debug_nglview.ipynb

{
 "cells": [
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   "cell_type": "code",
   "execution_count": 1,
   "id": "c1c7d8b6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Python 3.9.16\r\n"
     ]
    }
   ],
   "source": [
    "!python --version"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "2bde38ab",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'8.0.0'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import ipywidgets\n",
    "\n",
    "ipywidgets.__version__"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "2ff29482",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d8985e420e4842d9a0dd19297ec6776c",
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       "version_minor": 0
      },
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import MDAnalysis as mda\n",
    "import nglview as nv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "1266ee97",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'3.0.6'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nv.__version__"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "a5562835",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2.2.0'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mda.__version__"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a5447c9c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 898 atoms>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u = mda.Universe(\n",
    "    topology=\"/Users/xperrylinn/Desktop/demo_data/3_nvt_simulation/topology.pdb\",\n",
    "    coordinates=\"/Users/xperrylinn/Desktop/demo_data/3_nvt_simulation/trajectory.dcd\",\n",
    ")\n",
    "u"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "c03c1c9f",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "e3c1e8ad56c5468a9b5d124db4893c9e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view = nv.show_mdanalysis(u.atoms)\n",
    "view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c59dd4b6",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "debug_nglview",
   "language": "python",
   "name": "debug_nglview"
  },
  "language_info": {
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    "version": 3
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   "file_extension": ".py",
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   "name": "python",
   "nbconvert_exporter": "python",
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   "version": "3.9.16"
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