# HG changeset patch
# User chemteam
# Date 1649866916 0
# Node ID 24bf162ef74b926ac0028b146e5f7edfed725c38

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"

diff -r 000000000000 -r 24bf162ef74b pdbfixer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pdbfixer.xml	Wed Apr 13 16:21:56 2022 +0000
@@ -0,0 +1,189 @@
+<tool id="pdbfixer" name="PDBFixer"  version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>to automatically fix a PDB file before performing molecular dynamics simulation</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.8.1</token>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <requirements>
+         <requirement type="package" version="@TOOL_VERSION@">pdbfixer</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        pdbfixer
+            '$pdb_input'
+            ## --pdbid and --url not implemented here, users can use the get_pdb tool
+            --output '$output'
+            --add-atoms='$add_atoms'             ## which missing atoms to add: all, heavy, hydrogen, or none [default: all]
+            --keep-heterogens='$keep_heterogens' ## which heterogens to keep: all, water, or none [default: all]
+            $replace_nonstandard                 ## replace nonstandard residues with standard equivalents
+            $add_residues                        ## add missing residues
+            --ph='$ph'                           ## the pH to use for adding missing hydrogens [default: 7.0]
+
+            #if $solvent.box.water_box == "true":
+                --water-box=$solvent.box.x $solvent.box.y $solvent.box.z ## add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]
+                --positive-ion='$solvent.positive_ion' ##   positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]
+                --negative-ion='$solvent.negative_ion' ## negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]
+                --ionic-strength='$solvent.ionic_strength' ## molar concentration of ions to add to the water box [default: 0.0]
+            #end if
+            --verbose
+
+    ]]></command>
+    <inputs>
+        <param format="pdb" name="pdb_input" type="data" label="PDB input file"/>
+        <param name="add_atoms" type="select" label="Missing atoms to be added">
+            <option value="all" selected="true">All</option>
+            <option value="heavy">Heavy atoms only</option>
+            <option value="hydrogen">Hydrogen atoms only</option>
+            <option value="none">None</option>
+        </param>
+        <param name="keep_heterogens" type="select" label="Which heterogens to keep">
+            <option value="all" selected="true">All</option>
+            <option value="water">Only water</option>
+            <option value="none">None</option>
+        </param>
+        <param name="replace_nonstandard" type="boolean" label="Replace nonstandard residues with standard equivalents?" truevalue="--replace-nonstandard" falsevalue="" value=""/>
+        <param name="add_residues" type="boolean" label="Add missing residues?" truevalue="--add-residues" falsevalue="" value=""/>
+        <param name="ph" type="float" min="0" max="14" value="7" label="pH" help="Ignored if not adding hydrogen atoms"/>
+        <section name="solvent" title="Solvent parameters" help="Note that you may prefer to modify solvent parameters using other tools.">
+            <conditional name="box">
+                <param name="water_box" type="select" label="Add a water box?" help="Dimensions in nanometers">
+                    <option value="true">Yes</option>
+                    <option value="false" selected="true">No</option>
+                </param>
+                <when value="true">
+                    <param name="x" type="float" min="0" value="0" label="Size in X dimension"/>
+                    <param name="y" type="float" min="0" value="0" label="Size in Y dimension"/>
+                    <param name="z" type="float" min="0" value="0" label="Size in Z dimension"/>
+                </when>
+                <when value="false" />
+            </conditional>
+            <param name="positive_ion" type="select" label="Type of positive ion to add">
+                <option value="Li+">Lithium (Li+)</option>
+                <option value="Na+" selected="true">Sodium (Na+)</option>
+                <option value="K+">Potassium (K+)</option>
+                <option value="Rb+">Rubidium (Rb+)</option>
+                <option value="Cs+">Cesium (Cs+)</option>
+            </param>
