Attached the original list from Jonathan of the 861 SLN hits.
S.
On 26/08/2015 13:08 , Greg Landrum wrote:
On Wed, Aug 26, 2015 at 2:32 AM, Simon Saubern <simon.saub...@csiro.au
<mailto:simon.saub...@csiro.au>> wrote:
Thanks for doing this Greg.
Fixing those SMARTS queries always looked like it would be a
real...pain.
:-)
I've dropped your Github file into the KNIME workflow, and the
RDKit version of the workflow (using nodes RDKit
2.5.0.201505221301) now hits 770 structures in the WEHI-10k test set.
For what it's worth, I now get 888 matches across the WEHI-10K set
when running my Python test script. I am not 100% sure that the KNIME
nodes are doing (or can do) the mergeQueryHs step; that's something
else for me to follow up on.
But that includes 19 false positives that weren't being caught by
the SLN filters.
One filter alone is responsible for 17 of those false positives:
anil_di_alk_C(246)
old:
c:1:c:c(:c:c:c:1-[#8]-[#6;X4])-[#7](-[#6;X4])-[$([#1]),$([#6;X4])]
new: c:1:c:c(:c:c:c:1-[#8]-[#6;X4])-[#7;!H0,$([#7]-[#6;X4])]-[#6;X4]
An example of one of the false positive structures is the aniline
sulfonamide WEHI-18518.
I've checked with Johnathan, and the intention of that query is
that "... that the nitrogen has a single bond to a carbon that has
four atoms bonded to it (i.e. sp3), and that the other atom singly
bonded to the nitrogen atom is anything so long as it is either H
or an sp3 carbon".
So no to sulfonamides, and also some of the acetamide (sp2 C)
showing up as hits.
Thanks for pointing that out and providing the clarification about
what is expected!
I just committed a fix for this:
https://github.com/rdkit/rdkit/commit/e2487ffe79c393a6b0e472882bfb6eb66a3bcb8b
As an aside: If you could provide a text file that has the matches
found for each pattern in the WEHI-10k test set when you use the SLN
version of the PAINS, I would be very happy to use that to further
refine these patterns and to incorporate those results into the tests.
-greg
WEHI-0002757
WEHI-0003718
WEHI-0004345
WEHI-0005047
WEHI-0005752
WEHI-0006137
WEHI-0006195
WEHI-0006607
WEHI-0006892
WEHI-0007328
WEHI-0007435
WEHI-0007798
WEHI-0008187
WEHI-0008558
WEHI-0009314
WEHI-0011538
WEHI-0011957
WEHI-0012384
WEHI-0012615
WEHI-0012702
WEHI-0012773
WEHI-0012790
WEHI-0012829
WEHI-0012939
WEHI-0013053
WEHI-0013276
WEHI-0013384
WEHI-0013507
WEHI-0013892
WEHI-0013909
WEHI-0014006
WEHI-0014370
WEHI-0014546
WEHI-0014816
WEHI-0014836
WEHI-0014902
WEHI-0014937
WEHI-0015069
WEHI-0015806
WEHI-0015833
WEHI-0016142
WEHI-0016145
WEHI-0016287
WEHI-0016293
WEHI-0016316
WEHI-0016680
WEHI-0016735
WEHI-0016897
WEHI-0016957
WEHI-0016962
WEHI-0016985
