annotate ramachandran_plots.xml @ 4:70a2d548e62c draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"

<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- calculate and plot the distribution of two dihedrals in a trajectory</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.5.2">scipy</requirement>
        <requirement type="package" version="0.10.0">seaborn</requirement>
        <requirement type="package" version="2.0.0">nbdime</requirement>
        <requirement type="package" version="5.3.1">pyyaml</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/ramachandran_plots.py'
        --itraj '$trajin'
        --istr '$strin'
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --iyml '$ymlin'
        --output   '$output'
        --oramachandran_plot '$ramachandran_plot'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs" />
        <section name="ymlparam" title="Torsion Parameters" expanded="False">
            <param format="txt" name="ymlin" type="data" label="Torsion parameters in yml format" help="Information in YAML format about the segid, resid, and name for atoms 1-4 of the phi and psi angles. Example formatting included in the main help text"/>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="Ramachandran Plot raw data" />
        <data format="png" name="ramachandran_plot" label="Ramachandran Plot" />
    </outputs>
    <tests>
        <test>
            <param name="trajin" value="test.dcd" ftype="dcd" />
            <param name="strin" value="test.pdb" ftype="pdb" />
            <section name="ymlparam">
                <param name="ymlin" value="test.yml" />
            </section>
            <output name="output">
                <assert_contents>
                    <has_text text="-144.503" />
                    <has_text text="-140.553" />
                </assert_contents>
            </output>
            <output name="ramachandran_plot">
                <assert_contents>
                    <has_size value="18522" delta="2000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

A Ramachandran plot ([φ,ψ] plot) was originally developed as a way to visualize the energetically allowed regions for backbone dihedral angles ψ and φ of an amino acid.
It can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (Ramachandran plot) of user-defined φ and ψ angles of a trajectory.


_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Text file in YAML format with Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.

Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.

  - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html
  - For glycan φ and ψ dihedral definitions, see
     - `Glycan Structure Website`_ - The glycosidic torsion angle definition is adopted from the crystallographic definition; O5-C1-O1-C'x (Φ; phi), C1-O1-C'x-C'x-1 (Ψ; psi), and O1-C'6-C'5-O'5 (ω; omega). The torsion angle between the first residue of the N-glycan chain and the side chain of the asparagine residue is defined as O5-C1-N'D2-C'G (Φ; phi) and C1-N'D2-C'G-C'B (Ψ; psi). The torsion angle between the first residue of the O-glycan chain and the side chain of the serine residue is defined as O5-C1-O'G-C'B (Φ; phi) and C1-O'G-C'B-C'A (Ψ; psi). For threonine residue, OG1 is used instead of OG. The atom names are based on the CHARMM topology.
     - `Glycosciences Website`_ - NMR definition - Φ phi: H1-C1-O1-C′X Ψ psi: C1-O1-C′X-H′X ω omega: O1-C′6-C′5-H′5  Crystallographic definition - Φ phi: O5-C1-O1-C′X Ψ psi: C1-O1-C′X-C′X+1 ω omega: O1-C′6-C′5-O′5

  - An example of a yaml formatted selection for φ-ψ of a small glycoprotein called PROF with a carbohydrate portion called CARA where φ=O5-C1-OG1-CB1 and ψ=C1-OG1-CB-CA for the selected segment and residue ids.

    .. code-block:: yaml

      ramachandran1:
        phi:
          atom1:
           segid: CARA
           resid: 1
           name: O5
          atom2:
           segid: CARA
           resid: 1
           name: C1
          atom3:
           segid: PROF
           resid: 4
           name: OG1
          atom4:
           segid: PROF
           resid: 4
           name: CB
        psi:
          atom1:
           segid: CARA
           resid: 1
           name: C1
          atom2:
           segid: PROF
           resid: 4
           name: OG1
          atom3:
           segid: PROF
           resid: 4
           name: CB
          atom4:
           segid: PROF
           resid: 4
           name: CA
        comment: pick visually using VMD using labels. Go to labels, dihedral to see the information about resname resid and atomname and then lookup the segname for ach atom.

_____


.. class:: infomark

**Output**

       - Tab-separated file of raw data of the φ,ψ angles over time.
       - Image (as png) of the Ramachandran plot.

    .. _`Glycan Structure Website`: http://www.glycanstructure.org/fragment-db/howto
    .. _`Glycosciences Website`: http://www.glycosciences.de/tools/glytorsion/
    ]]></help>
    <expand macro="citations" />
</tool>