+            <param name="negative_ion" type="select" label="Type of negative ion to add">
+                <option value="Cl-" selected="true">Chloride (Cl-)</option>
+                <option value="Br-">Bromide (Br-)</option>
+                <option value="F-">Fluoride (F-)</option>
+                <option value="I-">Iodide (I-)</option>
+            </param>
+            <param name="ionic_strength" type="float" min="0" max="10" value="0" label="Ionic strength" help="Molar concentration of ions to add to the water box"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="pdb"/>
+    </outputs>
+    <tests>
+        <!-- pdbfixer test-data/broken.pdb -add-atoms=all -keep-heterogens=all -replace-nonstandard -->
+        <test>
+            <param name="pdb_input" value="broken.pdb"/>
+            <param name="add_atoms" value="all"/>
+            <param name="keep_heterogens" value="all"/>
+            <param name="replace_nonstandard" value="true"/>
+            <param name="add_residues" value="false"/>
+            <param name="ph" value="7"/>
+            <output name="output">
+                <assert_contents>
+                    <has_n_lines n="162"/>
+                    <!-- check LYS8 is fixed  -->
+                    <has_text text="CD  LYS A   8"/>
+                    <has_text text="CE  LYS A   8"/>
+                    <!-- check hydration -->
+                    <has_text_matching expression="H  \n" n="81"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- pdbfixer test-data/broken.pdb -add-atoms=heavy -keep-heterogens=all -replace-nonstandard -add-residues -->
+        <test>
+            <param name="pdb_input" value="broken.pdb"/>
+            <param name="add_atoms" value="heavy"/>
+            <param name="keep_heterogens" value="all"/>
+            <param name="replace_nonstandard" value="true"/>
+            <param name="add_residues" value="false"/>
+            <output name="output">
+                <assert_contents>
+                    <has_n_lines n="81"/>
+                    <!-- check LYS8 is fixed  -->
+                    <has_text text="CD  LYS A   8"/>
+                    <has_text text="CE  LYS A   8"/>
+                    <!-- check no hydration -->
+                    <has_text_matching expression="H  \n" negate="true"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="pdb_input" value="broken.pdb"/>
+            <param name="add_atoms" value="all"/>
+            <param name="keep_heterogens" value="all"/>
+            <param name="replace_nonstandard" value="true"/>
+            <param name="add_residues" value="false"/>
+            <param name="ph" value="14"/>
+            <param name="water_box" value="true"/>
+            <param name="x" value="5"/>
+            <param name="y" value="5"/>
+            <param name="z" value="5"/>
+            <param name="positive_ion" value="Li+"/>
+            <param name="negative_ion" value="I-"/>
+            <param name="ionic_strength" value="2"/>
+            <output name="output">
+                <assert_contents>
+                    <!-- seems insertion of water is random and not fully reproducible  -->
+                    <has_n_lines n="11482" delta="100"/>
+                    <!-- check LYS8 is fixed  -->
+                    <has_text text="CD  LYS A   8"/>
+                    <has_text text="CE  LYS A   8"/>
+                    <!-- check hydration one less due to raised pH -->
+                    <has_text_matching expression="ATOM.* H  \n" n="80"/>
+                    <!-- check water and ions -->
+                    <has_text_matching expression="HOH" n="11041" delta="100"/>
+                    <has_text_matching expression=" I .*\n" n="144"/>
+                    <has_text_matching expression=" Li .*\n" n="144"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>  
+    <help><![CDATA[   
+.. class:: infomark
+ 
+**What it does**
+
+Fixes any issues in a PDB file (for example, adding missing residues, or missing atoms) prior to performing molecular dynamics simulations.
+
+PDBFixer can do any or all of the following:
+
+    - Add missing heavy atoms.
+    - Add missing hydrogen atoms.
+    - Build missing loops.
+    - Convert non-standard residues to their standard equivalents.
+    - Select a single position for atoms with multiple alternate positions listed.
+    - Delete unwanted chains from the model.
+    - Delete unwanted heterogens.
+    - Build a water box for explicit solvent simulations.
