"""
RMSD Analysis
"""
import logging
import sys
from collections import deque
from typing import ClassVar
import matplotlib.pyplot as plt
import numpy as np
from joblib import delayed
from matplotlib.backends.backend_agg import FigureCanvasAgg
from MDAnalysis.analysis import rms
from mdadash.backend.widgets.base import WidgetBase
logger = logging.getLogger(__name__)
[docs]
class RMSD(WidgetBase):
"""
**RMSD Analysis**
This widget uses `MDAnalysis.analysis.rms.rmsd`_ to calculate `RMSD`_ of a
selection. The reference positions used by this widget are the initial
positions of the selection available for the trajectory from the reference
timestep (:attr:`~mdadash.backend.kernel.core.BufferedTrajectory.ref_u`).
.. note:: If you use trajectory data from simulations performed under periodic boundary
conditions then you must make your molecules whole before performing RMSD calculations so
that the centers of mass of the mobile and reference structure are properly superimposed.
You can add custom transformations to the universe in the Universe Configuration section
in the Settings page of the dasboard.
.. _MDAnalysis.analysis.rms.rmsd: https://docs.mdanalysis.org/stable/
documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.rmsd
.. _RMSD: https://userguide.mdanalysis.org/stable/
examples/analysis/alignment_and_rms/rmsd.html
**Inputs**
Run frequency
.. compound::
The frequency with which the widget is run - `every-frame` or `batch`
Default: ``every-frame``
Run mode
The mode in which the widget is run - `serial` or `parallel`
Default: ``serial``
Selection
MDAnalysis selection phrase
Default: ``protein``
Center
Subtract center of geometry before calculation
Default: ``False``
Superposition:
Perform a rotational and translational superposition with the fast QCP algorithm
Default: ``False``
Weights:
Weights to use to compute weighted average.
One of ``None``, ``masses``, ``charges``, ``Custom function``
Default: ``None``
Custom weights function:
Name of the custom weights function to use to obtain weights. This is applicable
only when the Weights input above is set to ``Custom function``.
A custom function can be defined using the Notebook interface. The function should
take one parameter (MDAnalysis ``AtomGroup``) as input and should return a 1D array
of weights of the same length as the passed in selection ``AtomGroup``.
Example:
.. code-block:: python
import numpy as np
def rmsd_custom_weights_function(ag):
return np.sqrt(ag.masses)
Default: ''
Custom title
Custom title for the plot
Default: ''
Max values
Max values to show in plot
Default: ``100``
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``
Reset on connect
Reset the plot on every connect
Default: ``False``
X-axis
X-axis value - `time` or `step`
Default: ``time``
**Output**
Here is an example output plot of this widget:
.. figure:: /_static/images/rmsd_output.jpg
:alt: RMSD output
.. tip::
This widget supports batching and can run in parallel
"""
name = "RMSD"
description = "RMSD of a selection"
_doclink = (
"https://mdadash.readthedocs.io/en/latest/autosummary/"
"mdadash.backend.analyses.rmsd.html"
)
_notes = (
"If simulations are performed under periodic boundary conditions "
"then you must make your molecules whole before performing RMSD "
"calculations so that the centers of mass of the mobile and reference "
"structure are properly superimposed. You can add custom transformations "
"to the universe in the Universe Configuration section in the Settings page.\n\n"
"Note: The reference positions used by this widget are the initial positions "
"of the selection available for the trajectory from the reference "
"timestep (`u.trajectory.ref_u`)."
)
_inputs: ClassVar = [
{
"attribute": "_run_frequency",
"name": "Run frequency",
"description": "The frequency with which the widget is run",
"type": "select",
"items": [
"every-frame",
"batch",
],
},
{
"attribute": "_run_mode",
"name": "Run mode",
"description": "The mode in which the widget is run",
"type": "select",
"items": [
"serial",
"parallel",
],
},
{
"attribute": "selection",
"name": "Selection",
"description": "MDAnalysis selection phrase",
"type": "str",
"validations": ["required"],
},
{
"attribute": "center",
"name": "Center",
"description": "Subtract center of geometry before calculation",
"type": "bool",
},
{
"attribute": "superposition",
"name": "Superposition",
"description": (
"Perform a rotational and translational superposition with the fast QCP algorithm"
),
"type": "bool",
},
{
"attribute": "weights",
"name": "Weights",
"description": "Weights to use to compute weighted average",
"type": "select",
"items": [
"None",
"masses",
"charges",
"Custom function",
],
},
{
"attribute": "weights_function",
"name": "Custom weights function",
"description": "Custom function to obtain weights",
"type": "str",
},
{
"attribute": "custom_title",
"name": "Custom title",
"description": "Custom title for the plot",
"type": "str",
},
{
"attribute": "maxlen",
"name": "Max values",
"description": "Max values to show in plot",
"type": "int",
"validations": ["min:0"],
},
{
"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"],
},
{
