Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison prepare_box.xml @ 6:8f766d9652a2 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 15694de1df8abe053d0fa0953262dfef419d2936"
author bgruening
date Wed, 01 Sep 2021 09:38:09 +0000
parents 668c60aa4799
children
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5:668c60aa4799 6:8f766d9652a2
1 <tool id="prepare_box" name="Calculate the box parameters using RDKit" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="prepare_box" name="Calculate the box parameters using RDKit" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">2021.03.4</token> 3 <token name="@TOOL_VERSION@">2021.03.5</token>
4 <token name="@GALAXY_VERSION@">0</token> 4 <token name="@GALAXY_VERSION@">0</token>
5 </macros> 5 </macros>
6 <description>for an AutoDock Vina job from a ligand input file (confounding box)</description> 6 <description>for an AutoDock Vina job from a ligand or pocket input file (confounding box)</description>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
9 <requirement type="package" version="1.19.1">numpy</requirement> 9 <requirement type="package" version="1.19.1">numpy</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
22 #if $seed_value: 22 #if $seed_value:
23 --seed '$seed_value' 23 --seed '$seed_value'
24 #end if 24 #end if
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand" 27 <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand or pocket"
28 help="The input ligand with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/> 28 help="The input ligand or pocket with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
29 <param name="bufx" type="float" value="0" label="x-axis buffer" 29 <param name="bufx" type="float" value="0" label="x-axis buffer"
30 help="Buffer in the x direction (in angs.)"/> 30 help="Buffer in the x direction (in angs.)"/>
31 <param name="bufy" type="float" value="0" label="y-axis buffer" 31 <param name="bufy" type="float" value="0" label="y-axis buffer"
32 help="Buffer in the y direction (in angs.)"/> 32 help="Buffer in the y direction (in angs.)"/>
33 <param name="bufz" type="float" value="0" label="z-axis buffer" 33 <param name="bufz" type="float" value="0" label="z-axis buffer"
79 79
80 .. class:: infomark 80 .. class:: infomark
81 81
82 **Description** 82 **Description**
83 83
84 This tool calculates a confounding box around an input ligand and 84 This tool calculates a confounding box around an input ligand or pocket and
85 uses it to generate the input parameters for an AutoDock Vina job. 85 uses it to generate the input parameters for an AutoDock Vina job.
86
87 If you already know the coordinates of a ligand which binds to the protein, you can simply
88 use this file as the tool input. Alternatively, you can search for pockets using the fpocket
89 tool and use one of the output PDB files as an input.
86 90
87 The output file can be fed into the AutoDock Vina tool as an alternative to creating the 91 The output file can be fed into the AutoDock Vina tool as an alternative to creating the
88 parameter file manually. 92 parameter file manually.
89 93
90 ----- 94 -----
93 97
94 **Inputs:** 98 **Inputs:**
95 99
96 This tool requires: 100 This tool requires:
97 101
98 * An input ligand - This should be a file (MOL, SDF, PDB or MOL2 format) representing the ligand you wish to dock. 102 * An input file (MOL, SDF, PDB or MOL2 format) representing either a ligand, or a pocket found with the fpocket tool.
99 103
100 * (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore. 104 * (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore.
101 105
102 106
103 ----- 107 -----