| Next changeset 1:5f73eb32ddbf (2020-03-17) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645" |
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added:
rbcavity.xml rdock_macros.xml test-data/ligand.mol test-data/ligand.sdf test-data/ligands_names.sdf test-data/ligands_nonames.sdf test-data/receptor.as test-data/receptor.mol2 |
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| diff -r 000000000000 -r 06f376dc117a rbcavity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbcavity.xml Wed Oct 02 12:34:26 2019 -0400 |
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| @@ -0,0 +1,92 @@ +<tool id="rdock_rbcavity" name="rDock cavity definition" version="0.1"> + <description>- generate the active site definition needed for rDock docking</description> + <macros> + <import>rdock_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ + ln -s '$receptor_prm' ./receptor.prm && + ln -s '$receptor' receptor.mol2 && + ln -s '$ligand' ligand.sdf && + rbcavity -was -d -r receptor.prm + ]]></command> + + <configfiles> + <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00 +RECEPTOR_FILE receptor.mol2 +RECEPTOR_FLEX 3.0 +SECTION MAPPER + SITE_MAPPER RbtLigandSiteMapper + REF_MOL ligand.sdf + RADIUS $radius + SMALL_SPHERE $sphere + MIN_VOLUME $min_volume + MAX_CAVITIES 1 + VOL_INCR $vol_incr + GRIDSTEP $gridstep +END_SECTION +SECTION CAVITY + SCORING_FUNCTION RbtCavityGridSF + WEIGHT $weight +END_SECTION + </configfile> + </configfiles> + + <inputs> + <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (Mol2 format)."/> + <param type="data" name="ligand" format="mol,sdf" label="Reference ligand" help="Single ligand in Mol or SDF format"/> + <param name="radius" type="float" value="6.0" min="0" label="Mapper sphere radius" + help="Mapper radius of large sphere in angstroms; rDock will search for cavities to the small sphere but not to the large sphere"/> + <param name="sphere" type="float" value="1.0" min="0" label="Mapper small sphere radius" + help="Mapper radius of small sphere in angstroms; rDock will search for cavities accessible to the small sphere but not to the large sphere"/> + <param name="min_volume" type="integer" value="100" min="0" label="Mapper minimum volume" + help="Mapper minimum volume in cubic angstroms. rDock will ignore cavities which are smaller than this value"/> + <param name="vol_incr" type="float" value="0.0" min="0" label="Mapper volume increment" + help="Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rDock will temporarily increase the radius of receptor atoms by this amount"/> + <param name="gridstep" type="float" value="0.5" min="0" label="Mapper grid step" help="Grid resolution for mapping in angstroms"/> + <param name="weight" type="float" value="1.0" min="0" label="Cavity weight" help="Cavity weight"/> + </inputs> + <outputs> + <data name="activesite" format="rdock_as" from_work_dir="receptor.as" label="rbcavity active site on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="receptor" value="receptor.mol2"/> + <param name="ligand" value="ligand.sdf"/> + <output name="activesite" file="receptor.as" compare="sim_size"/> + </test> + <test> + <param name="receptor" value="receptor.mol2"/> + <param name="ligand" value="ligand.mol"/> + <output name="activesite" file="receptor.as" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +This tool generates the cavity definition for