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
|
####################################################################################################################
# SMARTS evaluation definitions:
# SMARTSpattern SMARTSdescription moleculeList
#
# where moleculeList can be of type:
# mol1 mol2 mol3 which means that this SMARTSpattern should NOT occure in these molecules
# mol1#1#5#22 which means that this SMARTSpattern should occure at atoms 1,5 and 22 of this molecule
# mol1#1 mol2#8 which means that this SMARTSpattern should occure at molecule1/atom 1 and molecule2/atom 8
# mol1#1 mol2 which means that this SMARTSpattern should occure at molecule1/atom 1 and NOT in molecule2
# mol1#-1 mol2#-1 which means that this SMARTSpattern should occure at molecule1 and in molecule2, in both with undefined atom positions
# mol1#-1 mol2 which means that this SMARTSpattern should occure at molecule1 and NOT in molecule2
#
####################################################################################################################
###############################
## cis/trans detection
###############################
CC=CC a_carbon_in_abcd_with_trans butene#1#4 trans-butene#1#4 cis-butene#1#4
C\C=C/C a_carbon_in_abcd_with_trans butene trans-butene
C/C=C\C a_carbon_in_abcd_with_trans butene trans-butene
C/C=C/C a_carbon_in_abcd_with_trans butene trans-butene#1#4
C/?C=C/?C a_carbon_in_abcd_with_trans butene#1#4 trans-butene#1#4
C\C=C\C a_carbon_in_abcd_with_cis butene cis-butene
C/C=C/C a_carbon_in_abcd_with_cis butene cis-butene
C/C=C\C a_carbon_in_abcd_with_cis butene cis-butene#1
C\C=C/C a_carbon_in_abcd_with_cis butene cis-butene#4
C/?C=C\?C a_carbon_in_abcd_with_cis butene#1#4 cis-butene#1
C\?C=C/?C a_carbon_in_abcd_with_cis butene#1#4 cis-butene#4
# this can not be found for MDL SDF import, because JOELib's auto-assign method assign C/C=C/C !!!
C\C=C\C a_carbon_in_abcd_with_trans butene trans-butene
###############################
## misc
###############################
[#8][#1] hydroxy_group_explicit_h 8-amino-3H-phenoxazin-3-ol#17
[#8;H1] hydroxy_group 8-amino-3H-phenoxazin-3-ol#17 6-iminocyclohexa-1,4-diene-1,3-diol#4#9 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#1
[*;!#6;r3] heteroatoms_in_3-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#10
[*;r3] 3_ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#8#9#10
[*;r4] 4_ring 5-cyclobutyl-2-cycloheptylphosphinane#1#2#3#4
[*;r7] 7_ring 5-cyclobutyl-2-cycloheptylphosphinane#11#12#13#14#15#16#17
[*;!#6;r6] hetero_in_6-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#17#18
[#7;!#6;r6] N_in_6-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#18
[#15;!#6;r6] P_in_6-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#17
[*;!#6;H1] het_atoms_with_H 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#1#10#18#17