WEHI-0017369
WEHI-0017518
WEHI-0017809
WEHI-0017964
WEHI-0018024
WEHI-0018269
WEHI-0018910
WEHI-0018941
WEHI-0018980
WEHI-0019026
WEHI-0019035
WEHI-0019132
WEHI-0019903
WEHI-0020161
WEHI-0020193
WEHI-0020284
WEHI-0020337
WEHI-0020458
WEHI-0020926
WEHI-0020933
WEHI-0020934
WEHI-0020935
WEHI-0020941
WEHI-0021184
WEHI-0023024
WEHI-0023287
WEHI-0023407
WEHI-0023681
WEHI-0023788
WEHI-0023867
WEHI-0023878
WEHI-0023997
WEHI-0024471
WEHI-0024472
WEHI-0024647
WEHI-0024825
WEHI-0024863
WEHI-0024880
WEHI-0024921
WEHI-0025079
WEHI-0025267
WEHI-0025330
WEHI-0025376
WEHI-0025383
WEHI-0025388
WEHI-0025503
WEHI-0025579
WEHI-0025580
WEHI-0025582
WEHI-0025928
WEHI-0026032
WEHI-0026074
WEHI-0026076
WEHI-0026387
WEHI-0026861
WEHI-0026867
WEHI-0027388
WEHI-0027950
WEHI-0028261
WEHI-0028555
WEHI-0029002
WEHI-0029119
WEHI-0029150
WEHI-0029798
WEHI-0030010
WEHI-0030096
WEHI-0030547
WEHI-0030565
WEHI-0030575
WEHI-0030680
WEHI-0030930
WEHI-0030934
WEHI-0030951
WEHI-0030982
WEHI-0031003
WEHI-0031038
WEHI-0031099
WEHI-0031466
WEHI-0031501
WEHI-0031558
WEHI-0031567
WEHI-0031580
WEHI-0031588
WEHI-0031724
WEHI-0031740
WEHI-0031760
WEHI-0031812
WEHI-0031877
WEHI-0031964
WEHI-0032008
WEHI-0032062
WEHI-0032098
WEHI-0032137
WEHI-0032203
WEHI-0032316
WEHI-0032441
WEHI-0032550
WEHI-0032578
WEHI-0032654
WEHI-0032721
WEHI-0032885
WEHI-0032911
WEHI-0033083
WEHI-0033129
WEHI-0033323
WEHI-0033330
WEHI-0033335
WEHI-0033533
WEHI-0033701
WEHI-0033845
WEHI-0033898
WEHI-0033908
WEHI-0033945
WEHI-0034021
WEHI-0034271
WEHI-0034396
WEHI-0034445
WEHI-0034452
WEHI-0034461
WEHI-0034530
WEHI-0034703
WEHI-0034822
WEHI-0034838
WEHI-0034845
WEHI-0035236
WEHI-0035238
WEHI-0035255
WEHI-0035272
WEHI-0035277
WEHI-0035450
WEHI-0035595
WEHI-0035597
WEHI-0035630
WEHI-0035869
WEHI-0035912
WEHI-0036028
WEHI-0036184
WEHI-0036307
WEHI-0036313
WEHI-0036341
WEHI-0036510
WEHI-0036533
WEHI-0036558
WEHI-0036724
WEHI-0036737
WEHI-0036751
WEHI-0036982
WEHI-0037607
WEHI-0037998
WEHI-0038095
WEHI-0038687
WEHI-0038931
WEHI-0039118
WEHI-0039383
WEHI-0039450
WEHI-0039487
WEHI-0039519
WEHI-0039633
WEHI-0040000
WEHI-0040073
WEHI-0040109
WEHI-0040114
WEHI-0040305
WEHI-0040558
WEHI-0040725
WEHI-0040837
WEHI-0041008
WEHI-0041069
WEHI-0041267
WEHI-0041687
WEHI-0041730
WEHI-0041885
WEHI-0042364
WEHI-0042454
WEHI-0042811
WEHI-0042874
WEHI-0043005
WEHI-0043070
WEHI-0043178
WEHI-0043233
WEHI-0043344
WEHI-0043348
WEHI-0043559
WEHI-0043675
WEHI-0043832
WEHI-0043947
WEHI-0044144
WEHI-0044359
WEHI-0044468
WEHI-0044768
WEHI-0044802
WEHI-0045179
WEHI-0045191
WEHI-0045303
WEHI-0045380
WEHI-0045674
WEHI-0045735
WEHI-0045801
WEHI-0046123
WEHI-0046361
WEHI-0046374
WEHI-0046428
WEHI-0046485
WEHI-0046556
