# HG changeset patch # User bgruening # Date 1595863874 14400 # Node ID 0eb24d808e75ab3473c648bd81257f62575e58e8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae" diff -r 000000000000 -r 0eb24d808e75 featurestein.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featurestein.xml Mon Jul 27 11:31:14 2020 -0400 @@ -0,0 +1,76 @@ + + feature overlay scoring + + macros.xml + 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 0eb24d808e75 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 27 11:31:14 2020 -0400 @@ -0,0 +1,37 @@ + + 1.1.4 + + + 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 0eb24d808e75 test-data/Kinase_inhibs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Kinase_inhibs.sdf Mon Jul 27 11:31:14 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 0.0000 C 0 0 + 0.0000 -1.3190 0.0000 O 0 0 + 1.2274 -0.6045 0.0000 C 0 0 + 2.4732 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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 + +$$$$ + + 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C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6829 0.6686 0.1210 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0232 -0.7224 1.2041 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6748 -1.0475 1.3649 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 4 1 0 + 4 5 2 0 + 4 6 1 0 + 6 7 2 0 + 7 8 1 0 + 8 9 2 0 + 9 10 1 0 + 9 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 2 0 + 13 15 1 0 + 15 16 1 0 + 16 17 2 0 + 17 18 1 0 + 18 19 2 0 + 19 20 1 0 + 19 21 1 0 + 21 22 2 0 + 12 6 1 0 + 22 16 1 0 +M END +> (183) +3b7018fc-2ce3-4c44-9a60-c7924fd56af0 + +> (183) +33509b1f-56f4-4a43-bc9f-5aea174b9dad + +> (183) +0.10055473735156038 + +> (183) +92 + +> (183) +1 + +$$$$ + + RDKit 3D + + 22 23 0 0 0 0 0 0 0 0999 V2000 + 4.2333 4.6187 2.7097 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0089 3.5668 1.9130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0791 4.0769 0.2016 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 4.3909 2.1886 2.0154 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4701 1.9698 2.8506 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8859 1.0624 1.1848 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2725 0.8458 1.0930 C 0 0 0 0 0 0 0 0 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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V2000 + 3.9712 0.1501 0.5844 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5166 0.3848 0.3204 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6474 -0.7021 0.6617 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2473 -0.5387 0.4677 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2286 -0.2315 -0.8004 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4500 0.4259 -0.8610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3911 0.0755 0.0992 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0310 -0.7738 1.1372 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6867 -1.0391 1.3639 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6323 0.7131 0.1820 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0373 1.5357 0.5544 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 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 + 8 9 2 0 + 7 10 1 0 + 2 11 2 0 + 9 4 1 0 +M END +> (1) +[{, uuid, 8239add3-47ea-40a0-a326-d93c45f9cfb2, source, CC(=O)Cl, format, smiles, }, {, uuid, 33509b1f-56f4-4a43-bc9f-5aea174b9dad, source, Nc1ccc(O)cc1, format, smiles, }] + +> (1) +[{, uuid, c5420e1a-a5fe-4ca6-b815-0d243a87c559, source, Nc1ccc(O)cc1, format, smiles, }, {, uuid, 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