<tool id="prepare_box" name="Calculate the box parameters using RDKit" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <macros>
        <token name="@TOOL_VERSION@">2021.03.5</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <description>for an AutoDock Vina job from a ligand or pocket input file (confounding box)</description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
        <requirement type="package" version="1.19.1">numpy</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/calc_vina_box_params.py'
        --ligand '$ligand'
        --ftype '${ligand.ext}'
        --config '$output'
        --bufx '$bufx'
        --bufy '$bufy'
        --bufz '$bufz'
        #if $exh:
            --exh '$exh'
        #end if
        #if $seed_value:
            --seed '$seed_value'
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="ligand" format="mol,sdf,pdb,mol2" label="Input ligand or pocket"
            help="The input ligand or pocket with three-dimensional coordinates (MOL, SDF, PDB and MOL formats supported)."/>
        <param name="bufx" type="float" value="0" label="x-axis buffer"
            help="Buffer in the x direction (in angs.)"/>
        <param name="bufy" type="float" value="0" label="y-axis buffer"
            help="Buffer in the y direction (in angs.)"/>
        <param name="bufz" type="float" value="0" label="z-axis buffer"
            help="Buffer in the z direction (in angs.)"/>
        <param name="exh" type="integer" optional="true" label="Exhaustiveness (optional)"
            help="Exhaustiveness of global search (optional, default = 8)"/>
        <param type="integer" name="seed_value" optional="true" label="Random seed (optional)" 
            help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="ligand" value="NUDT5A-x0114_2.mol" ftype="mol"/>
            <param name="bufx" value="1" />
            <param name="bufy" value="2" />
            <param name="bufz" value="3" />
            <output name="output" file="box_params_1.txt" />
        </test>
        <test>
            <param name="ligand" value="NUDT5A-x0114_2.sdf" ftype="sdf"/>
            <param name="bufx" value="1" />
            <param name="bufy" value="2" />
            <param name="bufz" value="3" />
            <param name="exh" value="10" />
            <param name="seed_value" value="1" />
            <output name="output" file="box_params_2.txt" />
        </test>
        <test>
            <param name="ligand" value="NUDT5A-x0114_2.mol2"/>
            <param name="bufx" value="1" />
            <param name="bufy" value="2" />
            <param name="bufz" value="3" />
            <output name="output" file="box_params_1.txt" />
        </test>
        <test>
            <param name="ligand" value="NUDT5A-x0114_2.pdb" ftype="pdb"/>
            <param name="bufx" value="1" />
            <param name="bufy" value="2" />
            <param name="bufz" value="3" />
            <param name="exh" value="10" />
            <param name="seed_value" value="1" />
            <output name="output" file="box_params_2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**Description**

This tool calculates a confounding box around an input ligand or pocket and
uses it to generate the input parameters for an AutoDock Vina job.

If you already know the coordinates of a ligand which binds to the protein, you can simply
use this file as the tool input. Alternatively, you can search for pockets using the fpocket
tool and use one of the output PDB files as an input.

The output file can be fed into the AutoDock Vina tool as an alternative to creating the
parameter file manually.

-----

.. class:: infomark

**Inputs:**

This tool requires:

* An input file (MOL, SDF, PDB or MOL2 format) representing either a ligand, or a pocket found with the fpocket tool.

* (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.


-----

.. class:: infomark

**Output:**

The output for this tool is a txt file containing the parameters needed to run an autodock
vina docking calculation with the docking tool. For example: ::

    size_x =  12.443000000000001
    size_y =  11.888
    size_z =  9.290999999999997
    center_x =  -29.8395
    center_y =  4.364
    center_z =  -64.5925
    num_modes = 9999
    energy_range = 9999
    exhaustiveness = 10
    cpu = 4
    seed = 1

The values for num_modes, energy range, cpu and seed are set to default values here.

This file can be used as the box parameter for the docking tool.

]]>
    </help>
    <citations>
        <citation type="bibtex">
            @article{rdkit,
                author = {Greg Landrum},
                title = {RDKit: Open-source cheminformatics},
                url ={http://www.rdkit.org}
            }</citation>
    </citations>
</tool>