Update .gitignore and tutorials

ZhangGroup-MITChemistry · Jul 9, 2023 · 1d2f13e · 1d2f13e
1 parent d04cf35
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diff --git a/.gitignore b/.gitignore
@@ -15,3 +15,5 @@ examples/minimal-example/
 dist/
 openabc.egg-info/
 
+.ipynb_checkpoints/
+
diff --git a/tutorials/HPS-protein-condensate/DDX4.ipynb b/tutorials/HPS-protein-condensate/DDX4.ipynb
@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -12,7 +11,20 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "b7a111b53ee34e5a8773645803b6b9e4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "# load packages\n",
     "import numpy as np\n",
@@ -26,6 +38,11 @@
     "    import simtk.openmm as mm\n",
     "    import simtk.openmm.app as app\n",
     "    import simtk.unit as unit\n",
+    "import mdtraj\n",
+    "try:\n",
+    "    import nglview\n",
+    "except ImportError:\n",
+    "    print('Please install nglview to visualize molecules in the jupyter notebooks.')\n",
     "\n",
     "sys.path.append('../../')\n",
     "from openabc.forcefields.parsers import HPSParser\n",
@@ -37,7 +54,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -68,7 +84,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -93,11 +108,11 @@
       "Set water dielectric as 80.0.\n",
       "Use platform: CPU\n",
       "#\"Step\",\"Time (ps)\",\"Potential Energy (kJ/mole)\",\"Kinetic Energy (kJ/mole)\",\"Total Energy (kJ/mole)\",\"Temperature (K)\",\"Speed (ns/day)\"\n",
-      "100,1.0000000000000007,447.53549761014756,779.044497497912,1226.5799951080594,265.8085571550383,0\n",
-      "200,2.0000000000000013,486.8404272736629,926.2961924995544,1413.1366197732173,316.05056606817516,138\n",
-      "300,2.99999999999998,501.57864499170245,993.0885992430132,1494.6672442347156,338.8400130412459,129\n",
-      "400,3.9999999999999587,509.68876815099037,923.0584351486611,1432.7472032996516,314.945849184065,128\n",
-      "500,4.999999999999938,464.9724526697726,904.4309334315047,1369.4033861012774,308.59017968027825,115\n"
+      "100,1.0000000000000007,426.4861149069394,864.7997214241839,1291.2858363311234,295.0680826552625,0\n",
+      "200,2.0000000000000013,494.52917464130536,807.7471804554941,1302.2763550967995,275.60186006384146,453\n",
+      "300,2.99999999999998,543.3895317584377,819.7461130785344,1363.135644836972,279.69587392078347,457\n",
+      "400,3.9999999999999587,490.5923645594664,851.3156034074129,1341.9079679668794,290.4673262593729,457\n",
+      "500,4.999999999999938,594.9643276032544,872.0971948033958,1467.0615224066503,297.55796722031056,460\n"
      ]
     }
    ],
@@ -121,13 +136,35 @@
     "protein.simulation.context.setVelocitiesToTemperature(temperature)\n",
     "protein.simulation.step(500)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Show HP1alpha dimer slab simulation trajectory.\n"
+     ]
+    }
+   ],
+   "source": [
+    "try:\n",
+    "    traj = mdtraj.load_dcd(output_dcd, top=ca_pdb)\n",
+    "    nglview.show_mdtraj(traj)\n",
+    "    print('Show HP1alpha dimer slab simulation trajectory.')\n",
+    "except NameError:\n",
+    "    print('Please install nglview to visualize molecules in the jupyter notebooks.')"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py38",
+   "display_name": "Python [conda env:.conda-py39]",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-.conda-py39-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -141,13 +178,12 @@
    "pygments_lexer": "ipython3",
    "version": "3.9.16"
   },
-  "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
     "hash": "95d07581651f3c45a5651aa035df7e4a83b5587ddccf2e46662da40695cb8d28"
    }
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/tutorials/HPS-protein-condensate/DDX4_condensate.ipynb b/tutorials/HPS-protein-condensate/DDX4_condensate.ipynb
@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -10,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,6 +26,11 @@
     "    import simtk.openmm as mm\n",
     "    import simtk.openmm.app as app\n",
     "    import simtk.unit as unit\n",
+    "import mdtraj\n",
+    "try:\n",
+    "    import nglview\n",
+    "except ImportError:\n",
+    "    print('Please install nglview to visualize molecules in the jupyter notebooks.')\n",
     "\n",
     "sys.path.append('../../')\n",
     "from openabc.forcefields.parsers import HPSParser\n",
@@ -39,7 +43,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -48,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -68,7 +71,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -77,18 +79,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Check contact with FastNS method. \n",
-      "Successfully inserted 10 molecules.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# insert molecules into the simulation box randomly\n",
     "n_mol = 10\n",
@@ -97,7 +90,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -106,7 +98,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -122,11 +114,11 @@
       "Set water dielectric as 80.0.\n",
       "Use platform: CPU\n",
       "#\"Step\",\"Time (ps)\",\"Potential Energy (kJ/mole)\",\"Kinetic Energy (kJ/mole)\",\"Total Energy (kJ/mole)\",\"Temperature (K)\",\"Speed (ns/day)\"\n",
-      "100,1.0000000000000007,2400.4719434697204,5926.867498388963,8327.339441858683,201.45211588453614,0\n",
-      "200,2.0000000000000013,2872.814568603486,5477.84798418303,8350.662552786516,186.19010247950905,49.8\n",
-      "300,2.99999999999998,2863.9280415233243,5521.199733759883,8385.127775283207,187.66361301132497,48.9\n",
-      "400,3.9999999999999587,2835.6026344951633,5601.691907684705,8437.294542179869,190.39951334209988,48.7\n",
-      "500,4.999999999999938,2702.3308074140296,5789.900599375048,8492.231406789077,196.79665975699544,47.8\n"
+      "100,1.0000000000000007,2600.623669551789,5956.331977768012,8556.9556473198,202.45360304718304,0\n",
+      "200,2.0000000000000013,3081.0428007288133,5521.044159836187,8602.086960565,187.6583251090539,323\n",
+      "300,2.99999999999998,2912.410144432957,5789.632299945443,8702.0424443784,196.7875403549168,324\n",
+      "400,3.9999999999999587,2817.8429803771583,5934.708888941865,8752.551869319022,201.7186419573374,323\n",
+      "500,4.999999999999938,2649.3505835466144,6163.174527363165,8812.525110909779,209.48410765728644,321\n"
      ]
     }
    ],
@@ -153,13 +145,36 @@
     "protein.simulation.context.setVelocitiesToTemperature(temperature)\n",
     "protein.simulation.step(500)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Show DDX4 simulation trajectory.\n"
+     ]
+    }
+   ],
+   "source": [
+    "# view trajectory\n",
+    "try:\n",
+    "    traj = mdtraj.load_dcd(output_dcd, top='start.pdb')\n",
+    "    nglview.show_mdtraj(traj)\n",
+    "    print('Show DDX4 simulation trajectory.')\n",
+    "except NameError:\n",
+    "    print('Please install nglview to visualize molecules in the jupyter notebooks.')"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py38",
+   "display_name": "Python [conda env:.conda-py39]",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-.conda-py39-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -173,13 +188,12 @@
    "pygments_lexer": "ipython3",
    "version": "3.9.16"
   },
-  "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
     "hash": "95d07581651f3c45a5651aa035df7e4a83b5587ddccf2e46662da40695cb8d28"
    }
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }