| Next changeset 1:07309bad01df (2020-04-25) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" |
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added:
rbdock.py rbdock.xml rdock_macros.xml test-data/broken_ligand.sdf test-data/ligand.mol test-data/ligand.sdf test-data/ligands_names.sdf test-data/ligands_nonames.sdf test-data/poses-ascending.sdf test-data/poses-descending.sdf test-data/poses.sdf test-data/receptor.as test-data/receptor.mol2 |
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| diff -r 000000000000 -r 35ee2e002bb0 rbdock.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.py Sat Apr 04 15:00:22 2020 -0400 |
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| @@ -0,0 +1,28 @@ +import subprocess +import argparse + +def main(): + parser = argparse.ArgumentParser(description='Simple wrapper for rbdock') + parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate') + parser.add_argument('-s', '--seed', type=int, help='Random seed') + args = parser.parse_args() + + cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output'] + if args.seed != None: + cmd += ['-s', str(args.seed)] + + ps = subprocess.Popen(cmd, stdout=subprocess.PIPE) + + error_counter = 0 + for stdout_line in iter(ps.stdout.readline, ''): + if 'RBT_DOCKING_ERROR' in str(stdout_line): + error_counter += 1 + if error_counter == 10: + print(ps.stdout) + exit(23) + if ps.poll() != None: + print(ps.stdout) + exit(int(ps.poll())) + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 35ee2e002bb0 rbdock.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.xml Sat Apr 04 15:00:22 2020 -0400 |
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| b'@@ -0,0 +1,357 @@\n+<tool id="rxdock_rbdock" name="rxDock docking" version="0.1.3" profile="19.01">\n+ <description>- perform protein-ligand docking with rxDock</description>\n+ <macros>\n+ <import>rdock_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command><![CDATA[\n+ln -s \'$active_site\' receptor.as &&\n+ln -s \'$receptor\' receptor.mol2 &&\n+ln -s $receptor_prm receptor.prm &&\n+#if $name == \'Y\':\n+ sdmodify -f_REC \'$ligands\' > ligands.sdf &&\n+#else\n+ ln -s \'$ligands\' ligands.sdf &&\n+#end if\n+\n+python \'$__tool_directory__/rbdock.py\'\n+ -n \'$num\'\n+ #if $seed:\n+ -s \'$seed\'\n+ #end if\n+ &&\n+\n+cat rdock_output.sd \n+\n+#if $filter.filter_select == "filter":\n+ #if $filter.score:\n+ | sdfilter -f\'\\$SCORE <= ${filter.score}\'\n+ #end if\n+ #if $filter.nscore:\n+ | sdfilter -f\'\\$SCORE.norm <= ${filter.nscore}\'\n+ #end if\n+ #if $filter.top\n+ | sdsort -n -s -fSCORE | sdfilter -f\'\\$_COUNT <= $filter.top\'\n+ #end if\n+#end if\n+\n+ > \'$output\'\n+\n+ ]]></command>\n+\n+ <configfiles>\n+ <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00\n+RECEPTOR_FILE receptor.mol2\n+RECEPTOR_FLEX 3.0\n+ </configfile>\n+ </configfiles>\n+\n+ <inputs>\n+ <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>\n+ <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>\n+ <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/>\n+ <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>\n+ <conditional name="filter">\n+ <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter">\n+ <option value="filter">Show filter options</option>\n+ <option value="no_filter">No filtering</option>\n+ </param>\n+ <when value="filter">\n+ <param name="score" type="float" optional="true" label="Score filter"\n+ help="Exclude poses with score greater than this value"/>\n+ <param name="nscore" type="float" optional="true" label="Normalised score filter"\n+ help="Exclude poses with normalised score greater than this value"/>\n+ <param name="top" type="integer" value="1" optional="true" min="1" label="Number of best poses"\n+ help="Number of best scoring poses to keep"/>\n+ </when>\n+ <when value="no_filter"/>\n+ </conditional>\n+ <param name="name" type="boolean" label="Generate name field" truevalue="Y" falsevalue="N" checked="false"\n+ help="Generate the name field (first line) for cases where this is empty"/>\n+ <param argument="-seed" type="integer" optional="true" label="Random seed" help=""/>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="sdf" label="rxDock on ${on_string}"/>\n+ </outputs>\n+ <tests>\n+ <!