WEHI-0046605
WEHI-0046634
WEHI-0046792
WEHI-0046827
WEHI-0046951
WEHI-0047047
WEHI-0047098
WEHI-0047117
WEHI-0047322
WEHI-0047597
WEHI-0047680
WEHI-0047690
WEHI-0047757
WEHI-0047972
WEHI-0048046
WEHI-0048105
WEHI-0048187
WEHI-0048454
WEHI-0048665
WEHI-0048917
WEHI-0049364
WEHI-0049668
WEHI-0050027
WEHI-0050089
WEHI-0050112
WEHI-0050192
WEHI-0050349
WEHI-0050663
WEHI-0050885
WEHI-0051127
WEHI-0051263
WEHI-0051346
WEHI-0051434
WEHI-0051464
WEHI-0051501
WEHI-0051505
WEHI-0051514
WEHI-0051524
WEHI-0051539
WEHI-0051554
WEHI-0051593
WEHI-0051611
WEHI-0051613
WEHI-0051773
WEHI-0051841
WEHI-0051908
WEHI-0051988
WEHI-0051989
WEHI-0052188
WEHI-0052194
WEHI-0052409
WEHI-0052425
WEHI-0052472
WEHI-0052492
WEHI-0052509
WEHI-0052633
WEHI-0052678
WEHI-0052720
WEHI-0052773
WEHI-0053140
WEHI-0053427
WEHI-0053430
WEHI-0053585
WEHI-0053629
WEHI-0054036
WEHI-0054045
WEHI-0054085
WEHI-0054151
WEHI-0054296
WEHI-0054344
WEHI-0054479
WEHI-0054820
WEHI-0055176
WEHI-0055748
WEHI-0055838
WEHI-0055920
WEHI-0055968
WEHI-0056027
WEHI-0056124
WEHI-0056192
WEHI-0056202
WEHI-0056237
WEHI-0056333
WEHI-0056440
WEHI-0056464
WEHI-0056541
WEHI-0056571
WEHI-0056822
WEHI-0057105
WEHI-0057885
WEHI-0058132
WEHI-0058360
WEHI-0058420
WEHI-0058648
WEHI-0058661
WEHI-0058845
WEHI-0059076
WEHI-0059437
WEHI-0059440
WEHI-0059789
WEHI-0059877
WEHI-0060173
WEHI-0060402
WEHI-0060403
WEHI-0060427
WEHI-0060570
WEHI-0061121
WEHI-0061162
WEHI-0061290
WEHI-0061353
WEHI-0061569
WEHI-0061570
WEHI-0061618
WEHI-0061710
WEHI-0061985
WEHI-0062032
WEHI-0062063
WEHI-0062121
WEHI-0062353
WEHI-0062362
WEHI-0062380
WEHI-0062381
WEHI-0062568
WEHI-0062584
WEHI-0062638
WEHI-0062844
WEHI-0062876
WEHI-0062921
WEHI-0062965
WEHI-0062967
WEHI-0062979
WEHI-0062989
WEHI-0063018
WEHI-0063020
WEHI-0063179
WEHI-0063336
WEHI-0063371
WEHI-0063432
WEHI-0063709
WEHI-0063789
WEHI-0063820
WEHI-0063850
WEHI-0063895
WEHI-0064132
WEHI-0064268
WEHI-0064354
WEHI-0064376
WEHI-0064391
WEHI-0064435
WEHI-0064615
WEHI-0064827
WEHI-0064902
WEHI-0064964
WEHI-0064972
WEHI-0064989
WEHI-0065074
WEHI-0065083
WEHI-0065092
WEHI-0065352
WEHI-0065462
WEHI-0065480
WEHI-0065534
WEHI-0065540
WEHI-0065565
WEHI-0065575
WEHI-0065599
WEHI-0065666
WEHI-0065688
WEHI-0065741
WEHI-0065792
WEHI-0065834
WEHI-0065980
WEHI-0066017
WEHI-0066271
WEHI-0066396
WEHI-0066418
WEHI-0066481
WEHI-0066651
WEHI-0066840
WEHI-0066975
WEHI-0067052
WEHI-0067102
WEHI-0067228
WEHI-0067322
WEHI-0067334
WEHI-0067340
WEHI-0067384
WEHI-0067403
WEHI-0067424
WEHI-0067434
WEHI-0067505
WEHI-0067818
WEHI-0067849
WEHI-0067892
WEHI-0067996
WEHI-0068156
WEHI-0068157
WEHI-0068222
WEHI-0068271
WEHI-0068277
WEHI-0068303
WEHI-0068322
WEHI-0068525
