Add Tutorial for Analyzing MD Trajectories Using Deeptime

examples/md_trajectory_tutorial.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Tutorial: Analyzing MD Trajectories with Deeptime\n",
+    "\n",
+    "This tutorial demonstrates how to analyze Molecular Dynamics (MD) trajectories using Deeptime. We will perform Time-lagged Independent Component Analysis (TICA) on an example trajectory using MDAnalysis and Deeptime.\n",
+    "\n",
+    "### Prerequisites\n",
+    "- Install Deeptime: `pip install deeptime`\n",
+    "- Install MDAnalysis: `pip install MDAnalysis`\n",
+    "\n",
+    "### Steps\n",
+    "1. Load MD trajectory using MDAnalysis.\n",
+    "2. Perform TICA using Deeptime.\n",
+    "3. Visualize the results.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Requirement already satisfied: pip in c:\\users\\aster\\appdata\\local\\programs\\python\\python37\\lib\\site-packages (24.0)\n",
+      "Requirement already satisfied: setuptools in c:\\users\\aster\\appdata\\local\\programs\\python\\python37\\lib\\site-packages (68.0.0)\n",
+      "Collecting Cython\n",
+      "  Downloading Cython-3.0.10-cp37-cp37m-win_amd64.whl.metadata (3.2 kB)\n",
+      "Downloading Cython-3.0.10-cp37-cp37m-win_amd64.whl (2.7 MB)\n",
+      "   ---------------------------------------- 2.7/2.7 MB 828.5 kB/s eta 0:00:00\n",
+      "Installing collected packages: Cython\n",
+      "Successfully installed Cython-3.0.10\n"
+     ]
+    }
+   ],
+   "source": [
+    "\n",
+    "\n",
+    "# Upgrade pip and setuptools\n",
+    "!pip install --upgrade pip setuptools\n",
+    "\n",
+    "# Install Cython\n",
+    "!pip install Cython\n",
+    "\n",
+    "# Install MDAnalysis\n",
+    "!pip install MDAnalysis\n",
+    "\n",
+    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load an example trajectory using MDAnalysis\n",
+    "u = mda.Universe('topology_file.pdb', 'trajectory_file.xtc')\n",
+    "\n",
+    "# Select atoms or residues to analyze (e.g., protein)\n",
+    "atoms = u.select_atoms('protein')\n",
+    "\n",
+    "# Create a matrix to store the data\n",
+    "data = []\n",
+    "\n",
+    "# Iterate through trajectory frames and store positions\n",
+    "for ts in u.trajectory:\n",
+    "    data.append(atoms.positions)\n",
+    "\n",
+    "# Convert data to numpy array\n",
+    "data = np.array(data)\n",
+    "\n",
+    "# Perform TICA\n",
+    "tica = TICA(lag_time=10, dim=2)\n",
+    "tica_model = tica.fit(data).fetch_model()\n",
+    "\n",
+    "# Transform the data\n",
+    "transformed_data = tica_model.transform(data)\n",
+    "\n",
+    "# Plot the transformed data\n",
+    "plt.scatter(transformed_data[:, 0], transformed_data[:, 1])\n",
+    "plt.xlabel('TIC 1')\n",
+    "plt.ylabel('TIC 2')\n",
+    "plt.title('TICA of MD Trajectory')\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
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+ "nbformat": 4,
+ "nbformat_minor": 5
+}