-- broken ligand test -->\n+ <test expect_failure="true" expect_exit_code="23">\n+ <param name="receptor" value="receptor.mol2"/>\n+ <param name="ligands" value="broken_ligand.sdf"/>\n+ <param name="active_site" value="receptor.as"/>\n+ <param name="num" value="3"/>\n+ <param name="seed" value="3"/>\n+ <conditional name="filter">\n+ <param name="filter_select" value="filter"/>\n+ <param name="top" value="1"/>\n+ </conditional>\n+ <param name="name" value="false"/>\n+ </test>\n+ <test>\n+ <param name="receptor" value="receptor.mol2"/>\n+ <param name="ligands" value="ligands_names.sdf"/>\n+ <param name="active_site" value="receptor.as"/>\n+ <param name="num" value="3"/>\n+ <param na'..b'your results contain only one record\n+ then the name field is probably absent and must be generated.\n+\n+You will need to perform some test dockings to establish suitable values for the score filters.\n+The score is a number with lower values being better. Values can be negative.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Outputs**\n+\n+An SDF file is produced as output. The binding affinity scores are contained within the SDF file.::\n+\n+ 1-pyrimethamine\n+ rDOCK(R) 3D\n+ libRbt.so/2013.1/901 2013/11/27\n+ 21 22 0 0 0 0 0 0 0 0999 V2000\n+ -5.1897 17.8912 17.9590 N 0 0 0 0 0 0\n+ -3.9121 17.9973 18.3210 C 0 0 0 0 0 0\n+ -3.2404 19.1465 18.3804 N 0 0 0 0 0 0\n+ -3.8989 20.2829 18.0453 C 0 0 0 0 0 0\n+ -5.2389 20.2802 17.6553 C 0 0 0 0 0 0\n+ -5.8448 19.0235 17.6464 C 0 0 0 0 0 0\n+ -5.9601 21.5065 17.2850 C 0 0 0 0 0 0\n+ -6.2108 22.5074 18.2382 C 0 0 0 0 0 0\n+ -6.8903 23.6771 17.8851 C 0 0 0 0 0 0\n+ -7.3267 23.8556 16.5746 C 0 0 0 0 0 0\n+ -7.0903 22.8744 15.6151 C 0 0 0 0 0 0\n+ -6.4107 21.7051 15.9695 C 0 0 0 0 0 0\n+ -3.2455 16.8582 18.6507 N 0 0 0 0 0 0\n+ -7.1550 18.8446 17.2393 N 0 0 0 0 0 0\n+ -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0\n+ -2.9891 22.1828 19.5033 C 0 0 0 0 0 0\n+ -3.1112 21.5771 18.1096 C 0 0 0 0 0 0\n+ -2.2766 16.9101 18.9273 H 0 0 0 0 0 0\n+ -3.7237 15.9703 18.6154 H 0 0 0 0 0 0\n+ -7.8809 19.3992 17.6807 H 0 0 0 0 0 0\n+ -7.4159 17.8951 16.9940 H 0 0 0 0 0 0\n+ 1 2 2 0 0 0\n+ 1 6 1 0 0 0\n+ 2 3 1 0 0 0\n+ 2 13 1 0 0 0\n+ 3 4 2 0 0 0\n+ 4 5 1 0 0 0\n+ 4 17 1 0 0 0\n+ 5 6 2 0 0 0\n+ 5 7 1 0 0 0\n+ 6 14 1 0 0 0\n+ 7 8 2 0 0 0\n+ 7 12 1 0 0 0\n+ 8 9 1 0 0 0\n+ 9 10 2 0 0 0\n+ 10 11 1 0 0 0\n+ 10 15 1 0 0 0\n+ 11 12 2 0 0 0\n+ 13 18 1 0 0 0\n+ 13 19 1 0 0 0\n+ 14 20 1 0 0 0\n+ 14 21 1 0 0 0\n+ 16 17 1 0 0 0\n+ M END\n+ > <CHROM.0>\n+ -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150\n+\n+ > <CHROM.1>\n+ -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835\n+ 0.96119776,0.49809360,-3.12917831\n+\n+ > <Rbt.Current_Directory>\n+ /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock\n+\n+ > <Rbt.Executable>\n+ rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)\n+\n+ > <Rbt.Library>\n+ libRbt.so (2013.1, Build901 2013/11/27)\n+\n+ > <Rbt.Parameter_File>\n+ /rDock_2013.1/data/scripts/dock.prm\n+\n+ > <Rbt.Receptor>\n+ receptor.prm\n+\n+ > <SCORE>\n+ 0.445364\n+\n+ > <SCORE.INTER>\n+ 8.4\n+\n+ > <SCORE.INTER.CONST>\n+ 1\n+\n+ > <SCORE.INTER.POLAR>\n+ 0\n+\n+ > <SCORE.INTER.REPUL>\n+ 0\n+\n+ > <SCORE.INTER.ROT>\n+ 3\n+\n+ > <SCORE.INTER.VDW>\n+ 0\n+\n+ > <SCORE.INTER.norm>\n+ 0.494118\n+\n+ > <SCORE.INTRA>\n+ -1.38672\n+\n+ > <SCORE.INTRA.DIHEDRAL>\n+ -0.818539\n+\n+ > <SCORE.INTRA.DIHEDRAL.0>\n+ 6.01924\n+\n+ > <SCORE.INTRA.POLAR>\n+ 0\n+\n+ > <SCORE.INTRA.POLAR.0>\n+ 0\n+\n+ > <SCORE.INTRA.REPUL>\n+ 0\n+\n+ > <SCORE.INTRA.REPUL.0>\n+ 0\n+\n+ > <SCORE.INTRA.VDW>\n+ -0.977448\n+\n+ > <SCORE.INTRA.VDW.0>\n+ -1.0079\n+\n+ > <SCORE.INTRA.norm>\n+ -0.0815716\n+\n+ > <SCORE.RESTR>\n+\n+ > <SCORE.RESTR.norm>\n+ 0\n+\n+ > <SCORE.SYSTEM>\n+ -6.56792\n+\n+ > <SCORE.SYSTEM.CONST>\n+ 0\n+\n+ > <SCORE.SYSTEM.DIHEDRAL>\n+ 1.50415\n+\n+ > <SCORE.SYSTEM.POLAR>\n+ -2.3289\n+\n+ > <SCORE.SYSTEM.VDW>\n+ 0.59827\n+\n+ > <SCORE.SYSTEM.norm>\n+ -0.386348\n+\n+ > <SCORE.heavy>\n+ 17\n+\n+ > <SCORE.norm>\n+ 0.0261979\n+\n+ $$$$\n+\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 35ee2e002bb0 rdock_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdock_macros.xml Sat Apr 04 15:00:22 2020 -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_b93747f3">rxdock</requirement> + </requirements> + </xml> +</macros> |
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| diff -r 000000000000 -r 35ee2e002bb0 test-data/broken_ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/broken_ligand.sdf Sat Apr 04 15:00:22 2020 -0400 |