rDock docking (the receptor.as file) using the rbcavity program. +See http://rdock.sourceforge.net/ for more details about rDock and associated programs. +Only a subset of the parameters are currently exposed. Read the rDock docs for a full understanding. + +----- + +.. class:: infomark + +**Inputs** + +1. The protein receptor to dock into as a file in Mol2 format. +2. A reference ligand used to define the location of the active site in Molfile or SDF format. +3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all. + +----- + +.. class:: infomark + +**Outputs** + +An active site definition binary file (receptor.as) that is needed by the rDock docking program to guide the docking. + + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 06f376dc117a rdock_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdock_macros.xml Wed Oct 02 12:34:26 2019 -0400 |
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| @@ -0,0 +1,12 @@ +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1003571</citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2013.1-0">rdock</requirement> + </requirements> + </xml> +</macros> |
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| diff -r 000000000000 -r 06f376dc117a test-data/ligand.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.mol Wed Oct 02 12:34:26 2019 -0400 |
| b |
| @@ -0,0 +1,115 @@ +1S3V + OpenBabel07031809403D + + 54 56 0 0 1 0 0 0 0 0999 V2000 + -0.0237 32.0851 0.4630 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0257 32.5701 2.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5816 31.2781 2.5290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2645 30.7721 3.8370 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1514 29.5300 3.5680 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.3824 28.4990 2.7070 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7845 29.0260 1.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3126 30.4241 1.4480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6244 28.9840 4.9610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2442 26.5599 4.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1391 25.6479 4.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.8561 24.2849 4.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.0120 23.8848 3.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6611 23.8468 4.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5581 22.0928 3.4830 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7132 24.7349 5.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4583 25.1339 6.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0123 26.0899 5.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4676 30.8241 0.4170 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8412 32.3751 -0.5420 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2388 32.9722 1.4960 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2847 33.4632 3.4970 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.6273 27.9210 4.8320 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8230 23.4168 3.6560 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1441 22.5778 4.6930 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5192 24.2169 5.6340 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0522 28.2910 4.7350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8817 31.5647 4.