[#7][#1] N_explicit_h 8-amino-3H-phenoxazin-3-ol#11 8-amino-3H-phenoxazin-3-one#11
[#7]:c N_in_aromatic_bonds_with_C pyridine#6 8-amino-3H-phenoxazin-3-one#3
[n] aromatic_N pyridine#6
[a] aromatic pyridine#1#2#3#4#5#6 8-amino-3H-phenoxazin-3-one#1#2#3#4#5#6#7#8#9#10#13#14#15#16
[a] aromatic pyridine#-1 8-amino-3H-phenoxazin-3-one#-1 phenol#-1
*@*!@*@* ring_nbr_of_non-ring_bonds_that_connect_rings 5-cyclobutyl-2-cycloheptylphosphinane#1#4#6#7#8#9#12#13
[*;r]!@[*;r] non-ring_bonds_that_connect_rings 5-cyclobutyl-2-cycloheptylphosphinane#3#5#10#11
O!:a:a O_in_non-aromatic_bonds_to_an_a phenol#7 8-amino-3H-phenoxazin-3-one#17
[*;!#6;!#1]~[*;!#6;!#1] het-het_bonds 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#1#2#3 8-amino-3H-phenoxazin-3-ol
[*;!#6;!#1]~[*;!#6;!#1] het-het_bonds {(Z)-1-(1-hydrazinopropyl)-2-[(hydroxythio)oxy]-2-sulfinovinyl}(oxo)sulfonium#2#3#4#5#6#7#12#13#14#15
[O]-[O] peroxide_NoKey peroxide#1#2
[OH1]-[OH1] hydroperoxide_NoKey peroxide#1#2
[*;r4] atoms_in_4_ring_Key11 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#1#2#3#4
[#7](~[#8])(~[#6])~[#6] N_connected_to_1_O_and_2_C_Key13 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#5
[#16]-[#16] S_atoms_in_S-S_groups_Key14 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#8#9
[#6](~[#8])(~[#8])~[#8] C_connected_to_3_O_Key15 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#10
[*;!#6;!#1;r3] heteroatoms_in_3-membered_rings_Key16 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#15#16
###############################
## ALTANA Pharma, Germany Tests
###############################
[#6][NH][OH,O-] hydroxylamin hydroxylamin#1 TEST_1#10
[#6][NH][OH,O-] hydroxylamin hydroxylamin_H#1 TEST_1_H#10
[*;!#1;!#5;!#6;!#14;!#7;!#15;!#8;!#16;!#9;!#17;!#35;!#53] metal hydroxylamin phenol pyridine 5-cyclobutyl-2-cycloheptylphosphinane 8-amino-3H-phenoxazin-3-ol
[#1] explicit_hydrogen water#2#3
[OH2] water water#1
[*;!#1] all_except_hydrogen water#1 8-amino-3H-phenoxazin-3-ol#1#2#3#4#5#6#7#8#9#10#11#13#14#15#16#17
O=[$(C);$(C-[*!r!N!O])]-[$(C);$(C-[*!r!N!O!S])]=[$(C);$(C-[*!r!N!O!S])] ab_unsat_carbonyl ab_unsat_carbonyl_h#4
O=[$(C);$(C-[*!r!N!O])]-[$(C);$(C-[*!r!N!O!S])]=[$(C);$(C-[*!r!N!O!S])] ab_unsat_carbonyl ab_unsat_carbonyl#4
[#6]1(~[*!r!G7])~[#6]([*!r!G7])~[#6](~[G7])~[#7]~[#6](~[#7]1)[*!r!G7] pyrimidin_derivat_with_nonHalogen_at_2_5_6_and_halogen_at_4_explicit_nbr pyrimidin_derivat#2
C[$([CH1]),$(CC)]([G7])([G7]) di_halogen_ethyl_connected_to_H_or_C di_halogen_ethyl#1#5#13
[$([#6]);$(*~[*!r!G7]),$([*!H0])]1~[$([#6]);$(*~[*!r!G7]),$([*!H0])]~[#6](~[G7])~[#7]~[$([#6]);$(*~[*!r!G7]),$([*!H0])]~[#7]1 pyrimidin_derivat_with_nonHalogen_at_2_5_6_and_halogen_at_4_h_allowed pyrimidin_derivat#2 4-chlorpyrimidin#2