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - PDB file
+
+_____
+
+       
+.. class:: infomark
+
+**Output**
+
+       - PDB file
+
+    ]]></help>
+    <citations>
+      <citation type="doi">10.1371/journal.pcbi.1005659</citation>
+      <citation type="bibtex">@misc{pdbfixer, author = {{Peter Eastman et al.}}, title = {PDBFixer}, url={https://github.com/openmm/PDBFixer}, abstract = {PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.}, urldate = {2022-03-25}, publisher = {GitHub}, year = {2022}, month = mar, }</citation>
+    </citations>
+</tool>
+
diff -r 000000000000 -r 24bf162ef74b test-data/broken.pdb
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/broken.pdb	Wed Apr 13 16:21:56 2022 +0000
@@ -0,0 +1,148 @@
+COMPND    /data/dnb05/galaxy_db/files/a/e/1/dataset_ae125e29-1e3c-4170-98b3-b4bfa9ea44ab.dat 
+AUTHOR    GENERATED BY OPEN BABEL 3.1.0
+ATOM      1  N   MET A   1      -1.471  35.518  -6.691  1.00  0.00           N  
+ATOM      2  CA  MET A   1      -1.910  34.141  -6.485  1.00  0.00           C  
+ATOM      3  C   MET A   1      -2.164  33.409  -7.811  1.00  0.00           C  
+ATOM      4  O   MET A   1      -3.080  33.757  -8.560  1.00  0.00           O  
+ATOM      5  CB  MET A   1      -3.164  34.104  -5.599  1.00  0.00           C  
+ATOM      6  CG  MET A   1      -3.723  32.707  -5.358  1.00  0.00           C  
+ATOM      7  SD  MET A   1      -5.149  32.703  -4.256  1.00  0.00           S  
+ATOM      8  CE  MET A   1      -5.972  34.205  -4.783  1.00  0.00           C  
+ATOM      9  N   LEU A   2      -1.342  32.398  -8.090  1.00  0.00           N  
+ATOM     10  CA  LEU A   2      -1.526  31.550  -9.263  1.00  0.00           C  
+ATOM     11  C   LEU A   2      -2.804  30.743  -9.107  1.00  0.00           C  
+ATOM     12  O   LEU A   2      -2.963  30.014  -8.134  1.00  0.00           O  
+ATOM     13  CB  LEU A   2      -0.324  30.624  -9.448  1.00  0.00           C  
+ATOM     14  CG  LEU A   2       1.001  31.349  -9.723  1.00  0.00           C  
+ATOM     15  CD1 LEU A   2       2.173  30.375  -9.719  1.00  0.00           C  
+ATOM     16  CD2 LEU A   2       0.952  32.131 -11.039  1.00  0.00           C  
+ATOM     17  N   ASP A   3      -3.717  30.888 -10.062  1.00  0.00           N  
+ATOM     18  CA  ASP A   3      -5.063  30.335  -9.928  1.00  0.00           C  
+ATOM     19  C   ASP A   3      -5.073  28.812  -9.891  1.00  0.00           C  
+ATOM     20  O   ASP A   3      -4.491  28.155 -10.748  1.00  0.00           O  
+ATOM     21  CB  ASP A   3      -5.977  30.843 -11.046  1.00  0.00           C  
+ATOM     22  CG  ASP A   3      -7.366  30.238 -10.982  1.00  0.00           C  
+ATOM     23  OD1 ASP A   3      -8.026  30.358  -9.929  1.00  0.00           O  
+ATOM     24  OD2 ASP A   3      -7.805  29.641 -11.988  1.00  0.00           O  
+ATOM     25  N   ALA A   4      -5.745  28.263  -8.886  1.00  0.00           N  
+ATOM     26  CA  ALA A   4      -5.828  26.821  -8.702  1.00  0.00           C  
+ATOM     27  C   ALA A   4      -5.989  26.064 -10.024  1.00  0.00           C  
+ATOM     28  O   ALA A   4      -5.329  25.051 -10.250  1.00  0.00           O  
+ATOM     29  CB  ALA A   4      -6.966  26.483  -7.755  1.00  0.00           C  
+ATOM     30  N   GLU A   5      -6.859  26.566 -10.895  1.00  0.00           N  
+ATOM     31  CA  GLU A   5      -7.238  25.852 -12.112  1.00  0.00           C  
+ATOM     32  C   GLU A   5      -6.055  25.641 -13.052  1.00  0.00           C  
+ATOM     33  O   GLU A   5      -6.076  24.755 -13.902  1.00  0.00           O  
+ATOM     34  CB  GLU A   5      -8.361  26.594 -12.840  1.00  0.00           C  
+ATOM     35  CG  GLU A   5      -9.491  25.689 -13.296  1.00  0.00           C  
+ATOM     36  CD  GLU A   5     -10.466  25.372 -12.172  1.00  0.00           C  
+ATOM     37  OE1 GLU A   5     -10.799  26.295 -11.396  1.00  0.00           O  
+ATOM     38  OE2 GLU A   5     -10.905  24.205 -12.067  1.00  0.00           O  
+ATOM     39  N   ARG A   6      -5.023  26.457 -12.887  1.00  0.00           N  
+ATOM     40  CA  ARG A   6      -3.821  26.365 -13.708  1.00  0.00           C  
+ATOM     41  C   ARG A   6      -2.815  25.349 -13.160  1.00  0.00           C  
+ATOM     42  O   ARG A   6      -1.684  25.263 -13.639  1.00  0.00           O  
+ATOM     43  CB  ARG A   6      -3.150  27.737 -13.778  1.00  0.00           C  
+ATOM     44  CG  ARG A   6      -3.941  28.787 -14.536  1.00  0.00           C  
+ATOM     45  CD  ARG A   6      -3.495  28.859 -15.983  1.00  0.00           C  
+ATOM     46  NE  ARG A   6      -4.209  29.895 -16.722  1.00  0.00           N  
+ATOM     47  CZ  ARG A   6      -3.682  30.592 -17.723  1.00  0.00           C  
+ATOM     48  NH1 ARG A   6      -2.424  30.376 -18.098  1.00  0.00           N  
+ATOM     49  NH2 ARG A   6      -4.407  31.513 -18.342  1.00  0.00           N  
+ATOM     50  N   LEU A   7      -3.216  24.583 -12.152  1.00  0.00           N  
+ATOM     51  CA  LEU A   7      -2.263  23.726 -11.457  1.00  0.00           C  
+ATOM     52  C   LEU A   7      -2.667  22.264 -11.491  1.00  0.00           C  
+ATOM     53  O   LEU A   7      -1.975  21.419 -10.930  1.00  0.00           O  
+ATOM     54  CB  LEU A   7      -2.102  24.177  -9.997  1.00  0.00           C  
+ATOM     55  CG  LEU A   7      -1.945  25.680  -9.749  1.00  0.00           C  
+ATOM     56  CD1 LEU A   7      -2.124  26.012  -8.270  1.00  0.00           C  
+ATOM     57  CD2 LEU A   7      -0.611  26.185 -10.257  1.00  0.00           C  
+ATOM     58  N   LYS A   8      -3.791  21.963 -12.132  1.00  0.00           N  
+ATOM     59  CA  LYS A   8      -4.302  20.595 -12.151  1.00  0.00           C  
+ATOM     60  C   LYS A   8      -3.234  19.587 -12.586  1.00  0.00           C  
+ATOM     61  O   LYS A   8      -3.277  18.417 -12.186  1.00  0.00           O  
+ATOM     62  CB  LYS A   8      -5.543  20.491 -13.049  1.00  0.00           C  
+ATOM     63  N   HIS A   9      -2.276  20.055 -13.390  1.00  0.00           N  
+ATOM     64  CA  HIS A   9      -1.222  19.210 -13.959  1.00  0.00           C  
+ATOM     65  C   HIS A   9      -0.085  18.862 -12.995  1.00  0.00           C  
+ATOM     66  O   HIS A   9       0.712  17.970 -13.281  1.00  0.00           O  
+ATOM     67  CB  HIS A   9      -0.609  19.900 -15.181  1.00  0.00           C  
+ATOM     68  CG  HIS A   9       0.182  21.125 -14.839  1.00  0.00           C  
+ATOM     69  ND1 HIS A   9      -0.411  22.328 -14.524  1.00  0.00           N  
+ATOM     70  CD2 HIS A   9       1.516  21.327 -14.740  1.00  0.00           C  
+ATOM     71  CE1 HIS A   9       0.522  23.224 -14.256  1.00  0.00           C  
+ATOM     72  NE2 HIS A   9       1.702  22.642 -14.381  1.00  0.00           N  
+CONECT    1    2                                                      
+CONECT    2    3    1    5                                            
+CONECT    3    4    4    9    2                                       
+CONECT    4    3    3                                                 
+CONECT    5    2    6                                                 
+CONECT    6    5    7                                                 
+CONECT    7    6    8                                                 
+CONECT    8    7                                                      
+CONECT    9   10    3                                                 
+CONECT   10   13   11    9                                            
+CONECT   11   17   10   12   12                                       
+CONECT   12   11   11                                                 
+CONECT   13   14   10                                                 
+CONECT   14   16   15   13                                            
+CONECT   15   14                                                      
+CONECT   16   14                                                      
+CONECT   17   18   11                                                 