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4982 30.5088 4.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0329 29.7742 2.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0645 27.6908 2.4734 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5623 28.1183 3.3032 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5506 28.9693 0.5897 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9492 28.3958 1.0737 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0540 29.8010 5.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7656 28.5900 5.4903 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0962 26.0040 3.8974 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.7524 24.4932 2.1715 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6062 23.0393 2.7052 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5820 24.4781 3.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7376 22.7384 3.1952 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1884 21.0868 3.6389 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3042 22.0856 2.6981 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8011 25.7764 6.8076 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4051 24.5711 6.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1871 25.7386 5.1495 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2964 26.7805 5.6864 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2433 33.2980 -0.6110 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0822 31.6679 -1.2201 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8759 34.3850 3.4637 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8862 33.2055 4.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2045 28.9156 3.8635 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6528 27.3942 4.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3454 28.8348 5.6245 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 19 1 0 0 0 0 + 1 20 1 0 0 0 0 + 2 22 1 0 0 0 0 + 3 2 2 0 0 0 0 + 3 8 1 0 0 0 0 + 4 3 1 0 0 0 0 + 4 28 1 0 0 0 0 + 4 29 1 0 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 30 1 6 0 0 0 + 6 7 1 0 0 0 0 + 6 31 1 0 0 0 0 + 6 32 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 19 2 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 37 1 0 0 0 0 + 12 11 1 0 0 0 0 + 13 38 1 0 0 0 0 + 13 39 1 0 0 0 0 + 13 40 1 0 0 0 0 + 14 12 2 0 0 0 0 + 15 25 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 15 43 1 0 0 0 0 + 16 14 1 0 0 0 0 + 16 26 1 0 0 0 0 + 17 26 1 0 0 0 0 + 17 44 1 0 0 0 0 + 17 45 1 0 0 0 0 + 17 46 1 0 0 0 0 + 18 10 1 0 0 0 0 + 18 16 2 0 0 0 0 + 18 47 1 0 0 0 0 + 20 48 1 0 0 0 0 + 20 49 1 0 0 0 0 + 21 1 2 0 0 0 0 + 21 2 1 0 0 0 0 + 22 50 1 0 0 0 0 + 22 51 1 0 0 0 0 + 23 9 1 0 0 0 0 + 23 10 1 0 0 0 0 + 23 27 1 0 0 0 0 + 24 12 1 0 0 0 0 + 24 13 1 0 0 0 0 + 25 14 1 0 0 0 0 + 27 52 1 0 0 0 0 + 27 53 1 0 0 0 0 + 27 54 1 0 0 0 0 +M END |
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| diff -r 000000000000 -r 06f376dc117a test-data/ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.sdf Wed Oct 02 12:34:26 2019 -0400 |
| b |
