Mercurial > repos > bgruening > rxdock_rbdock
diff rbdock.xml @ 0:35ee2e002bb0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
| author | bgruening |
|---|---|
| date | Sat, 04 Apr 2020 15:00:22 -0400 |
| parents | |
| children | 07309bad01df |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rbdock.xml Sat Apr 04 15:00:22 2020 -0400 @@ -0,0 +1,357 @@ +<tool id="rxdock_rbdock" name="rxDock docking" version="0.1.3" profile="19.01"> + <description>- perform protein-ligand docking with rxDock</description> + <macros> + <import>rdock_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ +ln -s '$active_site' receptor.as && +ln -s '$receptor' receptor.mol2 && +ln -s $receptor_prm receptor.prm && +#if $name == 'Y': + sdmodify -f_REC '$ligands' > ligands.sdf && +#else + ln -s '$ligands' ligands.sdf && +#end if + +python '$__tool_directory__/rbdock.py' + -n '$num' + #if $seed: + -s '$seed' + #end if + && + +cat rdock_output.sd + +#if $filter.filter_select == "filter": + #if $filter.score: + | sdfilter -f'\$SCORE <= ${filter.score}' + #end if + #if $filter.nscore: + | sdfilter -f'\$SCORE.norm <= ${filter.nscore}' + #end if + #if $filter.top + | sdsort -n -s -fSCORE | sdfilter -f'\$_COUNT <= $filter.top' + #end if +#end if + + > '$output' + + ]]></command> + + <configfiles> + <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00 +RECEPTOR_FILE receptor.mol2 +RECEPTOR_FLEX 3.0 + </configfile> + </configfiles> + + <inputs> + <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/> + <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/> + <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/> + <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/> + <conditional name="filter"> + <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter"> + <option value="filter">Show filter options</option> + <option value="no_filter">No filtering</option> + </param> + <when value="filter"> + <param name="score" type="float" optional="true" label="Score filter" + help="Exclude poses with score greater than this value"/> + <param name="nscore" type="float" optional="true" label="Normalised score filter" + help="Exclude poses with normalised score greater than this value"/> + <param name="top" type="integer" value="1" optional="true" min="1" label="Number of best poses" + help="Number of best scoring poses to keep"/> + </when> + <when value="no_filter"/> + </conditional> + <param name="name" type="boolean" label="Generate name field" truevalue="Y" falsevalue="N" checked="false" + help="Generate the name field (first line) for cases where this is empty"/> + <param argument="-seed" type="integer" optional="true" label="Random seed" help=""/> + </inputs> + <outputs> + <data name="output" format="sdf" label="rxDock on ${on_string}"/> + </outputs> + <tests> + <!-- broken ligand test --> + <test expect_failure="true" expect_exit_code="23"> + <param name="receptor" value="receptor.mol2"/> + <param name="ligands" value="broken_ligand.sdf"/> + <param name="active_site" value="receptor.as"/> + <param name="num" value="3"/> + <param name="seed" value="3"/> + <conditional name="filter"> + <param name="filter_select" value="filter"/> + <param name="top" value="1"/> + </conditional> + <param name="name" value="false"/> + </test> + <test> + <param name="receptor" value="receptor.mol2"/> + <param name="ligands" value="ligands_names.sdf"/> + <param name="active_site" value="receptor.as"/> + <param name="num" value="3"/> + <param name="seed" value="3"/> + <conditional name="filter"> + <param name="filter_select" value="filter"/> + <param name="top" value="1"/> + </conditional> + <param name="name" value="false"/> + <output name="output"> + <assert_contents> + <has_text text="Rbt.Current_Directory"/> + <has_n_lines n="355"/> + </assert_contents> + </output> + </test> + <test> + <param name="receptor" value="receptor.mol2"/> + <param name="ligands" value="ligands_nonames.sdf"/> + <param name="active_site" value="receptor.as"/> + <param name="num" value="3"/> + <param name="seed" value="3"/> + <conditional name="filter"> + <param name="filter_select" value="filter"/> + <param name="top" value="1"/> + </conditional> + <param name="name" value="true"/> + <output name="output"> + <assert_contents> + <has_text text="Rbt.Current_Directory"/> + <has_n_lines n="355"/> + </assert_contents> + </output> + </test> + <!