"attribute": "reset_on_connect",
"name": "Reset on connect",
"description": "Reset the plot on every connect",
"type": "bool",
},
{
"attribute": "x_type",
"name": "X-axis",
"type": "toggle",
"options": [
{"name": "Time", "value": "time"},
{"name": "Step", "value": "step"},
],
},
]
def __init__(self):
super().__init__()
self.selection = "protein"
self.center = False
self.superposition = False
self.weights = "None"
self.weights_function = ""
self.ag = None
self.reference_positions = None
self.weights_array = None
self.title = "RMSD"
self.custom_title = None
self.default_maxlen = 100
self.maxlen = self.default_maxlen
self.plot_refresh_count = 1
self.plot_refresh_frequency = 1
self.reset_on_connect = False
self.x_type = "time"
self.x_values = None
self._setup_plot()
self._reset_plot_values()
def _setup_plot(self):
"""Setup matplotlib plot"""
self.fig, self.ax = plt.subplots()
self.canvas = FigureCanvasAgg(self.fig)
(self.plot,) = self.ax.plot([], [])
self.ax.set_ylabel("RMSD (Å)")
self.ax.grid(True)
self._set_title()
def _reset_plot_values(self):
"""Reset plot values"""
self.steps = deque(maxlen=self.maxlen)
self.times = deque(maxlen=self.maxlen)
self.y_values = deque(maxlen=self.maxlen)
self.plot_refresh_count = 1
self._set_x_values()
def _set_title(self):
"""Set plot title"""
self.ax.set_title(
self.custom_title.replace("\\n", "\n") if self.custom_title else self.title
)
def _set_x_values(self):
"""Set the values for the x-axis"""
if self.x_type == "step":
x_label = "Step"
self.x_values = self.steps
else:
x_label = "Time (ps)"
self.x_values = self.times
self.ax.set_xlabel(x_label)
def _get_weights(self):
if self.weights in ("masses", "charges"):
if not hasattr(self.ag, self.weights): # pragma: no cover
raise ValueError(f"{self.weights} not available")
return getattr(self.ag, self.weights)
if self.weights == "Custom function":
weights = None
main = sys.modules.get("__main__")
func_name = self.weights_function.strip()
if not hasattr(main, func_name):
raise ValueError(f"Custom function '{func_name}' not defined")
func = getattr(main, func_name)
if not callable(func):
raise ValueError(f"'{func_name}' is not a callable function")
try:
weights = func(self.ag)
except Exception as e: # pylint: disable=broad-exception-caught
raise ValueError("Error invoking custom weights function") from e
if np.shape(weights) != (len(self.ag),):
raise ValueError(f"Weights is not a 1D array of size {len(self.ag)}")
return weights
return None
def _update_selection(self):
"""Update atom groups when selection phrase changes"""
self.ag = self.u.select_atoms(self.selection)
# Use the reference universe to create the reference positions
ref_u = self.u.trajectory.ref_u
self.reference_positions = ref_u.select_atoms(self.selection).positions
# get weights
self.weights_array = self._get_weights()
# reset to current frame
self.reset_frame_latest()
self.title = f"RMSD of '{self.selection}'"
self._set_title()
self._update_plot(self._compute_current_frame())
[docs]
def on_post_create(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.on_post_create` handler"""
self._set_title()
self._reset_plot_values()
[docs]
def on_post_connect(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.on_post_connect` handler"""
self.plot_refresh_count = 1
if self.reset_on_connect: # pragma: no cover
self._reset_plot_values()
self._update_selection()
def _compute_current_frame(self):
"""Compute values for current frame"""
rmsd_value = rms.rmsd(
self.ag.positions,
self.reference_positions,
weights=self.weights_array,
center=self.center,
superposition=self.superposition,
)
return (
self.u.trajectory.ts.data["step"],
self.u.trajectory.ts.data["time"],
rmsd_value,
)
def _compute_batch(self):
"""Compute values for current batch"""
values = []
for i in range(self.u.trajectory.buffer_size):
_ = self.u.trajectory[i]
values.append(self._compute_current_frame())
return values
def _update_plot(self, values):
"""Append values and update plot"""
if isinstance(values, tuple):
values = [values]
# update plot points
for value in values:
(steps, times, v) = value
self.steps.append(steps)
self.times.append(times)
self.y_values.append(v)
# update plot
if self._run_frequency == "batch" or (
self.plot_refresh_count == 1
or self.plot_refresh_count % self.plot_refresh_frequency == 0
):
self.plot.set_data(self.x_values, self.y_values)
self.ax.relim()
self.ax.autoscale_view()
self.display_canvas(self.canvas)
self.plot_refresh_count += 1
[docs]
def run_every_frame(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.run_every_frame` handler"""
self._update_plot(self._compute_current_frame())
[docs]
def run_batch(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.run_batch` handler"""
self._update_plot(self._compute_batch())
[docs]
def get_parallel_job(self):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.get_parallel_job` handler"""
if self._run_frequency == "batch":
return delayed(self._compute_batch)()
return delayed(self._compute_current_frame)()
[docs]
def apply_parallel_results(self, values):
""":meth:`~mdadash.backend.widgets.base.WidgetBase.apply_parallel_results` handler"""
self._update_plot(values)