| @@ -0,0 +1,116 @@ +1S3V + OpenBabel07031809403D + + 54 56 0 0 1 0 0 0 0 0999 V2000 + -0.0237 32.0851 0.4630 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0257 32.5701 2.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5816 31.2781 2.5290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2645 30.7721 3.8370 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1514 29.5300 3.5680 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.3824 28.4990 2.7070 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7845 29.0260 1.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3126 30.4241 1.4480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6244 28.9840 4.9610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2442 26.5599 4.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1391 25.6479 4.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.8561 24.2849 4.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.0120 23.8848 3.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6611 23.8468 4.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5581 22.0928 3.4830 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7132 24.7349 5.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4583 25.1339 6.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0123 26.0899 5.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4676 30.8241 0.4170 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8412 32.3751 -0.5420 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2388 32.9722 1.4960 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2847 33.4632 3.4970 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.6273 27.9210 4.8320 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.8230 23.4168 3.6560 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1441 22.5778 4.6930 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5192 24.2169 5.6340 O 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0522 28.2910 4.7350 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8817 31.5647 4.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4982 30.5088 4.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0329 29.7742 2.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0645 27.6908 2.4734 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5623 28.1183 3.3032 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5506 28.9693 0.5897 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9492 28.3958 1.0737 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0540 29.8010 5.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7656 28.5900 5.4903 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.0962 26.0040 3.8974 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.7524 24.4932 2.1715 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6062 23.0393 2.7052 H 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5820 24.4781 3.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7376 22.7384 3.1952 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1884 21.0868 3.6389 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3042 22.0856 2.6981 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8011 25.7764 6.8076 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4051 24.5711 6.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1871 25.7386 5.1495 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2964 26.7805 5.6864 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2433 33.2980 -0.6110 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0822 31.6679 -1.2201 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8759 34.3850 3.4637 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8862 33.2055 4.