-- no filter test --> + <test> + <param name="receptor" value="receptor.mol2"/> + <param name="ligands" value="ligands_nonames.sdf"/> + <param name="active_site" value="receptor.as"/> + <param name="num" value="3"/> + <param name="seed" value="3"/> + <conditional name="filter"> + <param name="filter_select" value="no_filter"/> + </conditional> + <param name="name" value="true"/> + <output name="output"> + <assert_contents> + <has_text text="Rbt.Current_Directory"/> + <has_n_lines n="1059"/> + </assert_contents> + </output> + </test> + <test> + <param name="receptor" value="receptor.mol2"/> + <param name="ligands" value="ligands_names.sdf"/> + <param name="active_site" value="receptor.as"/> + <param name="num" value="1"/> + <param name="seed" value="3"/> + <conditional name="filter"> + <param name="filter_select" value="filter"/> + <param name="score" value="10"/> + <param name="nscore" value="1"/> + </conditional> + <param name="name"/> + <output name="output"> + <assert_contents> + <has_text text="Rbt.Current_Directory"/> + <has_n_lines n="355"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +This tool performs protein-ligand docking using the rxDock program. +See https://www.rxdock.org for more details about rxDock and associated programs. + +----- + +.. class:: infomark + +**Inputs** + +1. The protein receptor to dock into as a file in Mol2 format. +2. The active site definition as a file as generated by the rbcavity tool. +3. A set of ligands (collection or single file) to dock as a file in SDF format. +4. The number of docking poses to generate (integer). +5. The number of best scoring dockings to keep (integer). +6. The max score that is allowed. Poses with scores greater than this are excluded (float, optional). +7. The max normalised score (the score normalised by the number of heavy atoms) that is allowed. + Poses with normalised scores greater than this are excluded (float, optional). +8. Optionally generate the name field in the ligands SDF (this is the first line in the entry). + This field must be present and be unique for sorting and filtering to work. If your results contain only one record + then the name field is probably absent and must be generated. + +You will need to perform some test dockings to establish suitable values for the score filters. +The score is a number with lower values being better. Values can be negative. + +----- + +.. class:: infomark + +**Outputs** + +An SDF file is produced as output. The binding affinity scores are contained within the SDF file.:: + + 1-pyrimethamine + rDOCK(R) 3D + libRbt.so/2013.1/901 2013/11/27 + 21 22 0 0 0 0 0 0 0 0999 V2000 + -5.1897 17.8912 17.9590 N 0 0 0 0 0 0 + -3.9121 17.9973 18.3210 C 0 0 0 0 0 0 + -3.2404 19.1465 18.3804 N 0 0 0 0 0 0 + -3.8989 20.2829 18.0453 C 0 0 0 0 0 0 + -5.2389 20.2802 17.6553 C 0 0 0 0 0 0 + -5.8448 19.0235 17.6464 C 0 0 0 0 0 0 + -5.9601 21.5065 17.2850 C 0 0 0 0 0 0 + -6.2108 22.5074 18.2382 C 0 0 0 0 0 0 + -6.8903 23.6771 17.8851 C 0 0 0 0 0 0 + -7.3267 23.8556 16.5746 C 0 0 0 0 0 0 + -7.0903 22.8744 15.6151 C 0 0 0 0 0 0 + -6.4107 21.7051 15.9695 C 0 0 0 0 0 0 + -3.2455 16.8582 18.6507 N 0 0 0 0 0 0 + -7.1550 18.8446 17.2393 N 0 0 0 0 0 0 + -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0 + -2.9891 22.1828 19.5033 C 0 0 0 0 0 0 + -3.1112 21.5771 18.1096 C 0 0 0 0 0 0 + -2.2766 16.9101 18.9273 H 0 0 0 0 0 0 + -3.7237 15.9703 18.6154 H 0 0 0 0 0 0 + -7.8809 19.3992 17.6807 H 0 0 0 0 0 0 + -7.4159 17.8951 16.9940 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 + 9 10 2 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 13 18 1 0 0 0 + 13 19 1 0 0 0 + 14 20 1 0 0 0 + 14 21 1 0 0 0 + 16 17 1 0 0 0 + M END + > <CHROM.0> + -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150 + + > <CHROM.1> + -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835 + 0.96119776,0.49809360,-3.12917831 + + > <Rbt.Current_Directory> + /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock + + > <Rbt.Executable> + rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) + + > <Rbt.Library> + libRbt.so (2013.1, Build901 2013/11/27) + + > <Rbt.Parameter_File> + /rDock_2013.1/data/scripts/dock.prm + + > <Rbt.Receptor> + receptor.prm + + > <SCORE> + 0.445364 + + > <SCORE.INTER> + 8.4 + + > <SCORE.INTER.CONST> + 1 + + > <SCORE.INTER.POLAR> + 0 + + > <SCORE.INTER.REPUL> + 0 + + > <SCORE.INTER.ROT> + 3 + + > <SCORE.INTER.VDW> + 0 + + > <SCORE.INTER.norm> + 0.494118 + + > <SCORE.INTRA> + -1.38672 + + > <SCORE.INTRA.DIHEDRAL> + -0.818539 + + > <SCORE.INTRA.DIHEDRAL.0> + 6.01924 + + > <SCORE.INTRA.POLAR> + 0 + + > <SCORE.INTRA.POLAR.0> + 0 + + > <SCORE.INTRA.REPUL> + 0 + + > <SCORE.INTRA.REPUL.0> + 0 + + > <SCORE.INTRA.VDW> + -0.977448 + + > <SCORE.INTRA.VDW.0> + -1.0079 + + > <SCORE.INTRA.norm> + -0.0815716 + + > <SCORE.RESTR> + + > <SCORE.RESTR.norm> + 0 + + > <SCORE.SYSTEM> + -6.56792 + + > <SCORE.SYSTEM.CONST> + 0 + + > <SCORE.SYSTEM.DIHEDRAL> + 1.50415 + + > <SCORE.SYSTEM.POLAR> + -2.3289 + + > <SCORE.SYSTEM.VDW> + 0.59827 + + > <SCORE.SYSTEM.norm> + -0.386348 + + > <SCORE.heavy> + 17 + + > <SCORE.norm> + 0.0261979 + + $$$$ + + ]]></help> + <expand macro="citations"/> +</tool>