view pdbfixer.xml @ 0:24bf162ef74b draft default tip

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

<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>