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.2045 28.9156 3.8635 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6528 27.3942 4.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3454 28.8348 5.6245 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 19 1 0 0 0 0 + 1 20 1 0 0 0 0 + 2 22 1 0 0 0 0 + 3 2 2 0 0 0 0 + 3 8 1 0 0 0 0 + 4 3 1 0 0 0 0 + 4 28 1 0 0 0 0 + 4 29 1 0 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 30 1 6 0 0 0 + 6 7 1 0 0 0 0 + 6 31 1 0 0 0 0 + 6 32 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 33 1 0 0 0 0 + 7 34 1 0 0 0 0 + 8 19 2 0 0 0 0 + 9 35 1 0 0 0 0 + 9 36 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 37 1 0 0 0 0 + 12 11 1 0 0 0 0 + 13 38 1 0 0 0 0 + 13 39 1 0 0 0 0 + 13 40 1 0 0 0 0 + 14 12 2 0 0 0 0 + 15 25 1 0 0 0 0 + 15 41 1 0 0 0 0 + 15 42 1 0 0 0 0 + 15 43 1 0 0 0 0 + 16 14 1 0 0 0 0 + 16 26 1 0 0 0 0 + 17 26 1 0 0 0 0 + 17 44 1 0 0 0 0 + 17 45 1 0 0 0 0 + 17 46 1 0 0 0 0 + 18 10 1 0 0 0 0 + 18 16 2 0 0 0 0 + 18 47 1 0 0 0 0 + 20 48 1 0 0 0 0 + 20 49 1 0 0 0 0 + 21 1 2 0 0 0 0 + 21 2 1 0 0 0 0 + 22 50 1 0 0 0 0 + 22 51 1 0 0 0 0 + 23 9 1 0 0 0 0 + 23 10 1 0 0 0 0 + 23 27 1 0 0 0 0 + 24 12 1 0 0 0 0 + 24 13 1 0 0 0 0 + 25 14 1 0 0 0 0 + 27 52 1 0 0 0 0 + 27 53 1 0 0 0 0 + 27 54 1 0 0 0 0 +M END +$$$$ |
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| diff -r 000000000000 -r 06f376dc117a test-data/ligands_names.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_names.sdf Wed Oct 02 12:34:26 2019 -0400 |
| b |
| @@ -0,0 +1,170 @@ +1-pyrimethamine + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8357 0.2028 0.4209 N 0 0 0 0 0 0 + -2.8255 -1.1104 0.1969 C 0 0 0 0 0 0 + -1.7271 -1.8218 -0.0537 N 0 0 0 0 0 0 + -0.5417 -1.1654 -0.0884 C 0 0 0 0 0 0 + -0.4439 0.2086 0.1358 C 0 0 0 0 0 0 + -1.6550 0.8467 0.4052 C 0 0 0 0 0 0 + 0.8362 0.9302 0.0951 C 0 0 0 0 0 0 + 1.6327 1.0444 1.2466 C 0 0 0 0 0 0 + 2.8536 1.7244 1.2069 C 0 0 0 0 0 0 + 3.2885 2.2979 0.0146 C 0 0 0 0 0 0 + 2.5126 2.1980 -1.1375 C 0 0 0 0 0 0 + 1.2918 1.5178 -1.0966 C 0 0 0 0 0 0 + -4.0141 -1.7715 0.2232 N 0 0 0 0 0 0 + -1.7348 2.2137 0.6034 N 0 0 0 0 0 0 + 4.7918 3.1344 -0.0351 Cl 0 0 0 0 0 0 + 0.4261 -3.4744 -0.6318 C 0 0 0 0 0 0 + 0.6932 -1.9936 -0.3864 C 0 0 0 0 0 0 + 1.3065 0.6014 2.1872 H 0 0 0 0 0 0 + 3.4548 1.8000 2.1100 H 0 0 0 0 0 0 + 2.8462 2.6451 -2.0710 H 0 0 0 0 0 0 + 0.6948 1.4500 -2.0056 H 0 0 0 0 0 0 + -4.0348 -2.7663 0.0556 H 0 0 0 0 0 0 + -4.8657 -1.2631 0.4089 H 0 0 0 0 0 0 + -0.9674 2.6820 1.0738 H 0 0 0 0 0 0 + -2.6605 2.5780 0.8038 H 0 0 0 0 0 0 + 1.3655 -3.9964 -0.8406 H 0 0 0 0 0 0 + -0.2391 -3.6219 -1.4893 H 0 0 0 0 0 0 + -0.0337 -3.9462 0.2432 H 0 0 0 0 0 0 + 1.3880 -1.9081 0.4572 H 0 0 0 0 0 0 + 1.1868 -1.5858 -1.2763 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 10 2 0 0 0 + 9 19 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-pyrimethamine + +> <Family> +A + +> <PC_uM> +3.7 + +> <TG_uM> +0.39 + +> <RL_uM> +2.3 + +> <set> +1 + +$$$$ +1-3062 + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8168 0.2065 0.4735 N 0 0 0 0 0 0 + -2.8206 -1.1045 0.2371 C 0 0 0 0 0 0 + -1.7327 -1.8208 -0.0438 N 0 0 0 0 0 0 + -0.5439 -1.1720 -0.0988 C 0 0 0 0 0 0 + -0.4317 0.1989 0.1374 C 0 0 0 0 0 0 + -1.6324 0.8424 0.4390 C 0 0 0 0 0 0 + 0.8521 0.9130 0.0752 C 0 0 0 0 0 0 + 1.6858 0.9917 1.2029 C 0 0 0 0 0 0 + 2.9119 1.6650 1.1430 C 0 0 0 0 0 0 + 3.3184 2.2713 -0.0498 C 0 0 0 0 0 0 + 2.4965 2.2018 -1.1763 C 0 0 0 0 0 0 + 1.2730 1.5284 -1.1135 C 0 0 0 0 0 0 + -4.0128 -1.7579 0.2830 N 0 0 0 0 0 0 + -1.6980 2.2076 0.6534 N 0 0 0 0 0 0 + 4.8189 3.1175 -0.1945 Cl 0 0 0 0 0 0 + 0.3929 -3.4780 -0.7058 C 0 0 0 0 0 0 + 0.6782 -2.0057 -0.4320 C 0 0 0 0 0 0 + 3.8777 1.7088 2.5773 Cl 0 0 0 0 0 0 + 1.3763 0.5224 2.1357 H 0 0 0 0 0 0 + 2.7982 2.6697 -2.1110 H 0 0 0 0 0 0 + 0.6467 1.4886 -2.0046 H 0 0 0 0 0 0 + -4.0437 -2.7510 0.1067 H 0 0 0 0 0 0 + -4.8568 -1.2458 0.4914 H 0 0 0 0 0 0 + -0.9218 2.6660 1.1184 H 0 0 0 0 0 0 + -2.6181 2.5747 0.8742 H 0 0 0 0 0 0 + 1.3238 -4.0040 -0.9412 H 0 0 0 0 0 0 + -0.2872 -3.5999 -1.5556 H 0 0 0 0 0 0 + -0.0575 -3.9650 0.1657 H 0 0 0 0 0 0 + 1.3854 -1.9447 0.4035 H 0 0 0 0 0 0 + 1.1636 -1.5839 -1.3199 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 19 1 0 0 0 + 9 10 2 0 0 0 + 9 18 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-3062 + +> <Family> +A + +> <PC_uM> +1.08 + +> <TG_uM> +0.094 + +> <RL_uM> +0.19 + +> <set> +0 + +$$$$ |
| b |
| diff -r 000000000000 -r 06f376dc117a test-data/ligands_nonames.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_nonames.sdf Wed Oct 02 12:34:26 2019 -0400 |
| b |
| @@ -0,0 +1,170 @@ + + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8357 0.2028 0.4209 N 0 0 0 0 0 0 + -2.8255 -1.1104 0.1969 C 0 0 0 0 0 0 + -1.7271 -1.8218 -0.0537 N 0 0 0 0 0 0 + -0.5417 -1.1654 -0.0884 C 0 0 0 0 0 0 + -0.4439 0.2086 0.1358 C 0 0 0 0 0 0 + -1.6550 0.8467 0.4052 C 0 0 0 0 0 0 + 0.8362 0.9302 0.0951 C 0 0 0 0 0 0 + 1.6327 1.0444 1.2466 C 0 0 0 0 0 0 + 2.8536 1.7244 1.2069 C 0 0 0 0 0 0 + 3.2885 2.2979 0.0146 C 0 0 0 0 0 0 + 2.5126 2.1980 -1.1375 C 0 0 0 0 0 0 + 1.2918 1.5178 -1.0966 C 0 0 0 0 0 0 + -4.0141 -1.7715 0.2232 N 0 0 0 0 0 0 + -1.7348 2.2137 0.6034 N 0 0 0 0 0 0 + 4.7918 3.1344 -0.0351 Cl 0 0 0 0 0 0 + 0.4261 -3.4744 -0.6318 C 0 0 0 0 0 0 + 0.6932 -1.9936 -0.3864 C 0 0 0 0 0 0 + 1.3065 0.6014 2.1872 H 0 0 0 0 0 0 + 3.4548 1.8000 2.1100 H 0 0 0 0 0 0 + 2.8462 2.6451 -2.0710 H 0 0 0 0 0 0 + 0.6948 1.4500 -2.0056 H 0 0 0 0 0 0 + -4.0348 -2.7663 0.0556 H 0 0 0 0 0 0 + -4.8657 -1.2631 0.4089 H 0 0 0 0 0 0 + -0.9674 2.6820 1.0738 H 0 0 0 0 0 0 + -2.6605 2.5780 0.8038 H 0 0 0 0 0 0 + 1.3655 -3.9964 -0.8406 H 0 0 0 0 0 0 + -0.2391 -3.6219 -1.4893 H 0 0 0 0 0 0 + -0.0337 -3.9462 0.2432 H 0 0 0 0 0 0 + 1.3880 -1.9081 0.4572 H 0 0 0 0 0 0 + 1.1868 -1.5858 -1.2763 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 10 2 0 0 0 + 9 19 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-pyrimethamine + +> <Family> +A + +> <PC_uM> +3.7 + +> <TG_uM> +0.39 + +> <RL_uM> +2.3 + +> <set> +1 + +$$$$ + + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8168 0.2065 0.4735 N 0 0 0 0 0 0 + -2.8206 -1.1045 0.2371 C 0 0 0 0 0 0 + -1.7327 -1.8208 -0.0438 N 0 0 0 0 0 0 + -0.5439 -1.1720 -0.0988 C 0 0 0 0 0 0 + -0.4317 0.1989 0.1374 C 0 0 0 0 0 0 + -1.6324 0.8424 0.4390 C 0 0 0 0 0 0 + 0.8521 0.9130 0.0752 C 0 0 0 0 0 0 + 1.6858 0.9917 1.2029 C 0 0 0 0 0 0 + 2.9119 1.6650 1.1430 C 0 0 0 0 0 0 + 3.3184 2.2713 -0.0498 C 0 0 0 0 0 0 + 2.4965 2.2018 -1.1763 C 0 0 0 0 0 0 + 1.2730 1.5284 -1.1135 C 0 0 0 0 0 0 + -4.0128 -1.7579 0.2830 N 0 0 0 0 0 0 + -1.6980 2.2076 0.6534 N 0 0 0 0 0 0 + 4.8189 3.1175 -0.1945 Cl 0 0 0 0 0 0 + 0.3929 -3.4780 -0.7058 C 0 0 0 0 0 0 + 0.6782 -2.0057 -0.4320 C 0 0 0 0 0 0 + 3.8777 1.7088 2.5773 Cl 0 0 0 0 0 0 + 1.3763 0.5224 2.1357 H 