annotate hbonds/hbonds.xml @ 0:8aa5e465b043 draft default tip

"planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"

<tool id="vmd_hbonds" name="Hydrogen Bond Analysis using VMD" version="1.9.3">
    <description>between two segments of a trajectory</description>
    <requirements>
        <requirement type="package" version="1.9.3">vmd</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
     ln -s '$__tool_directory__/hbonds.tcl' ./hbonds.tcl &&
#if $trajin.is_of_type("dcd"):
     vmd  -pdb '$strin' -dcd '$trajin' -dispdev text -e '$hbonds_inp' &>> verbose.txt
#elif $trajin.is_of_type("xtc"):
     vmd  -gro '$strin' -xtc '$trajin' -dispdev text -e '$hbonds_inp' &>> verbose.txt
#end if 
]]></command>
    <configfiles>
         <configfile name="hbonds_inp">
source hbonds.tcl

set sele1 [atomselect $molid "$sele1"]
set sele2 [atomselect $molid "$sele2"]

hbonds -sel1 \$sele1 -sel2 \$sele2 -writefile yes -ang $angle -dist $distance -plot no -DA both -type all -outfile hbond.txt -detailout detail.txt
quit
         </configfile>
    </configfiles> 
    <inputs>
        <param format="dcd,xtc" name="trajin" type="data" label="DCD/XTC trajectory input"/>
        <param format="pdb,gro" name="strin" type="data" label="PDB/GRO input"/>
        <param name="molid"  type="integer" value="0" label="Molecule ID"/>
        <param name="sele1"  type="text" value="segid PRO" label="Selection 1" help="Definition of a segment with VMD atom selection language"/>
        <param name="sele2"  type="text" value="segid HET" label="Selection 2" help="Definition of a segment with VMD atom selection language"/>
        <param name="angle"  type="float" value="20.0" label="Angle cutoff"/>
        <param name="distance"  type="float" value="3.0" label="Distance cutoff"/>
    </inputs>
    <outputs> 
        <data format="txt" name="detail" from_work_dir="detail.txt" label="Percentage occupancy of the H-bond"/>
        <data format="txt" name="hbond"  from_work_dir="hbond.txt" label="Number of H-bonds"/>
        <data name="report" format="txt" from_work_dir="verbose.txt"/>
    </outputs>
    <tests>
        <test>
            <param name="trajin" value="test.dcd" ftype="dcd"/>
            <param name="strin" value="test.pdb" ftype="pdb"/>
            <param name="molid" value="0"/>
            <param name="distance" value="3.0"/>
            <param name="angle" value="20.0"/>
            <param name="sele1" value="water"/>
            <param name="sele2" value="not water"/>
	    <output name="hbond" value="Number_of_H-bonds.txt"/>
        </test>
        <test>
            <param name="trajin" value="test.xtc" ftype="xtc"/>
            <param name="strin" value="test.gro" ftype="gro"/>
            <param name="molid" value="0"/>
            <param name="distance" value="3.0"/>
            <param name="angle" value="20.0"/>
            <param name="sele1" value="water"/>
            <param name="sele2" value="not water"/>
	    <output name="hbond" value="Number_of_H-bonds_gro.txt"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
This tool calculates hydrogen bonds between two segments of a system in a molecular dynamics trajectory.

_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD/XTC).
       - PDB or GRO file.
       - Atom selection commands for two regions to be compared - e.g. 'not water' or 'segid PRO'. See here_ for more information on the VMD atom selection language.

.. _here: https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html    

_____

        
.. class:: infomark

**Output**

       - Number of H-bonds for each time step and and their occupancy.


    ]]></help>
    <citations>
      <citation type="doi">10.1016/0263-7855(96)00018-5</citation>
      <citation type="doi">10.1093/bioinformatics/btz107</citation>
    </citations>
</tool>