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| @@ -0,0 +1,159 @@ +Cc1ccsc1C1(O)CCOC1 + OpenBabel03262013053D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 2.6244 -0.3204 0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1487 -0.0653 -0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5577 1.2199 0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7851 1.2166 -0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4005 -0.3714 0.0020 S 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1829 -0.9540 -0.0102 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7593 -3.2703 1.1063 C 0 0 3 0 0 0 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7298 -2.3113 -0.2964 C 0 0 0 0 0 2 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 C 0 0 0 0 0 2 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3797 -2.5572 0.0072 C 0 0 0 0 0 2 0 0 0 0 0 0 + 3.1460 0.6144 0.0045 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8955 -0.8785 -0.8702 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8896 -0.8781 0.8782 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1148 2.0915 0.0058 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3714 2.0694 -0.0084 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6424 -1.9351 0.5862 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 13 1 0 0 0 0 + 1 14 1 0 0 0 0 + 1 15 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 16 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 17 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 12 1 0 0 0 0 + 8 18 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 1 0 0 0 0 +M END +$$$$ +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 35ee2e002bb0 test-data/ligand.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.mol Sat Apr 04 15:00:22 2020 -0400 |
| b |
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| diff -r 000000000000 -r 35ee2e002bb0 test-data/ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.sdf Sat Apr 04 15:00:22 2020 -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 35ee2e002bb0 test-data/ligands_names.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_names.sdf Sat Apr 04 15:00:22 2020 -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 35ee2e002bb0 test-data/ligands_nonames.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_nonames.sdf Sat Apr 04 15:00:22 2020 -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 + +$$$$ + + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8168 0.2065 0.4735 N 0 0 0 0 0 0 + -2.8206 -1.1045 0.2371 C 0 0 0 0 0 0 + -1.7327 -1.8208 -0.0438 N 0 0 0 0 0 0 + -0.5439 -1.1720 -0.0988 C 0 0 0 0 0 0 + -0.4317 0.1989 0.1374 C 0 0 0 0 0 0 + -1.6324 0.8424 0.4390 C 0 0 0 0 0 0 + 0.8521 0.9130 0.0752 C 0 0 0 0 0 0 + 1.6858 0.9917 1.2029 C 0 0 0 0 0 0 + 2.9119 1.6650 1.1430 C 0 0 0 0 0 0 + 3.3184 2.2713 -0.0498 C 0 0 0 0 0 0 + 2.4965 2.2018 -1.1763 C 0 0 0 0 0 0 + 1.2730 1.5284 -1.1135 C 0 0 0 0 0 0 + -4.0128 -1.7579 0.2830 N 0 0 0 0 0 0 + -1.6980 2.2076 0.6534 N 0 0 0 0 0 0 + 4.8189 3.1175 -0.1945 Cl 0 0 0 0 0 0 + 0.3929 -3.4780 -0.7058 C 0 0 0 0 0 0 + 0.6782 -2.0057 -0.4320 C 0 0 0 0 0 0 + 3.8777 1.7088 2.5773 Cl 0 0 0 0 0 0 + 1.3763 0.5224 2.1357 H 0 0 0 0 0 0 + 2.7982 2.6697 -2.1110 H 0 0 0 0 0 0 + 0.6467 1.4886 -2.0046 H 0 0 0 0 0 0 + -4.0437 -2.7510 0.1067 H 0 0 0 0 0 0 + -4.8568 -1.2458 0.4914 H 0 0 0 0 0 0 + -0.9218 2.6660 1.1184 H 0 0 0 0 0 0 + -2.6181 2.5747 0.8742 H 0 0 0 0 0 0 + 1.3238 -4.0040 -0.9412 H 0 0 0 0 0 0 + -0.2872 -3.5999 -1.5556 H 0 0 0 0 0 0 + -0.0575 -3.9650 0.1657 H 0 0 0 0 0 0 + 1.3854 -1.9447 0.4035 H 0 0 0 0 0 0 + 1.1636 -1.5839 -1.3199 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 19 1 0 0 0 + 9 10 2 0 0 0 + 9 18 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END +> <Name> +1-3062 + +> <Family> +A + +> <PC_uM> +1.08 + +> <TG_uM> +0.094 + +> <RL_uM> +0.19 + +> <set> +0 + +$$$$ |
| b |
| diff -r 000000000000 -r 35ee2e002bb0 test-data/poses-ascending.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-ascending.sdf Sat Apr 04 15:00:22 2020 -0400 |
| b |
| @@ -0,0 +1,130 @@ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.1119 -3.9277 5.3225 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0310 -3.0413 5.0553 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9945 -3.7187 4.3397 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8246 -2.7535 4.0816 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.7024 -3.4607 3.3058 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3075 -2.0336 5.3805 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.2468 -0.9323 5.0952 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6163 -0.0866 6.5353 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9603 -2.9922 6.5383 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7490 -3.7097 6.5798 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4577 -4.5984 7.6187 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3584 -4.7793 8.6615 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.5372 -4.0453 8.6712 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.7688 -4.2708 10.0891 