annotate prepare_receptor.xml @ 1:8b9b960c9409 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e

<tool id="prepare_receptor" name="Prepare receptor" version="0.1.0">
    <description>Tool to prepare receptor for docking with Autodock Vina</description>
    <requirements>
        <requirement type="package" version="1.5.6">mgltools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1" />
    </stdio>
    <command><![CDATA[
        ln -s $receptor ./receptor.pdb && prepare_receptor4.py -r ./receptor.pdb -o "$file_output" -v -U nphs_lps -A hydrogens
    ]]></command>
    <inputs>
        <param type="data" name="receptor" format="pdb" label="Select a PDB file" />
    </inputs>
    <outputs>
        <data name="file_output" format="pdbqt" />
    </outputs>
    <tests>
        <test>
            <param name="receptor" value="3u1i_for_DM.pdb"/>
            <output name="file_output" file="3u1i_for_DM.pdbqt"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

This tool uses the MGLTools programming package to convert a pdb file to pdbqt file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom type modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added.

-----

.. class:: infomark

**Input**

A pdb input file is required.

* Example::

        ATOM      1  C   ACE A  49       7.007  -4.529   9.096  1.00  0.00           C  
        ATOM      2  O   ACE A  49       7.822  -3.710   8.650  1.00  0.00           O  
        ATOM      3  CH3 ACE A  49       6.132  -5.342   8.166  1.00  0.00           C  
        ATOM      4 1HH3 ACE A  49       6.747  -5.942   7.510  1.00  0.00           H  
        ATOM      5 2HH3 ACE A  49       5.492  -5.996   8.739  1.00  0.00           H  
        ATOM      6 3HH3 ACE A  49       5.518  -4.686   7.568  1.00  0.00           H  
        ATOM      7  N   ASP A  50       6.886  -4.713  10.549  1.00 65.94           N  
        ATOM      8  CA  ASP A  50       7.845  -3.806  11.248  1.00 64.98           C  
        ATOM      9  C   ASP A  50       8.508  -4.537  12.430  1.00 62.63           C  
        ATOM     10  O   ASP A  50       7.898  -5.423  13.032  1.00 63.05           O  
        ATOM     11  CB  ASP A  50       7.146  -2.511  11.685  1.00 66.87           C  
        ATOM     12  CG  ASP A  50       8.017  -1.267  11.465  1.00 68.22           C  
        ATOM     13  OD1 ASP A  50       9.140  -1.204  12.030  1.00 67.77           O  
        ATOM     14  OD2 ASP A  50       7.570  -0.351  10.729  1.00 69.97           O1-
        ATOM     15  N   LEU A  51       9.760  -4.189  12.730  1.00 60.07           N  
        ATOM     16  CA  LEU A  51      10.551  -4.934  13.712  1.00 57.24           C  
        ATOM     17  C   LEU A  51      10.592  -4.245  15.069  1.00 56.84           C  
        ATOM     18  O   LEU A  51      10.689  -3.020  15.157  1.00 57.09           O  
        ATOM     19  CB  LEU A  51      11.979  -5.179  13.205  1.00 55.78           C  
        ATOM     20  CG  LEU A  51      12.250  -6.074  11.987  1.00 54.47           C  
        ATOM     21  CD1 LEU A  51      13.717  -6.000  11.623  1.00 52.72           C  
        ATOM     22  CD2 LEU A  51      11.857  -7.523  12.233  1.00 53.53           C  
        ATOM     23  N   THR A  52      10.527  -5.061  16.117  1.00 55.68           N  
        ATOM     24  CA  THR A  52      10.525  -4.607  17.507  1.00 55.35           C  
        ATOM     25  C   THR A  52      11.729  -5.165  18.262  1.00 53.35           C  
        ATOM     26  O   THR A  52      12.413  -6.076  17.786  1.00 52.40           O  
        ATOM     27  CB  THR A  52       9.185  -4.964  18.195  1.00 56.95           C  

-----

.. class:: infomark

**Output**

The output is a pdbqt file - effectively the same as a pdb file, but with an extra column containing Gasteiger charges.

* Example::

        ATOM      1  C   ACE A  49       7.007  -4.529   9.096  1.00  0.00     0.214 C 
        ATOM      2  O   ACE A  49       7.822  -3.710   8.650  1.00  0.00    -0.274 OA
        ATOM      3  CH3 ACE A  49       6.132  -5.342   8.166  1.00  0.00     0.117 C 
        ATOM      4  N   ASP A  50       6.886  -4.713  10.549  1.00 65.94    -0.348 N 
        ATOM      5  HN  ASP A  50       6.246  -5.360  11.009  1.00  0.00     0.163 HD
        ATOM      6  CA  ASP A  50       7.845  -3.806  11.248  1.00 64.98     0.186 C 
        ATOM      7  C   ASP A  50       8.508  -4.537  12.430  1.00 62.63     0.241 C 
        ATOM      8  O   ASP A  50       7.898  -5.423  13.032  1.00 63.05    -0.271 OA
        ATOM      9  CB  ASP A  50       7.146  -2.511  11.685  1.00 66.87     0.147 C 
        ATOM     10  CG  ASP A  50       8.017  -1.267  11.465  1.00 68.22     0.175 C 
        ATOM     11  OD1 ASP A  50       9.140  -1.204  12.030  1.00 67.77    -0.648 OA
        ATOM     12  OD2 ASP A  50       7.570  -0.351  10.729  1.00 69.97    -0.648 OA
        ATOM     13  N   LEU A  51       9.760  -4.189  12.730  1.00 60.07    -0.346 N 
        ATOM     14  HN  LEU A  51      10.177  -3.384  12.264  1.00  0.00     0.163 HD
        ATOM     15  CA  LEU A  51      10.551  -4.934  13.712  1.00 57.24     0.177 C 
        ATOM     16  C   LEU A  51      10.592  -4.245  15.069  1.00 56.84     0.241 C 
        ATOM     17  O   LEU A  51      10.689  -3.020  15.157  1.00 57.09    -0.271 OA
        ATOM     18  CB  LEU A  51      11.979  -5.179  13.205  1.00 55.78     0.038 C 
        ATOM     19  CG  LEU A  51      12.250  -6.074  11.987  1.00 54.47    -0.020 C 
        ATOM     20  CD1 LEU A  51      13.717  -6.000  11.623  1.00 52.72     0.009 C 
        ATOM     21  CD2 LEU A  51      11.857  -7.523  12.233  1.00 53.53     0.009 C 
        ATOM     22  N   THR A  52      10.527  -5.061  16.117  1.00 55.68    -0.344 N 
        ATOM     23  HN  THR A  52      10.475  -6.064  15.941  1.00  0.00     0.163 HD


      ]]></help>
    <citations>
        <citation type="doi">10.1002/jcc.21334</citation>
    </citations>
</tool>