rxdock_rbdock: rbdock.xml annotate

annotate rbdock.xml @ 3:b34d068c2782 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

author	bgruening
date	Tue, 28 Jul 2020 08:45:49 -0400
parents	6fe6b0e10ed6
children

rev	line source
3 b34d068c2782 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	1 <tool id="rxdock_rbdock" name="rxDock docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	2 <description>- perform protein-ligand docking with rxDock</description>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	3 <macros>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	4 <import>rxdock_macros.xml</import>
3 b34d068c2782 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	5 <token name="@GALAXY_VERSION@">0</token>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	6 </macros>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	7 <expand macro="requirements"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	8 <command><![CDATA[
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	9 ln -s '$active_site' receptor.as &&
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	10 ln -s '$receptor' receptor.mol2 &&
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	11
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	12 #if $custom_rec.custom_rec_select == 'true':
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	13 ## simple check that the receptor file name is correct
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	14 grep -q 'RECEPTOR_FILE receptor.mol2' $custom_rec.prm_file \|\| (echo "Error: a custom receptor.prm file must contain the line 'RECEPTOR_FILE receptor.mol2'" >&2 && exit 1) &&
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	15 ln -s '$custom_rec.prm_file' receptor.prm &&
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	16 #else
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	17 ln -s '$receptor_prm' receptor.prm &&
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	18 #end if
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	19
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	20 #if $name == 'Y':
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	21 sdmodify -f_REC '$ligands' > ligands.sdf &&
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	22 #else
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	23 ln -s '$ligands' ligands.sdf &&
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	24 #end if
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	25
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	26 rbdock -i ligands.sdf
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	27 -r receptor.prm
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	28 -p dock.prm
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	29 -n '$num'
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	30 -o rdock_output
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	31 #if $seed:
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	32 -s '$seed'
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	33 #end if
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	34 &&
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	35
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	36 cat rdock_output.sd
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	37
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	38 #if $filter.filter_select == "filter":
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	39 #if $filter.score:
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	40 \| sdfilter -f'\$SCORE <= ${filter.score}'
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	41 #end if
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	42 #if $filter.nscore:
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	43 \| sdfilter -f'\$SCORE.norm <= ${filter.nscore}'
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	44 #end if
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	45 #if $filter.top
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	46 \| sdsort -n -s -fSCORE \| sdfilter -f'\$_COUNT <= $filter.top'
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	47 #end if
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	48 #end if
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	49
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	50 > '$output'
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	51
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	52 ]]></command>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	53
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	54 <configfiles>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	55 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	56 RECEPTOR_FILE receptor.mol2
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	57 #if $custom_rec.custom_rec_select == 'false':
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	58 RECEPTOR_FLEX $custom_rec.flex
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	59 #end if
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	60 </configfile>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	61 </configfiles>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	62
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	63 <inputs>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	64 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	65 <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	66 <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	67 <conditional name="custom_rec">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	68 <param name="custom_rec_select" type="select" label="Use a custom receptor.prm file?" help="Useful for more advanced use-cases, such as tethered docking.">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	69 <option value="true">Use custom receptor.prm file</option>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	70 <option value="false" selected="true">Use default options (no user upload required)</option>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	71 </param>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	72 <when value="true">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	73 <param type="data" name="prm_file" format="txt" label="Receptor prm file" help="Note the file must contain the line 'RECEPTOR_FILE receptor.mol2', else the tool will fail."/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	74 </when>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	75 <when value="false">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	76 <param name="flex" type="float" value="3.0" min="0.0" label="Receptor flex" help="Value for RECEPTOR_FLEX (default 3)"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	77 </when>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	78 </conditional>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	79
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	80 <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	81 <conditional name="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	82 <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	83 <option value="filter">Show filter options</option>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	84 <option value="no_filter">No filtering</option>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	85 </param>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	86 <when value="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	87 <param name="score" type="float" optional="true" label="Score filter"
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	88 help="Exclude poses with score greater than this value"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	89 <param name="nscore" type="float" optional="true" label="Normalised score filter"
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	90 help="Exclude poses with normalised score greater than this value"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	91 <param name="top" type="integer" value="1" optional="true" min="1" label="Number of best poses"