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8278 -3.1495 7.6389 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 6 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.000052 + +$$$$ +COCC(C)C(CO)c1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 8.0891 -17.4910 5.6428 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7776 -17.2166 6.8572 O 0 0 0 0 0 0 0 0 0 0 0 0 + 9.8614 -18.1239 7.0701 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.5740 -17.7750 8.3957 C 0 0 1 0 0 0 0 0 0 0 0 0 + 9.6152 -18.0787 9.5619 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.9364 -18.5267 8.5391 C 0 0 1 0 0 0 0 0 0 0 0 0 + 11.7889 -20.0488 8.2998 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0437 -20.6799 9.3396 O 0 0 0 0 0 0 0 0 0 0 0 0 + 13.0327 -17.9696 7.6253 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1839 -17.4039 8.2015 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.2110 -16.8983 7.4013 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0973 -16.9557 6.0161 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.4814 -16.2619 4.9318 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 13.9696 -17.5220 5.4242 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.9423 -18.0292 6.2262 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.5383 -20.5488 10.1686 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 6 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 16 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CO)c1ccc(Br)cc1 + +> <TransFSScore> +0.000113 + +$$$$ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + -3.9406 -3.6524 26.0345 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0091 -3.2577 25.0376 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6782 -3.1793 25.5508 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7080 -2.7487 24.4377 C 0 0 1 0 0 0 0 0 0 0 0 0 + -1.0018 -1.3118 24.0009 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6316 -2.8817 24.9410 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0553 -4.2385 25.0759 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3836 -4.2980 25.8222 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7118 -5.6728 26.0281 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8212 -5.9445 26.7790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9743 -5.1619 26.8458 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0387 -5.5484 27.6691 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9457 -6.7188 28.4197 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3792 -7.2299 29.5403 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8038 -7.5103 28.3520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7442 -7.1209 27.5286 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.029289 + +$$$$ |
| b |
| diff -r 000000000000 -r 35ee2e002bb0 test-data/poses-descending.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses-descending.sdf Sat Apr 04 15:00:22 2020 -0400 |
| b |
| @@ -0,0 +1,130 @@ +COCC(C)OCCOc1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.6650 -5.5958 25.3680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.1057 -4.4972 26.0732 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0785 -3.4881 26.3491 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4358 -2.3388 27.1440 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.9482 -2.8397 28.5054 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4151 -1.2967 27.2873 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6267 -0.5481 26.0900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3817 0.2676 25.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6866 1.1011 24.6394 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7821 0.4960 23.4174 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7162 -0.8770 23.1782 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8146 -1.3676 21.8707 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9820 -0.4818 20.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1007 -1.1472 19.0431 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0584 0.8879 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9602 1.3731 22.3447 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <Name> +COCC(C)OCCOc1ccc(Br)cc1 + +> <TransFSScore> +0.900000 + +$$$$ +COCC(C)C(CCl)c1cccc(Br)c1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 15 15 0 0 0 0 0 0 0 0999 V2000 + 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 1 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CCl)c1cccc(Br)c1 + +> <TransFSScore> +0.258377 + +$$$$ +COCC(C)C(CO)c1ccc(Br)cc1 + OpenBabel03162018053D +libRbt.so/2013.1/901 2013/11/27 + 16 16 