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Diffstat (limited to 'java/resources/smartsEvaluation/evaluation.txt')
| -rw-r--r-- | java/resources/smartsEvaluation/evaluation.txt | 130 |
1 files changed, 0 insertions, 130 deletions
diff --git a/java/resources/smartsEvaluation/evaluation.txt b/java/resources/smartsEvaluation/evaluation.txt deleted file mode 100644 index 6e7eec7..0000000 --- a/java/resources/smartsEvaluation/evaluation.txt +++ /dev/null @@ -1,130 +0,0 @@ -####################################################################################################################
-# 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
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