0 0 0 0 0 0 + 2.7982 2.6697 -2.1110 H 0 0 0 0 0 0 + 0.6467 1.4886 -2.0046 H 0 0 0 0 0 0 + -4.0437 -2.7510 0.1067 H 0 0 0 0 0 0 + -4.8568 -1.2458 0.4914 H 0 0 0 0 0 0 + -0.9218 2.6660 1.1184 H 0 0 0 0 0 0 + -2.6181 2.5747 0.8742 H 0 0 0 0 0 0 + 1.3238 -4.0040 -0.9412 H 0 0 0 0 0 0 + -0.2872 -3.5999 -1.5556 H 0 0 0 0 0 0 + -0.0575 -3.9650 0.1657 H 0 0 0 0 0 0 + 1.3854 -1.9447 0.4035 H 0 0 0 0 0 0 + 1.1636 -1.5839 -1.3199 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 19 1 0 0 0 + 9 10 2 0 0 0 + 9 18 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-3062 + +> <Family> +A + +> <PC_uM> +1.08 + +> <TG_uM> +0.094 + +> <RL_uM> +0.19 + +> <set> +0 + +$$$$ |
| b |
| diff -r 000000000000 -r 06f376dc117a test-data/receptor.as |
| b |
| Binary file test-data/receptor.as has changed |
| b |
| diff -r 000000000000 -r 06f376dc117a test-data/receptor.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.mol2 Wed Oct 02 12:34:26 2019 -0400 |
| b |
| b'@@ -0,0 +1,6069 @@\n+@<TRIPOS>MOLECULE\n+receptor.pdb\n+ 3013 3048 0 0 0\n+SMALL\n+GASTEIGER\n+\n+@<TRIPOS>ATOM\n+ 1 N 16.0520 41.0190 15.4650 N.4 1 VAL1 0.2275\n+ 2 CA 15.2450 42.0270 14.7460 C.3 1 VAL1 0.0555\n+ 3 C 14.1180 41.2820 14.0050 C.2 1 VAL1 0.2618\n+ 4 O 13.2440 40.5890 14.5350 O.2 1 VAL1 -0.2696\n+ 5 CB 16.0900 42.8220 13.7240 C.3 1 VAL1 0.0050\n+ 6 CG1 15.3310 44.0210 13.1490 C.3 1 VAL1 -0.0571\n+ 7 CG2 17.4520 43.2500 14.2510 C.3 1 VAL1 -0.0571\n+ 8 H1 16.8010 41.4790 15.9620 H 1 VAL1 0.2002\n+ 9 H2 15.4660 40.5250 16.1230 H 1 VAL1 0.2002\n+ 10 H3 16.4410 40.3630 14.8020 H 1 VAL1 0.2002\n+ 11 HA 14.8280 42.7360 15.4610 H 1 VAL1 0.0951\n+ 12 HB 16.4690 42.1440 12.9590 H 1 VAL1 0.0355\n+ 13 HG11 15.9670 44.5470 12.4370 H 1 VAL1 0.0234\n+ 14 HG12 14.4300 43.6730 12.6430 H 1 VAL1 0.0234\n+ 15 HG13 15.0550 44.6980 13.9570 H 1 VAL1 0.0234\n+ 16 HG21 17.9850 43.8020 13.4770 H 1 VAL1 0.0234\n+ 17 HG22 17.3200 43.8870 15.1250 H 1 VAL1 0.0234\n+ 18 HG23 18.0280 42.3680 14.5290 H 1 VAL1 0.0234\n+ 19 N 14.2650 41.4590 12.7080 N.am 2 GLY2 -0.3021\n+ 20 CA 13.3910 40.8770 11.6990 C.3 2 GLY2 0.0883\n+ 21 C 12.8860 42.0140 10.8100 C.2 2 GLY2 0.2308\n+ 22 O 13.3350 43.1700 10.8420 O.2 2 GLY2 -0.2741\n+ 23 H 15.0220 42.0290 12.3590 H 2 GLY2 0.1494\n+ 24 HA2 13.9510 40.1530 11.1070 H 2 GLY2 0.0558\n+ 25 HA3 12.5540 40.3770 12.1870 H 2 GLY2 0.0558\n+ 26 N 11.9410 41.5950 10.0180 N.am 3 SER3 -0.3008\n+ 27 CA 11.2600 42.4710 9.0470 C.3 3 SER3 0.1226\n+ 28 C 9.7770 42.0580 9.1450 C.2 3 SER3 0.2362\n+ 29 O 9.5540 40.9440 9.6580 O.2 3 SER3 -0.2737\n+ 30 CB 11.8720 42.2070 7.6870 C.3 3 SER3 0.0711\n+ 31 OG 12.1980 40.8290 7.5230 O.3 3 SER3 -0.3927\n+ 32 H 11.6440 40.6300 10.0520 H 3 SER3 0.1496\n+ 33 HA 11.4250 43.5130 9.3190 H 3 SER3 0.0618\n+ 34 HB2 11.1640 42.4900 6.9080 H 3 SER3 0.0580\n+ 35 HB3 12.7840 42.7940 7.5780 H 3 SER3 0.0580\n+ 36 HG 12.5830 40.6920 6.6540 H 3 SER3 0.2095\n+ 37 N 8.9500 42.9530 8.6670 N.am 4 LEU4 -0.3024\n+ 38 CA 7.5000 42.7870 8.6020 C.3 4 LEU4 0.0997\n+ 39 C 7.0610 42.3920 7.1710 C.2 4 LEU4 0.2340\n+ 40 O 7.2180 43.2070 6.2410 O.2 4 LEU4 -0.2738\n+ 41 CB 6.8560 44.1050 8.9850 C.3 4 LEU4 -0.0236\n+ 42 CG 5.4220 44.0040 9.4470 C.3 4 LEU4 -0.0446\n+ 43 CD1 5.2730 42.9590 10.5730 C.3 4 LEU4 -0.0626\n+ 44 CD2 5.0360 45.3300 10.1100 C.3 4 LEU4 -0.0626\n+ 45 H 9.3050 43.8290 8.3110 H 4 LEU4 0.1495\n+ 46 HA 7.1920 42.0030 9.2940 H 4 LEU4 0.0594\n+ 47 HB2 7.4160 44.5590 