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	92 help="Number of best scoring poses to keep"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	93 </when>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	94 <when value="no_filter"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	95 </conditional>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	96 <param name="name" type="boolean" label="Generate name field" truevalue="Y" falsevalue="N" checked="false"
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	97 help="Generate the name field (first line) for cases where this is empty"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	98 <param argument="-seed" type="integer" optional="true" label="Random seed" help=""/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	99 </inputs>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	100 <outputs>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	101 <data name="output" format="sdf" label="rxDock on ${on_string}"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	102 </outputs>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	103 <tests>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	104 <!-- broken ligand test -->
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	105 <test>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	106 <param name="receptor" value="receptor.mol2"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	107 <param name="ligands" value="broken_ligand.sdf"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	108 <param name="active_site" value="receptor.as"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	109 <param name="num" value="3"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	110 <param name="flex" value="3"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	111 <param name="seed" value="3"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	112 <conditional name="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	113 <param name="filter_select" value="filter"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	114 <param name="top" value="1"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	115 </conditional>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	116 <param name="name" value="false"/>
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	117 <output name="output">
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	118 <assert_contents>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	119 <has_text text="Rbt.Current_Directory"/>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	120 <has_n_lines n="181"/>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	121 <has_text_matching expression="^([^\$]+?\$\$\$\$){1}?$"/>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	122 </assert_contents>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	123 </output>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	124 </test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	125 <test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	126 <param name="receptor" value="receptor.mol2"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	127 <param name="ligands" value="ligands_names.sdf"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	128 <param name="active_site" value="receptor.as"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	129 <param name="num" value="3"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	130 <param name="flex" value="3"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	131 <param name="seed" value="3"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	132 <conditional name="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	133 <param name="filter_select" value="filter"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	134 <param name="top" value="1"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	135 </conditional>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	136 <param name="name" value="false"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	137 <output name="output">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	138 <assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	139 <has_text text="Rbt.Current_Directory"/>
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	140 <has_n_lines n="352"/>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	141 <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	142 </assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	143 </output>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	144 </test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	145 <test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	146 <param name="receptor" value="receptor.mol2"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	147 <param name="ligands" value="ligands_nonames.sdf"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	148 <param name="active_site" value="receptor.as"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	149 <param name="num" value="3"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	150 <param name="flex" value="3"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	151 <param name="seed" value="3"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	152 <conditional name="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	153 <param name="filter_select" value="filter"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	154 <param name="top" value="1"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	155 </conditional>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	156 <param name="name" value="true"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	157 <output name="output">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	158 <assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	159 <has_text text="Rbt.Current_Directory"/>
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	160 <has_n_lines n="352"/>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	161 <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	162 </assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	163 </output>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	164 </test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	165 <!-- no filter test -->
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	166 <test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	167 <param name="receptor" value="receptor.mol2"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	168 <param name="ligands" value="ligands_nonames.sdf"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	169 <param name="active_site" value="receptor.as"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	170 <param name="num" value="3"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	171 <param name="flex" value="3"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	172 <param name="seed" value="3"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	173 <conditional name="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	174 <param name="filter_select" value="no_filter"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	175 </conditional>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	176 <param name="name" value="true"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	177 <output name="output">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	178 <assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	179 <has_text text="Rbt.Current_Directory"/>
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	180 <has_n_lines n="1056"/>