[$(c);$(*~[*!r!G7]),$([*!H0])]1~[$(c);$(*~[*!r!G7]),$([*!H0])]~c(~[G7])~n~[$([c]);$(*~[*!r!G7]),$([*!H0])]~n1 pyrimidin_with_nonHalogen_at_2_5_6_and_halogen_at_4_h_allowed pyrimidin_derivat#2 4-chlorpyrimidin#2
[*!r!G7,#1] notHalogenOrH 4-chlorpyrimidin 4-chlorpyrimidin_h#8#9#10
[$(C);!$(C~[*;R,N,O])] Knock65CNonRNO knockout65#1
###############################
#### recognize explicite hydrogens flag : FALSE ####
# joelib.smarts.ParseSmart.ParseSmart.anyRecognizesExpliciteHydrogens=false
* all_atoms hydroxylamin_H#1#2#3#4
#### recognize explicite hydrogens flag :TRUE ####
# joelib.smarts.ParseSmart.ParseSmart.anyRecognizesExpliciteHydrogens=true
#* all_atoms hydroxylamin_H#1#2#3#4#5#6#7#8#9#10#11
###############################
###############################
## Stephen Jelfs
###############################
[CH3Q1] terminal_methyl ethan#1#2
[CH3Q1] terminal_methyl propan#1#3
[CH3Q1] terminal_methyl butan#1#4
[CH3]C terminal_ethyl ethan#1#2
[CH3]C terminal_ethyl propan#1#3
[CH3]C terminal_ethyl butan#1#4
###############################
###############################
## aromaticity model
###############################
### inner ring problem
[a] aromatic pyrene-4,5-diol#2#3#5#6#7#8#9#10#11#12#13#14#15#16#17#18
[a] aromatic 9,10-dihydroxyphenanthrene#2#3#5#6#7#8#9#10#11#12#13#14#15#16
###misc
c1ccc2c(c1)C=CC(=O)O2 2H-chromen-2-one TEST_3
*!@* 2H-chromen-2-one TEST_3#1#2#3#6
[#6rQ3]=!@[!#6] 2H-chromen-2-one TEST_3#2
c1ccc2c(c1)C=CC(=O)O2 2H-chromen-2-one TEST_2
c1ccc2c(c1)C=CC(=O)O2 2H-chromen-2-one 2H-chromen-2-one
c1ccc2ocnc2c1 c1ccc2ocnc2c1 2-phenylnaphtho[1,2-d][1,3]oxazole#13
###############################
## RECAP-SMARTS pattern
###############################
[$([NX3]~*);!$([NX3]C=[G6]);!$([NX3]S(=O)=O)]~* amine-bond recap#1#7
[$([OD2;H0](C)C);!$([OD2](*)C=O)] etherO-bond recap#8
[NX4]~* quatN-bond recap#11
n-C nC-bond recap#19
c-c biphenyl-bond recap#25#26
[$([NX3]C=[G6]);!$([NX3]C(=O)[NX3])]C=O amideN-bond recap#35#56
[OD2]C=O esterO-bond recap#42
[NX3]C(=O)[NX3] ureaC-bond recap#47#49
C=C olefin-bond recap#52#53
[N;r6]([C;r6]=O)C lactamN-bond recap#56
[NX3]S(=O)=O sulphonamide-bond recap#65
###############################
## groups
###############################
[#89,#90,#91,#92,#93,#94,#95,#96,#97,#98,#99,#100,#101,#102,#103] Actinides_Key4 actinides#2#3#4#5#6#7#8#9#10#11#12#13#14#15#16
[#57,#58,#59,#60,#61,#62,#63,#64,#65,#66,#67,#68,#69,#70,#71] Lanthanides_Key6 lanthanides#1#2#3#4#5#6#7#8#9#10#11#12#13#14#15 lanthanides2#1#2#3#4#5#6#7#8#9#10#11#12#13#14#15
[#4,#12,#20,#38,#56,#88] alkaline_earth_elements_Key10 earth_alkanline#1#2#3#4#5#6
[#5,#13,#31,#49,#81] group_IIIA_elements_Key18 boron_group#1#2#3#4#5
[#3,#11,#19,#37,#55,#87] alkali_(group_IA)_elements_Key35 alkali_elements#1#2#3#4#5#6
[#2,#10,#18,#36,#54,#85,#86] other_elements_(He,Ne,Ar,Kr,Xe,Rn,At)_Key44 he_group#1#2#3#4#5#6
|
