Source code for mdadash.backend.analyses.janin

"""
Janin plot (Dihedral angles analysis)
"""

import logging
from typing import ClassVar

import matplotlib.pyplot as plt
from IPython.display import display
from MDAnalysis.analysis.dihedrals import Janin

from mdadash.backend.widgets.base import WidgetBase

logger = logging.getLogger(__name__)




class JaninPlot(WidgetBase):
    """

    **Janin Plot**

    This widget uses `MDAnalysis.analysis.dihedrals.Janin`_ for dihedral angles
    analysis and creates a `Janin plot`_.

    .. _MDAnalysis.analysis.dihedrals.Janin: https://docs.mdanalysis.org/stable/
        documentation_pages/analysis/dihedrals.html#MDAnalysis.analysis.dihedrals.Janin

    .. _Janin plot: https://userguide.mdanalysis.org/stable/
        examples/analysis/structure/dihedrals.html#Janin-analysis

    **Inputs**

    Selection
        MDAnalysis selection phrase
            Default: ``protein``

    Show reference
        Show allowed and marginally allowed regions
            Default: ``True``

    **Output**

    Here is an example output plot of this widget:

    .. figure:: /_static/images/janin_output.jpg
        :alt: Janin Plot output

    """

    name = "Janin Plot"
    description = "Dihedral angles analysis using Janin plot"

    _inputs: ClassVar = [
        {
            "attribute": "selection",
            "name": "Selection",
            "description": "MDAnalysis selection phrase",
            "type": "str",
            "validations": ["required"],
        },
        {
            "attribute": "ref",
            "name": "Show reference",
            "description": "Show allowed and marginally allowed regions",
            "type": "bool",
        },
    ]

    def __init__(self):
        super().__init__()
        self.selection = "protein"
        self.ref = True
        self.janin = None
        self._setup_plot()

    def _setup_plot(self):
        """Setup matplotlib plot"""
        self.fig, self.ax = plt.subplots()
        (self.plot,) = self.ax.plot([], [])
        self.ax.grid(True)

    def _update_selection(self):
        """Update atom groups when selection phrase changes"""
        self.janin = Janin(self.u.select_atoms(self.selection))



    def on_post_connect(self):
        """on_post_connect handler"""
        self._update_selection()




    def on_input_change(self, attribute, _old_value, new_value):
        """on_input_change handler"""
        if attribute == "selection":
            self._update_selection()


    def _do_nothing(self, *_args, **_kwargs):
        return None



    def run_every_frame(self):
        """every-frame run handler"""
        self.janin.run(frames=[self.u.trajectory.frame])
        # update plot
        self.ax.clear()
        # Using `set_major_formatter` causes a memory leak everytime this
        # loop is run. Hence remove the degree formatting and mention
        # the units in the x and y axis labels instead
        self.ax.xaxis.set_major_formatter = self._do_nothing
        self.ax.yaxis.set_major_formatter = self._do_nothing
        self.janin.plot(ax=self.ax, color="black", marker=".", ref=self.ref)
        self.ax.set_xlabel(r"$\chi_1$ (degrees)")
        self.ax.set_ylabel(r"$\chi_2$ (degrees)")
        self.fig.canvas.draw()
        display(self.fig)