Add widget for RMSD (MDAnalysis#56)

Author: PardhavMaradani

CHANGELOG.md

@@ -29,10 +29,15 @@ The rules for this file:
 
 <!-- New added features -->
 
+- Added widget for RMSD (PR #54)
+
 ### Fixed
 
 <!-- Bug fixes -->
 
+- Miscellaneous fixes (PR #50)
+- Minor UI fixes (PR #51)
+
 ### Changed
 
 <!-- Changes in existing functionality -->

mdadash/backend/analyses/__init__.py

@@ -11,6 +11,7 @@
     janin,
     msd,
     ramachandran,
+    rmsd,
     rog,
 )
 
@@ -23,5 +24,6 @@
     "janin",
     "msd",
     "ramachandran",
+    "rmsd",
     "rog",
 ]

mdadash/backend/analyses/rmsd.py

@@ -0,0 +1,186 @@
+"""
+RMSD Analysis
+"""
+
+import logging
+from collections import deque
+from typing import ClassVar
+
+import matplotlib.pyplot as plt
+from IPython.display import display
+from MDAnalysis.analysis import rms
+
+from mdadash.backend.widgets.base import WidgetBase
+
+logger = logging.getLogger(__name__)
+
+
+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 when the widget instance is created or the
+    initial positions whenever the selection is updated.
+
+    .. _MDAnalysis.analysis.rms.rmsd: https://docs.mdanalysis.org/stable/
+        documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.rmsd
+
+    """
+
+    name = "RMSD"
+    description = "RMSD of a selection"
+
+    _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 when the widget instance is created or the initial positions "
+        "whenever the selection is updated."
+    )
+
+    _inputs: ClassVar = [
+        {
+            "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": "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",
+        },
+        {
+            "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.ag = None
+        self.reference_positions = None
+        self.title = "RMSD"
+        self.custom_title = None
+        self.default_maxlen = 100
+        self.maxlen = self.default_maxlen
+        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.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._set_x_values()
+
+    def _set_title(self):
+        """Set plot title"""
+        self.ax.set_title(self.custom_title 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 _update_selection(self):
+        """Update atom groups when selection phrase changes"""
+        self.ag = self.u.select_atoms(self.selection)
+        self.reference_positions = self.ag.positions.copy()
+        self.title = f"RMSD of '{self.selection}'"
+        self._set_title()
+
+    def on_post_create(self):
+        """on_post_create handler"""
+        self._set_title()
+        self._reset_plot_values()
+
+    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"""
+        reset_plot = False
+        if attribute == "maxlen":
+            if new_value < 0:
+                self.maxlen = self.default_maxlen
+            reset_plot = True
+        elif attribute == "x_type":
+            self._set_x_values()
+        elif attribute == "custom_title":
+            self._set_title()
+        elif attribute in ("selection", "center", "superposition"):
+            self._update_selection()
+            reset_plot = True
+        if reset_plot:
+            self._reset_plot_values()
+
+    def run_every_frame(self):
+        """every-frame run handler"""
+        rmsd_value = rms.rmsd(
+            self.ag.positions,
+            self.reference_positions,
+            center=self.center,
+            superposition=self.superposition,
+        )
+        self.y_values.append(rmsd_value)
+        self.steps.append(self.u.trajectory.ts.data["step"])
+        self.times.append(self.u.trajectory.ts.data["time"])
+        # update plot
+        self.plot.set_data(self.x_values, self.y_values)
+        self.ax.relim()
+        self.ax.autoscale_view()
+        self.fig.canvas.draw()
+        display(self.fig)

mdadash/backend/tests/test_server.py

@@ -1,3 +1,4 @@
+# pylint: disable=too-many-lines
 import json
 import sys
 from unittest.mock import ANY, AsyncMock
@@ -984,3 +985,21 @@ async def test_utils_alert_pause(_client, imd_server):
     handler = sio.handlers["/"]["delete_all_alerts"]
     await run_task_until_done(handler("_sid"))
     await disconnect_from_simulation()
+
+
+async def test_widget_run_rmsd(_client, imd_server):
+    uuid = await add_widget("RMSD")
+    await connect_to_simulation(imd_server)
+    inputs = [
+        ("selection", "protein"),
+        ("center", True),
+        ("superposition", True),
+        ("maxlen", -1),
+        ("x_type", "step"),
+        ("custom_title", "Title"),
+    ]
+    await check_input_changes(uuid, inputs)
+    await resume_simulation(imd_server)
+    assert await sio_event_emitted(sio, "widgets:output", n=1)
+    await remove_widget(uuid)
+    await disconnect_from_simulation()