0 0 0 0 0 0 0 0999 V2000 + 5.1209 -3.0737 26.6189 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2470 -2.2997 25.4319 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6087 -2.1896 25.0116 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6915 -1.2882 23.7597 C 0 0 1 0 0 0 0 0 0 0 0 0 + 8.1245 -0.7354 23.6481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2475 -2.0456 22.4671 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.8752 -2.7399 22.6419 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9977 -4.0000 23.2991 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2126 -1.1502 21.2243 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1393 -1.7450 19.9523 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0915 -0.9617 18.7969 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1145 0.4251 18.9029 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0611 1.4863 17.3396 Br 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1760 1.0355 20.1544 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2225 0.2504 21.3109 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0953 -4.3353 23.4490 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 6 0 0 0 + 4 6 1 0 0 0 0 + 6 7 1 1 0 0 0 + 6 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 16 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 15 2 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 1 0 0 0 0 + 12 14 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END +> <Name> +COCC(C)C(CO)c1ccc(Br)cc1 + +> <TransFSScore> +0.173348 + +$$$$ |
| b |
| diff -r 000000000000 -r 35ee2e002bb0 test-data/poses.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses.sdf Sat Apr 04 15:00:22 2020 -0400 |
| b |
| b'@@ -0,0 +1,2730 @@\n+COCC(C)C(CCl)c1cccc(Br)c1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 10.5975 -1.6265 24.3456 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9876 -2.4972 23.3994 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5655 -2.3484 23.4275 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.9288 -3.2311 22.3401 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 8.0397 -4.7166 22.7175 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4621 -2.8051 21.9660 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 5.4266 -3.1085 23.0863 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5671 -2.0982 24.5513 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3532 -1.4007 21.3371 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4668 -0.2249 22.1042 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3963 1.0427 21.5193 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1859 1.1744 20.1518 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0190 0.0317 19.3806 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7201 0.1935 17.5198 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0801 -1.2369 19.9634 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 1 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 1 0 0 0\n+ 6 9 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 9 15 2 0 0 0 0\n+ 10 11 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)C(CCl)c1cccc(Br)c1\n+\n+> <TransFSScore>\n+0.258377\n+\n+$$$$\n+COCC(C)C(CCl)c1cccc(Br)c1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 5.6183 -0.0012 26.1615 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1674 -1.0474 25.3681 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1412 -1.6856 24.6032 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7556 -2.7964 23.7339 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 4.6702 -3.4858 22.8925 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.9796 -2.3138 22.8727 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 7.6828 -3.4659 22.0996 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.1636 -4.8702 23.0913 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7068 -1.0412 22.0446 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.9589 0.2496 22.5488 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7362 1.3947 21.7787 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2313 1.2861 20.4884 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9256 0.0281 19.9861 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2267 -0.1367 18.2360 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1388 -1.1182 20.7563 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 6 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 6 0 0 0\n+ 6 9 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 9 15 2 0 0 0 0\n+ 10 11 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 13 2 