{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "// Load the FFX libraries.\n",
    "%use @file[ffx.json]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "// Run the Energy script to calculate the current potential energy of ubiquitin.\n",
    "import ffx.potential.commands.Energy\n",
    "\n",
    "val energy = Energy(arrayOf(\"../examples/ubiquitin.xyz\")).run()\n",
    "println(\" Current Potential Energy\")\n",
    "println(energy.getForceFieldEnergy())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "// Plot the energy during a minimization of ubiquitin using Koltin DataFrame and Kandy.\n",
    "%use kandy\n",
    "%use dataframe\n",
    "import ffx.algorithms.commands.Minimize\n",
    "\n",
    "val minimize = Minimize(arrayOf(\"../examples/ubiquitin.xyz\", \"-e\", \"1.0\")).run()\n",
    "println(minimize.toString())\n",
    "\n",
    "val energies = minimize.getEnergyList()\n",
    "val length = energies.size\n",
    "val steps = (0 until length).toList()\n",
    "val df = dataFrameOf(\"Step\" to steps, \"Energy\" to energies)\n",
    "\n",
    "df.plot {\n",
    "    points {\n",
    "        x(steps) { axis.name = \"Step\" }\n",
    "        y(energies) { axis.name = \"Energy (kcal/mol)\" }\n",
    "    }\n",
    "    layout.title = \"Ubiquitin Minimization\"\n",
    "}\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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  "ktnbPluginMetadata": {
   "projectDependencies": [
    "ffx-algorithms",
    "ffx-crystal",
    "ffx-experiment",
    "ffx-numerics",
    "ffx-pj",
    "ffx-potential",
    "ffx-ui",
    "ffx-utilities",
    "forcefieldx",
    "jopenmm"
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