D2](*)#[#7,#8] OTH
[#6D2](=*)=[#7,#8] OTH
[#16D2](#*)-[#7,#8] OTH # buried sp S
[#16D2](*)#[#7,#8] OTH
[#16D2](=*)=[#7,#8] OTH
# misc fixups
[ND2](=*)=* OTH # sp buried
[ND2](*)#* OTH
[#7,#15,#33;D4]=[S,O] OTH
[ND3]P(=O) OTH
[OD1]-n ACC
n-[OD1] OTH
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