performance_comparison_pickle.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import MDAnalysis as mda"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from MDAnalysis.coordinates.PDB import PDBReader"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def iter_through_traj():\n",
    "    for time in range(u.trajectory.n_frames):\n",
    "        u.trajectory[time]\n",
    "        coord = u.atoms.positions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Develop Branch"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "89.3 ms ± 3.05 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit traj = PDBReader('test/test.pdb', n_atoms=47681)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/scottzhuang/mdanalysis/package/MDAnalysis/topology/guessers.py:148: UserWarning: Failed to guess the mass for the following atom types: DU\n",
      "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n",
      "/home/scottzhuang/mdanalysis/package/MDAnalysis/topology/PDBParser.py:327: UserWarning: Invalid elements found in the PDB file, elements attributes will not be populated.\n",
      "  warnings.warn(\"Invalid elements found in the PDB file, \"\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.31 s ± 10.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit u = mda.Universe('test_multi.pdb')  # 35 frames, 47681 atoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = mda.Universe('test_multi.pdb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.67 s ± 86.5 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit iter_through_traj()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Patched Branch"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "90.1 ms ± 2.23 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
     ]
    }
   ],
   "source": [
    "%timeit traj = PDBReader('test/test.pdb', n_atoms=47681)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/scottzhuang/mdanalysis/package/MDAnalysis/topology/guessers.py:80: UserWarning: Failed to guess the mass for the following atom types: DU\n",
      "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n",
      "/home/scottzhuang/mdanalysis/package/MDAnalysis/topology/PDBParser.py:327: UserWarning: Invalid elements found in the PDB file, elements attributes will not be populated.\n",
      "  warnings.warn(\"Invalid elements found in the PDB file, \"\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.51 s ± 10.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit u = mda.Universe('test_multi.pdb')  # 35 frames, 47681 atoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = mda.Universe('test_multi.pdb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.66 s ± 208 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
     ]
    }
   ],
   "source": [
    "%timeit iter_through_traj()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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