"""
Ramachandran 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 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``
**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"
_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.rama = 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.rama = Ramachandran(self.u.select_atoms(self.selection))
[docs]
def on_post_connect(self):
"""on_post_connect handler"""
self._update_selection()
def _do_nothing(self, *_args, **_kwargs):
return None
[docs]
def run_every_frame(self):
"""every-frame run handler"""
self.rama.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.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.fig.canvas.draw()
display(self.fig)