6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	181 <has_text_matching expression="^([^\$]+?\$\$\$\$){6}?$"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	182 </assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	183 </output>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	184 </test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	185 <test>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	186 <param name="receptor" value="receptor.mol2"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	187 <param name="ligands" value="ligands_names.sdf"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	188 <param name="active_site" value="receptor.as"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	189 <param name="num" value="1"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	190 <param name="flex" value="3"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	191 <param name="seed" value="3"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	192 <conditional name="filter">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	193 <param name="filter_select" value="filter"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	194 <param name="score" value="10"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	195 <param name="nscore" value="1"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	196 </conditional>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	197 <param name="name"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	198 <output name="output">
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	199 <assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	200 <has_text text="Rbt.Current_Directory"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	201 <has_n_lines n="355"/>
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	202 <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	203 </assert_contents>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	204 </output>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	205 </test>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	206 <!-- test with custom receptor.prm -->
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	207 <test>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	208 <param name="receptor" value="receptor.mol2"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	209 <param name="ligands" value="ligands_names.sdf"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	210 <param name="active_site" value="receptor.as"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	211 <param name="custom_rec_select" value="true"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	212 <param name="prm_file" value="receptor.prm"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	213 <param name="num" value="1"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	214 <param name="seed" value="3"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	215 <conditional name="filter">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	216 <param name="filter_select" value="filter"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	217 <param name="score" value="10"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	218 <param name="nscore" value="1"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	219 </conditional>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	220 <param name="name"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	221 <output name="output">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	222 <assert_contents>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	223 <has_text text="Rbt.Current_Directory"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	224 <has_n_lines n="355"/>
2 6fe6b0e10ed6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1" bgruening parents: 1 diff changeset	225 <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/>
1 07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	226 </assert_contents>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	227 </output>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	228 </test>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	229 <!-- test with custom but broken receptor.prm -->
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	230 <test expect_failure="true" expect_exit_code="1">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	231 <param name="receptor" value="receptor.mol2"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	232 <param name="ligands" value="ligands_names.sdf"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	233 <param name="active_site" value="receptor.as"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	234 <param name="custom_rec_select" value="true"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	235 <param name="prm_file" value="wrong_receptor.prm"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	236 <param name="num" value="1"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	237 <param name="seed" value="3"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	238 <conditional name="filter">
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	239 <param name="filter_select" value="no_filter"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	240 </conditional>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	241 <param name="name"/>
07309bad01df "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit e9c627440028cfd2c743462927672e0c5e3576aa" bgruening parents: 0 diff changeset	242 </test>
0 35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	243 </tests>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	244 <help><![CDATA[
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	245
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	246 .. class:: infomark
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	247
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	248 This tool performs protein-ligand docking using the rxDock program.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	249 See https://www.rxdock.org for more details about rxDock and associated programs.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	250
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	251 -----
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	252
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	253 .. class:: infomark
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	254
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	255 Inputs
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	256
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	257 1. The protein receptor to dock into as a file in Mol2 format.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	258 2. The active site definition as a file as generated by the rbcavity tool.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	259 3. A set of ligands (collection or single file) to dock as a file in SDF format.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	260 4. The number of docking poses to generate (integer).
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	261 5. The number of best scoring dockings to keep (integer).
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	262 6. The max score that is allowed. Poses with scores greater than this are excluded (float, optional).
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	263 7. The max normalised score (the score normalised by the number of heavy atoms) that is allowed.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	264 Poses with normalised scores greater than this are excluded (float, optional).
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	265 8. Optionally generate the name field in the ligands SDF (this is the first line in the entry).
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	266 This field must be present and be unique for sorting and filtering to work. If your results contain only one record
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	267 then the name field is probably absent and must be generated.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	268
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	269 You will need to perform some test dockings to establish suitable values for the score filters.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	270 The score is a number with lower values being better. Values can be negative.
