# HG changeset patch # User bgruening # Date 1595323391 14400 # Node ID e3c4312457b61c0d9a97a04bbc6122a52a74bed1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9" diff -r 000000000000 -r e3c4312457b6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 21 05:23:11 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 e3c4312457b6 rxn_maker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rxn_maker.xml Tue Jul 21 05:23:11 2020 -0400 @@ -0,0 +1,96 @@ + + using RDKit + + macros.xml + 0 + + + > $logfile && + cat outp_metrics.txt &>> $logfile && + gzip -d outp.sdf.gz + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + multi + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r e3c4312457b6 test-data/Kinase_inhibs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Kinase_inhibs.sdf Tue Jul 21 05:23:11 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 + 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0 0 0 0 0 0 0 0 0 0 + 7.0872 2.1867 1.2664 N 0 0 0 0 0 4 0 0 0 0 0 0 + 6.7000 3.3554 1.0584 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2452 1.9937 1.9833 O 0 0 0 0 0 1 0 0 0 0 0 0 + 4.8545 1.2396 0.8574 C 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 + 14 16 1 0 + 16 17 1 0 + 17 18 2 0 + 17 19 1 0 + 16 20 2 0 + 10 4 1 0 + 20 11 1 0 +M CHG 2 17 1 19 -1 +M END +> (65) +f8851b20-4f97-4a1c-a06e-129986c791fc + +> (65) +33509b1f-56f4-4a43-bc9f-5aea174b9dad + +> (65) +0.09910774864285887 + +> (65) +33 + +> (65) +1 + +$$$$ + + RDKit 3D + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 2.0601 1.5339 0.4810 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5372 0.3645 0.4883 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6537 -0.7537 0.6537 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2537 -0.6264 0.4088 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1949 -0.0608 -0.7882 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5110 0.3804 -0.8891 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4174 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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 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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