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)C(CCl)c1cccc(Br)c1\n+\n+> <TransFSScore>\n+0.047733\n+\n+$$$$\n+COCC(C)C(CCl)c1cccc(Br)c1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 15 15 0 0 0 0 0 0 0 0999 V2000\n+ 7.9912 -4.2501 22.2375 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3105 -3.3249 23.0780 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2107 -2.3148 23.5412 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.4791 -1.3723 24.5125 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 8.4280 -0.2734 25.0159 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1337 -0.7983 23.9352 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 5.3067 0.0046 24.9796 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6297 -0.9578 26.3221 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2752 -0.1245 22.5547 C 0 0 0 0 '..b'-1.1938 19.3289 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9926 -1.8088 20.5659 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 6 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 16 2 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)OCCOc1ccc(Br)cc1\n+\n+> <TransFSScore>\n+0.052545\n+\n+$$$$\n+COCC(C)OCCOc1ccc(Br)cc1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 1.5854 -4.4167 26.8713 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9171 -3.9650 27.0697 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3204 -3.0325 26.0654 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0629 -3.7637 24.9341 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 3.0725 -4.5314 24.0556 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7894 -2.7836 24.1743 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8770 -3.3338 23.4307 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3647 -2.3248 22.3968 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2636 -1.9969 21.5481 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5320 -1.2441 20.4392 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2993 -1.6247 19.1173 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6084 -0.7491 18.0695 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1526 0.5029 18.3492 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.5557 1.6873 16.9327 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3970 0.8871 19.6636 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0874 0.0098 20.7062 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 6 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 16 2 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)OCCOc1ccc(Br)cc1\n+\n+> <TransFSScore>\n+0.239591\n+\n+$$$$\n+COCC(C)OCCOc1ccc(Br)cc1\n+ OpenBabel03162018053D\n+libRbt.so/2013.1/901 2013/11/27\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 5.6650 -5.5958 25.3680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1057 -4.4972 26.0732 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0785 -3.4881 26.3491 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.4358 -2.3388 27.1440 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 4.9482 -2.8397 28.5054 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4151 -1.2967 27.2873 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.6267 -0.5481 26.0900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.3817 0.2676 25.7585 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6866 1.1011 24.6394 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7821 0.4960 23.4174 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7162 -0.8770 23.1782 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8146 -1.3676 21.8707 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9820 -0.4818 20.8080 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1007 -1.1472 19.0431 Br 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0584 0.8879 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9602 1.3731 22.3447 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 3 4 1 0 0 0 0\n+ 4 5 1 1 0 0 0\n+ 4 6 1 0 0 0 0\n+ 6 7 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 9 10 1 0 0 0 0\n+ 10 11 1 0 0 0 0\n+ 10 16 2 0 0 0 0\n+ 11 12 2 0 0 0 0\n+ 12 13 1 0 0 0 0\n+ 13 14 1 0 0 0 0\n+ 13 15 2 0 0 0 0\n+ 15 16 1 0 0 0 0\n+M END\n+> <Name>\n+COCC(C)OCCOc1ccc(Br)cc1\n+\n+> <TransFSScore>\n+0.900000\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 35ee2e002bb0 test-data/receptor.as |
| b |
| Binary file test-data/receptor.as has changed |
| b |
| diff -r 000000000000 -r 35ee2e002bb0 test-data/receptor.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/receptor.mol2 Sat Apr 04 15:00:22 2020 -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' |