WEHI-0068562
WEHI-0068612
WEHI-0068698
WEHI-0068804
WEHI-0068820
WEHI-0068833
WEHI-0068869
WEHI-0068904
WEHI-0068981
WEHI-0069107
WEHI-0069139
WEHI-0069165
WEHI-0069438
WEHI-0069477
WEHI-0069495
WEHI-0069623
WEHI-0069696
WEHI-0069819
WEHI-0070167
WEHI-0070428
WEHI-0070511
WEHI-0070594
WEHI-0070618
WEHI-0070623
WEHI-0070750
WEHI-0070766
WEHI-0071177
WEHI-0071312
WEHI-0071357
WEHI-0071359
WEHI-0071377
WEHI-0071424
WEHI-0071431
WEHI-0071450
WEHI-0071572
WEHI-0071634
WEHI-0071685
WEHI-0071754
WEHI-0071840
WEHI-0071844
WEHI-0071892
WEHI-0071968
WEHI-0071982
WEHI-0072239
WEHI-0072644
WEHI-0072711
WEHI-0072728
WEHI-0072896
WEHI-0073128
WEHI-0073150
WEHI-0073156
WEHI-0073511
WEHI-0073534
WEHI-0073869
WEHI-0073916
WEHI-0074014
WEHI-0074040
WEHI-0074057
WEHI-0074080
WEHI-0074168
WEHI-0074173
WEHI-0074368
WEHI-0074371
WEHI-0074484
WEHI-0074510
WEHI-0074558
WEHI-0074591
WEHI-0074603
WEHI-0074738
WEHI-0074918
WEHI-0074968
WEHI-0075061
WEHI-0075106
WEHI-0075240
WEHI-0075244
WEHI-0075249
WEHI-0075317
WEHI-0075432
WEHI-0075624
WEHI-0075646
WEHI-0075693
WEHI-0075723
WEHI-0076143
WEHI-0076176
WEHI-0076504
WEHI-0076517
WEHI-0076529
WEHI-0076558
WEHI-0076560
WEHI-0076597
WEHI-0076632
WEHI-0076636
WEHI-0076697
WEHI-0076739
WEHI-0076869
WEHI-0076971
WEHI-0077013
WEHI-0077090
WEHI-0077252
WEHI-0077292
WEHI-0077301
WEHI-0077450
WEHI-0077640
WEHI-0077641
WEHI-0078015
WEHI-0078052
WEHI-0078070
WEHI-0078083
WEHI-0078089
WEHI-0078133
WEHI-0078148
WEHI-0078168
WEHI-0078246
WEHI-0078251
WEHI-0078278
WEHI-0078282
WEHI-0078376
WEHI-0078812
WEHI-0078813
WEHI-0078927
WEHI-0078957
WEHI-0079129
WEHI-0079130
WEHI-0079163
WEHI-0079208
WEHI-0079219
WEHI-0079352
WEHI-0079390
WEHI-0079426
WEHI-0079457
WEHI-0079461
WEHI-0079504
WEHI-0079548
WEHI-0079598
WEHI-0079642
WEHI-0079645
WEHI-0079689
WEHI-0079731
WEHI-0079920
WEHI-0080015
WEHI-0080105
WEHI-0080238
WEHI-0080309
WEHI-0080339
WEHI-0080398
WEHI-0080416
WEHI-0080417
WEHI-0080429
WEHI-0080453
WEHI-0080456
WEHI-0080565
WEHI-0081094
WEHI-0081191
WEHI-0081297
WEHI-0081516
WEHI-0081595
WEHI-0081650
WEHI-0081738
WEHI-0081819
WEHI-0081905
WEHI-0081956
WEHI-0081978
WEHI-0082117
WEHI-0082167
WEHI-0082201
WEHI-0082219
WEHI-0082242
WEHI-0082256
WEHI-0082321
WEHI-0082380
WEHI-0082394
WEHI-0082581
WEHI-0082627
WEHI-0082819
WEHI-0082887
WEHI-0082973
WEHI-0082985
WEHI-0083031
WEHI-0083134
WEHI-0083140
WEHI-0083199
WEHI-0083263
WEHI-0083292
WEHI-0083339
WEHI-0083352
WEHI-0083391
WEHI-0083487
WEHI-0083499
WEHI-0083609
WEHI-0083740
WEHI-0083759
WEHI-0083804
WEHI-0083821
WEHI-0083841
WEHI-0083884
WEHI-0083892
WEHI-0083969
WEHI-0083981
WEHI-0084035
WEHI-0084273
WEHI-0084293
WEHI-0084354
WEHI-0084464
WEHI-0084492