+CONECT   18   21   17   19                                            
+CONECT   19   20   20   18   25                                       
+CONECT   20   19   19                                                 
+CONECT   21   22   18                                                 
+CONECT   22   24   24   21   23                                       
+CONECT   23   22                                                      
+CONECT   24   22   22                                                 
+CONECT   25   19   26                                                 
+CONECT   26   27   25   29                                            
+CONECT   27   30   28   28   26                                       
+CONECT   28   27   27                                                 
+CONECT   29   26                                                      
+CONECT   30   31   27                                                 
+CONECT   31   32   34   30                                            
+CONECT   32   33   33   39   31                                       
+CONECT   33   32   32                                                 
+CONECT   34   35   31                                                 
+CONECT   35   34   36                                                 
+CONECT   36   35   38   38   37                                       
+CONECT   37   36                                                      
+CONECT   38   36   36                                                 
+CONECT   39   40   32                                                 
+CONECT   40   43   41   39                                            
+CONECT   41   40   42   42   50                                       
+CONECT   42   41   41                                                 
+CONECT   43   44   40                                                 
+CONECT   44   45   43                                                 
+CONECT   45   46   44                                                 
+CONECT   46   47   47   45                                            
+CONECT   47   49   48   46   46                                       
+CONECT   48   47                                                      
+CONECT   49   47                                                      
+CONECT   50   41   51                                                 
+CONECT   51   50   52   54                                            
+CONECT   52   58   51   53   53                                       
+CONECT   53   52   52                                                 
+CONECT   54   51   55                                                 
+CONECT   55   57   54   56                                            
+CONECT   56   55                                                      
+CONECT   57   55                                                      
+CONECT   58   59   52                                                 
+CONECT   59   62   60   58                                            
+CONECT   60   63   61   61   59                                       
+CONECT   61   60   60                                                 
+CONECT   62   59                                                      
+CONECT   63   64   60                                                 
+CONECT   64   67   63   65                                            
+CONECT   65   64   66   66                                            
+CONECT   66   65   65                                                 
+CONECT   67   68   64                                                 
+CONECT   68   67   70   70   69                                       
+CONECT   69   68   71                                                 
+CONECT   70   68   68   72                                            
+CONECT   71   69   72   72                                            
+CONECT   72   70   71   71                                            
+MASTER        0    0    0    0    0    0    0    0   72    0   72    0
+END