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	271
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	272 -----
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	273
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	274 .. class:: infomark
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	275
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	276 Outputs
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	277
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	278 An SDF file is produced as output. The binding affinity scores are contained within the SDF file.::
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	279
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	280 1-pyrimethamine
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	281 rDOCK(R) 3D
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	282 libRbt.so/2013.1/901 2013/11/27
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	283 21 22 0 0 0 0 0 0 0 0999 V2000
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	284 -5.1897 17.8912 17.9590 N 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	285 -3.9121 17.9973 18.3210 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	286 -3.2404 19.1465 18.3804 N 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	287 -3.8989 20.2829 18.0453 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	288 -5.2389 20.2802 17.6553 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	289 -5.8448 19.0235 17.6464 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	290 -5.9601 21.5065 17.2850 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	291 -6.2108 22.5074 18.2382 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	292 -6.8903 23.6771 17.8851 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	293 -7.3267 23.8556 16.5746 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	294 -7.0903 22.8744 15.6151 C 0 0 0 0 0 0
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35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	296 -3.2455 16.8582 18.6507 N 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	297 -7.1550 18.8446 17.2393 N 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	298 -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	299 -2.9891 22.1828 19.5033 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	300 -3.1112 21.5771 18.1096 C 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	301 -2.2766 16.9101 18.9273 H 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	302 -3.7237 15.9703 18.6154 H 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	303 -7.8809 19.3992 17.6807 H 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	304 -7.4159 17.8951 16.9940 H 0 0 0 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	305 1 2 2 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	306 1 6 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	307 2 3 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	308 2 13 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	309 3 4 2 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	310 4 5 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	311 4 17 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	312 5 6 2 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	313 5 7 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	314 6 14 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	315 7 8 2 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	316 7 12 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	317 8 9 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	318 9 10 2 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	319 10 11 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	320 10 15 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	321 11 12 2 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	322 13 18 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	323 13 19 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	324 14 20 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	325 14 21 1 0 0 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	326 16 17 1 0 0 0
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35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	328 > <CHROM.0>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	329 -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150
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35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	331 > <CHROM.1>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	332 -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	333 0.96119776,0.49809360,-3.12917831
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	334
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	335 > <Rbt.Current_Directory>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	336 /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	337
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	338 > <Rbt.Executable>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	339 rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	340
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	341 > <Rbt.Library>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	342 libRbt.so (2013.1, Build901 2013/11/27)
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	343
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	344 > <Rbt.Parameter_File>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	345 /rDock_2013.1/data/scripts/dock.prm
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	346
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	347 > <Rbt.Receptor>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	348 receptor.prm
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	349
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	350 > <SCORE>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	351 0.445364
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	352
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	353 > <SCORE.INTER>
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35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	355
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	356 > <SCORE.INTER.CONST>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	357 1
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	358
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	359 > <SCORE.INTER.POLAR>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	360 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	361
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	362 > <SCORE.INTER.REPUL>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	363 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	364
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	365 > <SCORE.INTER.ROT>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	366 3
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	367
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	368 > <SCORE.INTER.VDW>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	369 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	370
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	371 > <SCORE.INTER.norm>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	372 0.494118
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	373
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	374 > <SCORE.INTRA>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	375 -1.38672
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	376
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	377 > <SCORE.INTRA.DIHEDRAL>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	378 -0.818539
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	379
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	380 > <SCORE.INTRA.DIHEDRAL.0>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	381 6.01924
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	382
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	383 > <SCORE.INTRA.POLAR>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	384 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	385
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	386 > <SCORE.INTRA.POLAR.0>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	387 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	388
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	389 > <SCORE.INTRA.REPUL>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	390 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	391
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	392 > <SCORE.INTRA.REPUL.0>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	393 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	394
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	395 > <SCORE.INTRA.VDW>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	396 -0.977448
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	397
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	398 > <SCORE.INTRA.VDW.0>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	399 -1.0079
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	400
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	401 > <SCORE.INTRA.norm>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	402 -0.0815716
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	403
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	404 > <SCORE.RESTR>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	405
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	406 > <SCORE.RESTR.norm>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	407 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	408
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	409 > <SCORE.SYSTEM>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	410 -6.56792
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	411
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	412 > <SCORE.SYSTEM.CONST>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	413 0
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	414
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	415 > <SCORE.SYSTEM.DIHEDRAL>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	416 1.50415
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	417
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	418 > <SCORE.SYSTEM.POLAR>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	419 -2.3289
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	420
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	421 > <SCORE.SYSTEM.VDW>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	422 0.59827
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	423
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	424 > <SCORE.SYSTEM.norm>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	425 -0.386348
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	426
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	427 > <SCORE.heavy>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	428 17
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	429
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	430 > <SCORE.norm>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	431 0.0261979
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	432
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	433 $$$$
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	434
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	435 ]]></help>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	436 <expand macro="citations"/>
35ee2e002bb0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5" bgruening parents: diff changeset	437 </tool>

Mercurial > repos > bgruening > rxdock_rbdock

annotate rbdock.xml @ 3:b34d068c2782 draft default tip