# HG changeset patch # User bgruening # Date 1595323459 14400 # Node ID fbfac03ce8c3e83f76f953eba8eaf00e46acd0ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9" diff -r 000000000000 -r fbfac03ce8c3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 21 05:24:19 2020 -0400 @@ -0,0 +1,37 @@ + + 1.1.3 + + + im-pipelines + + + + + + + + + + + + + + + + + + @article{rdkit, + author = {Greg Landrum and others}, + title = {RDKit: Open-source cheminformatics}, + url = {http://www.rdkit.org} + } + + @article{im-pipelines, + author = {Tim Dudgeon and others}, + title = {InformaticsMatters pipeline components for cheminformatics and computational chemistry.}, + url = {https://github.com/InformaticsMatters/pipelines} + } + + + + diff -r 000000000000 -r fbfac03ce8c3 standardize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/standardize.xml Tue Jul 21 05:24:19 2020 -0400 @@ -0,0 +1,71 @@ + + using RDKit + + macros.xml + 0 + + + > $logfile && + cat outp_metrics.txt &>> $logfile && + gzip -d outp.sdf.gz + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r fbfac03ce8c3 test-data/Kinase_inhibs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Kinase_inhibs.sdf Tue Jul 21 05:24:19 2020 -0400 @@ -0,0 +1,2823 @@ + + SciTegic01171120562D + + 26 30 0 0 0 0 999 V2000 + -8.6396 0.9568 0.0000 O 0 0 + -7.6023 1.5602 0.0000 C 0 0 + -7.6071 3.0602 0.0000 C 0 0 + -6.3104 3.8143 0.0000 C 0 0 + -5.0090 3.0685 0.0000 C 0 0 + -5.0040 1.5682 0.0000 C 0 0 + -6.3008 0.8143 0.0000 C 0 0 + -3.7006 0.8244 0.0000 C 0 0 + -3.7006 -0.6045 0.0000 N 0 0 + -2.4915 -1.3190 0.0000 C 0 0 + -2.5059 -2.8197 0.0000 N 0 0 + -1.2156 -3.5847 0.0000 C 0 0 + -1.2329 -5.0846 0.0000 C 0 0 + -2.5404 -5.8196 0.0000 O 0 0 + -3.8308 -5.0547 0.0000 C 0 0 + -3.8135 -3.5548 0.0000 C 0 0 + -1.2274 -0.6045 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C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2990 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6003 1.4977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8990 0.7455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.2007 1.4909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.4972 0.7364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.4920 -0.7636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1903 -1.5091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8939 -0.7546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.7876 -1.5212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -8.8299 -0.9266 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -7.7802 -3.0220 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -9.0758 -3.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -9.0707 -5.2796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -10.3671 -6.0341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -11.6687 -5.2886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -12.7059 -5.8922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -11.6740 -3.7886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -12.9748 -3.0401 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 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0 0 + 4.8722 1.2043 0.9283 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.3889 2.4131 1.3126 F 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 + 2 3 1 0 + 3 4 1 0 + 4 5 2 0 + 5 6 1 0 + 6 7 2 0 + 7 8 1 0 + 7 9 1 0 + 9 10 2 0 + 2 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 1 0 + 13 15 2 0 + 15 16 1 0 + 15 17 1 0 + 17 18 2 0 + 18 19 1 0 + 10 4 1 0 + 18 11 1 0 +M END +> (26) +fb8861f6-fa0a-4ac5-9c5e-32a8523da6d0 + +> (26) +33509b1f-56f4-4a43-bc9f-5aea174b9dad + +> (26) +0.09879091579514199 + +> (26) +13 + +> (26) +2 + +$$$$ + + RDKit 3D + + 23 24 0 0 0 0 0 0 0 0999 V2000 + 2.0618 1.5278 0.4716 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5391 0.3586 0.4992 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6516 -0.7608 0.6456 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2525 -0.6236 0.4084 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1966 -0.0586 -0.7883 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5127 0.3816 -0.8888 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4183 0.0942 0.1356 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6842 0.6690 0.1208 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0247 -0.7216 1.2041 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6765 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C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0020 0.1673 0.5318 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5906 -1.0916 0.2618 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9930 -1.2530 0.2968 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8273 -0.1629 0.5950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2248 1.0647 0.8471 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8749 1.2272 0.8156 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5720 2.5457 1.1062 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8012 3.2481 1.3305 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8353 3.7551 2.6160 F 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9469 4.2653 0.4061 F 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8311 2.2672 1.1561 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 + 2 3 1 0 + 3 4 1 0 + 4 5 2 0 + 5 6 1 0 + 6 7 2 0 + 7 8 1 0 + 7 9 1 0 + 9 10 2 0 + 2 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 2 0 + 14 15 1 0 + 15 16 2 0 + 16 17 1 0 + 17 18 1 0 + 18 19 1 0 + 18 20 1 0 + 18 21 1 0 + 10 4 1 0 + 16 11 1 0 + 21 15 1 0 +M END +> (86) +a276e2d6-08f5-48bf-969d-d2ae50edcd6f + +> (86) +33509b1f-56f4-4a43-bc9f-5aea174b9dad + +> (86) +0.09864699027416803 + +> (86) +43 + +> (86) +2 + +$$$$ + + 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C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7448 0.1791 -0.4778 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4197 0.2213 -0.8106 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2739 1.3950 -1.0244 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6062 1.3986 -1.3577 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2997 0.2178 -1.4904 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7497 0.1548 -1.8469 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.5859 0.1605 -0.6025 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.2638 1.2779 -0.1821 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.9887 1.1923 0.9490 N 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0615 0.0470 1.6675 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.8448 -0.0075 2.8699 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.3924 -1.0395 1.2436 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.6497 -1.0101 0.1158 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9399 -2.1833 -0.3230 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6016 -0.9632 -1.2753 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2642 -0.9687 -0.9407 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3598 -2.1766 -0.7431 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3323 -3.3966 -0.8755 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.3296 0.9336 1.3535 C 0 0 0 0 0 0 0 0 0 0 0 0 + 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0 0 + 7.3614 2.4686 -0.2051 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1024 0.3563 -1.4988 N 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2806 0.5114 -2.3310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2524 -0.6469 -1.5309 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2803 -0.4836 -0.6355 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1567 -1.2321 -0.2659 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8555 -1.4584 0.5688 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3903 -2.1124 -0.5507 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9150 -1.8754 -0.9408 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6883 -1.0372 -0.2452 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2546 -0.3986 0.8364 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0941 0.4734 1.5472 N 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4328 0.7756 1.2331 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1537 1.6494 2.0456 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.4671 1.9810 1.7869 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.1259 1.4586 0.7074 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5361 1.7733 0.3739 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.4280 0.5881 -0.1129 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1133 0.2571 0.1470 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2621 -0.0966 -1.5084 S 0 0 0 0 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0.5596 2.9559 N 0 0 0 0 0 0 0 0 0 0 0 0 + -6.5081 1.9186 3.0562 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.1363 2.4791 1.6887 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.1868 2.2895 0.7242 N 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6437 2.5627 -0.5921 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.5158 1.5916 -0.8134 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2263 1.9084 -0.4439 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2342 1.0092 -0.6582 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4801 -0.2149 -1.2362 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.7670 -0.5344 -1.6064 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8035 0.3709 -1.3974 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3703 -1.1669 -1.4524 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5666 -2.2840 -1.9747 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0494 -0.8271 -1.0675 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0324 -1.7135 -1.2601 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2097 -2.9393 -1.8380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8211 -3.8139 -2.0346 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1016 -3.4830 -1.6608 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2370 -4.4619 -1.8842 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3403 -2.2622 -1.0858 C 0 0 0 0 0 0 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0 + 18 19 2 0 + 19 20 1 0 + 19 21 1 0 + 21 22 1 0 + 22 23 1 0 + 23 24 2 0 + 24 25 1 0 + 25 26 2 0 + 26 27 1 0 + 27 28 2 0 + 23 28 1 0 + 27 29 1 0 + 29 30 2 0 + 30 31 1 0 + 31 32 2 0 + 32 33 1 0 + 33 34 2 0 + 29 34 1 0 + 21 35 2 0 + 16 35 1 0 + 5 36 1 0 + 36 37 1 0 + 2 37 1 0 +M END +> (31) +2087 + +> (31) +CN1CCN(Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3)CC1 + +> (31) +0.64258755577353022 + +> (31) +3.3210457878649953 + +> (31) +12.931972470655383 + +$$$$ + + RDKit 3D + + 27 29 0 0 0 0 0 0 0 0999 V2000 + -2.2024 1.1996 -0.0682 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3292 0.0812 -0.1081 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0301 0.1638 -0.0828 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5087 -1.0874 -0.1601 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8370 -1.5579 -0.1729 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8979 -0.6001 -0.0933 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2222 -0.9876 -0.1000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2334 -0.0527 -0.0227 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9824 1.3006 0.0643 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6573 1.6824 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6409 0.7523 -0.0065 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2902 2.4650 0.1614 S 0 0 0 0 0 0 0 0 0 0 0 0 + 7.5188 1.8389 0.7809 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8548 3.6901 0.8821 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7623 2.9738 -1.4377 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5625 -1.8838 -0.2289 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7017 -1.1943 -0.1984 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9579 -1.8122 -0.2861 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0915 -3.0479 -0.4616 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1709 -1.0276 -0.1756 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0607 -1.0131 -1.2462 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.7180 -1.7235 -2.3554 F 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2401 -0.3122 -1.1937 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.5305 0.3844 -0.0494 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.6817 0.4003 1.0377 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.5086 -0.3109 0.9566 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6804 -0.3211 2.0468 F 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 2 0 + 3 4 1 0 + 4 5 1 0 + 5 6 1 0 + 6 7 2 0 + 7 8 1 0 + 8 9 2 0 + 9 10 1 0 + 10 11 2 0 + 6 11 1 0 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17 39 1 0 + 39 40 2 0 + 14 40 1 0 +M END +> (33) +2424686 + +> (33) +CS(=O)(=O)CCNCc1ccc(o1)c2ccc3ncnc(Nc4ccc(OCc5cccc(F)c5)c(Cl)c4)c3c2 + +> (33) +1.0134371241903675 + +> (33) +24.147545727793705 + +> (33) +28.028352372577782 + +> (33) +5.7710971238846867 + +$$$$ + + RDKit 3D + + 35 40 0 0 1 0 0 0 0 0999 V2000 + 4.6561 3.9065 -0.6910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9485 2.6025 -0.6682 N 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4187 1.7988 -1.7759 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0420 2.0666 0.6166 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1551 0.7211 0.7953 C 0 0 2 0 0 0 0 0 0 0 0 0 + 3.3978 0.1262 -0.7248 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2589 -1.3310 -0.4498 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9060 -1.7864 -0.2188 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8183 -1.2839 -0.7740 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2935 -1.9874 -0.3164 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6659 -1.7064 -0.7305 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2791 -0.5563 -0.8022 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6751 -0.7743 -1.2711 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.5862 0.0917 -1.4687 O 0 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