"""
Ramachandran plot (Dihedral angles analysis)
"""
import logging
from typing import ClassVar
import matplotlib.pyplot as plt
from matplotlib.backends.backend_agg import FigureCanvasAgg
from MDAnalysis.analysis.dihedrals import Ramachandran
from mdadash.backend.widgets.base import WidgetBase
logger = logging.getLogger(__name__)
[docs]
class RamachandranPlot(WidgetBase):
"""
**Ramachandran Plot**
This widget uses `MDAnalysis.analysis.dihedrals.Ramachandran`_ for dihedral angles
analysis and creates a `Ramachandran plot`_.
.. _MDAnalysis.analysis.dihedrals.Ramachandran: https://docs.mdanalysis.org/stable/
documentation_pages/analysis/dihedrals.html#MDAnalysis.analysis.dihedrals.Ramachandran
.. _Ramachandran plot: https://userguide.mdanalysis.org/stable/
examples/analysis/structure/dihedrals.html#Ramachandran-analysis
**Inputs**
Selection
MDAnalysis selection phrase
Default: ``protein``
Show reference
Show allowed and marginally allowed regions
Default: ``True``
Custom title
Custom title for the plot
Default: ''
Plot refresh frequency
The frequency with which the plot is refreshed (every n frames).
This only applies when the run frequency is ``every-frame``
Default: ``1``
**Output**
Here is an example output plot of this widget:
.. figure:: /_static/images/ramachandran_output.jpg
:alt: Ramachandran Plot output
"""
name = "Ramachandran Plot"
description = "Dihedral angles analysis using Ramachandran plot"
_doclink = (
"https://mdadash.readthedocs.io/en/latest/autosummary/"
"mdadash.backend.analyses.ramachandran.html"
)
_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",
},
{
"attribute": "custom_title",
"name": "Custom title",
"description": "Custom title for the plot",
"type": "str",
},
{
"attribute": "plot_refresh_frequency",
"name": "Plot refresh frequency",
"description": "The frequency with which the plot is refreshed (every n frames)",
"type": "int",
"validations": ["min:1"],
},
]
def __init__(self):
super().__init__()
self.selection = "protein"
self.ref = True
self.rama = None
self.title = "protein"
self.custom_title = None
self.plot_refresh_count = 1
self.plot_refresh_frequency = 1
self._setup_plot()
def _setup_plot(self):
"""Setup matplotlib plot"""
self.fig, self.ax = plt.subplots()
self.canvas = FigureCanvasAgg(self.fig)
(self.plot,) = self.ax.plot([], [])
def _update_selection(self):
"""Update atom groups when selection phrase changes"""
self.rama = Ramachandran(self.u.select_atoms(self.selection))
self.title = f"{self.selection}"
[docs]
def on_post_connect(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.on_post_connect` handler"""
self._update_selection()
self.plot_refresh_count = 1
def _do_nothing(self, *_args, **_kwargs):
return None
[docs]
def run_every_frame(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.run_every_frame` handler"""
self.rama.run(frames=[self.u.trajectory.frame])
# update plot
if (
self.plot_refresh_count == 1
or self.plot_refresh_count % self.plot_refresh_frequency == 0
):
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.rama.plot(ax=self.ax, color="black", marker=".", ref=self.ref)
self.ax.set_xlabel(r"$\phi$ (degrees)")
self.ax.set_ylabel(r"$\psi$ (degrees)")
self.ax.set_title(
self.custom_title.replace("\\n", "\n")
if self.custom_title
else self.title
)
self.display_canvas(self.canvas)
self.plot_refresh_count += 1