WEHI-0084518
WEHI-0084538
WEHI-0084569
WEHI-0084574
WEHI-0084643
WEHI-0084688
WEHI-0084746
WEHI-0084828
WEHI-0084854
WEHI-0084896
WEHI-0084945
WEHI-0085287
WEHI-0085763
WEHI-0085834
WEHI-0085909
WEHI-0085993
WEHI-0086087
WEHI-0086184
WEHI-0086187
WEHI-0086206
WEHI-0086262
WEHI-0086352
WEHI-0086357
WEHI-0086377
WEHI-0086391
WEHI-0086406
WEHI-0086419
WEHI-0086737
WEHI-0086796
WEHI-0086896
WEHI-0087078
WEHI-0087143
WEHI-0087627
WEHI-0087646
WEHI-0087668
WEHI-0087703
WEHI-0087815
WEHI-0087835
WEHI-0088030
WEHI-0088060
WEHI-0088101
WEHI-0088105
WEHI-0088355
WEHI-0088521
WEHI-0088668
WEHI-0088851
WEHI-0088883
WEHI-0088958
WEHI-0089030
WEHI-0089232
WEHI-0089240
WEHI-0089276
WEHI-0089325
WEHI-0089373
WEHI-0089414
WEHI-0089452
WEHI-0089498
WEHI-0089507
WEHI-0089525
WEHI-0089540
WEHI-0089730
WEHI-0089780
WEHI-0089841
WEHI-0089856
WEHI-0090032
WEHI-0090215
WEHI-0090293
WEHI-0090392
WEHI-0090599
WEHI-0090652
WEHI-0090846
WEHI-0090926
WEHI-0090942
WEHI-0091121
WEHI-0091251
WEHI-0091338
WEHI-0091396
WEHI-0091501
WEHI-0091601
WEHI-0091678
WEHI-0091697
WEHI-0092346
WEHI-0092381
WEHI-0092528
WEHI-0092529
WEHI-0092660
WEHI-0092813
WEHI-0092814
WEHI-0092817
WEHI-0092907
WEHI-0092975
WEHI-0092976
WEHI-0093066
WEHI-0093099
WEHI-0093452
WEHI-0093488
WEHI-0093732
WEHI-0094040
WEHI-0094194
WEHI-0094203
WEHI-0094422
WEHI-0094427
WEHI-0094525
WEHI-0094570
WEHI-0094594
WEHI-0094650
WEHI-0094665
WEHI-0094684
WEHI-0094713
WEHI-0094724
WEHI-0094732
WEHI-0094738
WEHI-0094914
WEHI-0094945
WEHI-0095078
WEHI-0095084
WEHI-0095085
WEHI-0095173
WEHI-0095186
WEHI-0095246
WEHI-0095718
WEHI-0095903
WEHI-0095925
WEHI-0096000
WEHI-0096167
WEHI-0096201
WEHI-0096202
WEHI-0096239
WEHI-0096372
WEHI-0096388
WEHI-0096406
WEHI-0096407
WEHI-0096416
WEHI-0096487
WEHI-0096501
WEHI-0096510
WEHI-0096644
WEHI-0096822
WEHI-0096895
WEHI-0096941
WEHI-0097085
WEHI-0097290
WEHI-0097431
WEHI-0097492
WEHI-0097493
WEHI-0097548
WEHI-0097560
WEHI-0097577
WEHI-0097588
WEHI-0097596
WEHI-0097746
WEHI-0097754
WEHI-0097800
WEHI-0097978
WEHI-0098409
WEHI-0098426
WEHI-0098429
WEHI-0098531
WEHI-0098552
WEHI-0098581
WEHI-0098703
WEHI-0098719
WEHI-0098884
WEHI-0098917
WEHI-0098962
WEHI-0099250
WEHI-0099298
WEHI-0099427
WEHI-0100071
WEHI-0100247
WEHI-0100301
WEHI-0100302
WEHI-0100338
WEHI-0100363
WEHI-0100413
WEHI-0100432
WEHI-0100437
WEHI-0100518
WEHI-0100533
WEHI-0100565
WEHI-0100714
WEHI-0100721
WEHI-0100737
WEHI-0101036
WEHI-0101165
WEHI-0101190
WEHI-0101358
WEHI-0101476
WEHI-0101514
WEHI-0101584
WEHI-0101627
WEHI-0101628
WEHI-0101853
WEHI-0101977
WEHI-0101979
WEHI-0102124
WEHI-0102262
WEHI-0103052
WEHI-0103091
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