Mercurial > repos > bgruening > autodock_vina_prepare_receptor

changeset 1:8b9b960c9409 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:32:31 -0400
parents d15e5a2a7558
children 05a13d377b28
files prepare_receptor.xml
diffstat 1 files changed, 26 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/prepare_receptor.xml	Sat Jun 04 12:37:59 2016 -0400
+++ b/prepare_receptor.xml	Tue May 07 13:32:31 2019 -0400
@@ -1,5 +1,5 @@
 <tool id="prepare_receptor" name="Prepare receptor" version="0.1.0">
-    <description>Tool to prepare receptor for Autodock Vina</description>
+    <description>Tool to prepare receptor for docking with Autodock Vina</description>
     <requirements>
         <requirement type="package" version="1.5.6">mgltools</requirement>
     </requirements>
@@ -22,14 +22,23 @@
         </test>
     </tests>
     <help><![CDATA[
-        ** What it does? **
+
+.. class:: infomark
 
-        This tool uses the MGLTools programming packages to convert a pdb molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. 
+**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.
+
+-----
 
-        ** input **
+.. class:: infomark
+
+**Input**
 
-        It's required at least one pdb dataset in history, what is informed in ligand field, for use the tool. The pdb molecule file looks like the following example:
-        
+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  
@@ -58,9 +67,15 @@
         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  
 
-        ** output **
+-----
+
+.. class:: infomark
 
-        The output is a pdbqt molecule file converted from a pdb molecule file. The pdbqt molecule file looks like the following example:
+**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
@@ -85,7 +100,9 @@
         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>
+
+
+      ]]></help>
     <citations>
         <citation type="doi">10.1002/jcc.21334</citation>
     </citations>