9.8020 H 4 LEU4 0.0290\n+ 48 HB3 6.8600 44.7750 8.1260 H 4 LEU4 0.0290\n+ 49 HG 4.8070 43.6030 8.6410 H 4 LEU4 0.0296\n+ 50 HD11 4.2300 42.9080 10.8860 H 4 LEU4 0'..b' 2889 1693 1698 1\n+ 2890 1386 1387 2\n+ 2891 1675 1674 1\n+ 2892 1587 1597 1\n+ 2893 1587 1596 1\n+ 2894 1587 1585 1\n+ 2895 1356 1358 am\n+ 2896 1459 1461 2\n+ 2897 1459 1460 1\n+ 2898 1329 1323 1\n+ 2899 1461 1473 1\n+ 2900 1592 1585 1\n+ 2901 1406 1408 ar\n+ 2902 1700 1697 1\n+ 2903 1409 1411 ar\n+ 2904 1581 1589 1\n+ 2905 1472 1460 1\n+ 2906 1460 1471 1\n+ 2907 1723 1732 1\n+ 2908 1723 1724 1\n+ 2909 1614 1617 1\n+ 2910 1614 1615 1\n+ 2911 1575 1565 1\n+ 2912 1585 1586 1\n+ 2913 1697 1701 1\n+ 2914 1697 1702 1\n+ 2915 1358 1365 1\n+ 2916 1358 1366 1\n+ 2917 1331 1326 1\n+ 2918 1574 1564 1\n+ 2919 1324 1323 1\n+ 2920 1324 1325 2\n+ 2921 1565 1564 1\n+ 2922 1565 1576 1\n+ 2923 1437 1428 1\n+ 2924 1564 1573 1\n+ 2925 1617 1625 1\n+ 2926 1617 1624 1\n+ 2927 1428 1438 1\n+ 2928 1428 1439 1\n+ 2929 1268 1269 2\n+ 2930 1268 1285 am\n+ 2931 1323 1326 1\n+ 2932 1323 1322 1\n+ 2933 1707 1714 1\n+ 2934 1707 1713 1\n+ 2935 1707 1708 1\n+ 2936 1310 1309 2\n+ 2937 1330 1326 1\n+ 2938 1326 1327 1\n+ 2939 1709 1708 2\n+ 2940 1411 1420 1\n+ 2941 1411 1410 ar\n+ 2942 1408 1417 1\n+ 2943 1408 1410 ar\n+ 2944 1662 1661 2\n+ 2945 1674 1682 1\n+ 2946 1674 1661 am\n+ 2947 1738 1725 1\n+ 2948 1294 1285 1\n+ 2949 1734 1724 1\n+ 2950 1724 1725 1\n+ 2951 1724 1735 1\n+ 2952 1708 1710 am\n+ 2953 1285 1286 1\n+ 2954 1615 1616 2\n+ 2955 1615 1628 am\n+ 2956 1637 1628 1\n+ 2957 1586 1593 1\n+ 2958 1586 1594 1\n+ 2959 1586 1595 1\n+ 2960 1309 1322 am\n+ 2961 1309 1308 1\n+ 2962 1322 1328 1\n+ 2963 1661 1660 1\n+ 2964 1410 1419 1\n+ 2965 1316 1307 1\n+ 2966 1725 1737 1\n+ 2967 1725 1736 1\n+ 2968 1628 1629 1\n+ 2969 1672 1664 1\n+ 2970 1298 1290 1\n+ 2971 1320 1312 1\n+ 2972 1333 1327 1\n+ 2973 1327 1328 1\n+ 2974 1327 1332 1\n+ 2975 1631 1630 2\n+ 2976 1303 1292 1\n+ 2977 1307 1308 1\n+ 2978 1307 1287 am\n+ 2979 1710 1716 1\n+ 2980 1710 1715 1\n+ 2981 1328 1334 1\n+ 2982 1328 1335 1\n+ 2983 1286 1295 1\n+ 2984 1286 1287 1\n+ 2985 1286 1289 1\n+ 2986 1308 1317 1\n+ 2987 1308 1311 1\n+ 2988 1671 1663 1\n+ 2989 1302 1292 1\n+ 2990 1299 1290 1\n+ 2991 1290 1289 1\n+ 2992 1290 1291 1\n+ 2993 1639 1632 1\n+ 2994 1664 1663 1\n+ 2995 1664 1665 1\n+ 2996 1664 1673 1\n+ 2997 1660 1663 1\n+ 2998 1660 1669 1\n+ 2999 1660 1659 1\n+ 3000 1667 1665 ar\n+ 3001 1312 1321 1\n+ 3002 1312 1313 1\n+ 3003 1312 1311 1\n+ 3004 1287 1288 2\n+ 3005 1630 1629 1\n+ 3006 1630 1645 am\n+ 3007 1292 1291 1\n+ 3008 1292 1293 1\n+ 3009 1629 1632 1\n+ 3010 1629 1638 1\n+ 3011 1663 1670 1\n+ 3012 1665 1666 ar\n+ 3013 1296 1289 1\n+ 3014 1648 1647 2\n+ 3015 1289 1297 1\n+ 3016 1315 1313 ar\n+ 3017 1313 1314 ar\n+ 3018 1304 1293 1\n+ 3019 1659 1647 am\n+ 3020 1659 1668 1\n+ 3021 1311 1318 1\n+ 3022 1311 1319 1\n+ 3023 1642 1633 1\n+ 3024 1632 1640 1\n+ 3025 1632 1633 1\n+ 3026 1291 1300 1\n+ 3027 1291 1301 1\n+ 3028 1647 1646 1\n+ 3029 1293 1305 1\n+ 3030 1293 1306 1\n+ 3031 1645 1646 1\n+ 3032 1645 1651 1\n+ 3033 1652 1646 1\n+ 3034 1633 1641 1\n+ 3035 1633 1634 1\n+ 3036 1646 1649 1\n+ 3037 1658 1651 1\n+ 3038 1634 1635 2\n+ 3039 1634 1636 am\n+ 3040 1644 1636 1\n+ 3041 1651 1657 1\n+ 3042 1651 1650 1\n+ 3043 1636 1643 1\n+ 3044 1653 1649 1\n+ 3045 1649 1650 1\n+ 3046 1649 1654 1\n+ 3047 1650 1655 1\n+ 3048 1650 1656 1\n' |