mdtraj_learning.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import mdtraj as md"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/jaeohshin/cadd'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mdtraj_learning.ipynb  topology.pdb           trajectory.xtc\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<mdtraj.Trajectory with 1000 frames, 52754 atoms, 16257 residues, and unitcells>\n"
     ]
    }
   ],
   "source": [
    "t = md.load('trajectory.xtc', top='topology.pdb')\n",
    "print(t)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<mdtraj.Trajectory with 9 frames, 52754 atoms, 16257 residues, and unitcells>\n"
     ]
    }
   ],
   "source": [
    "print (t[1:10])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(1000, 52754, 3)\n"
     ]
    }
   ],
   "source": [
    "print(t.xyz.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[22.04 22.06 22.08 22.1  22.12 22.14 22.16 22.18 22.2  22.22]\n"
     ]
    }
   ],
   "source": [
    "print(t.time[0:10])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'Trajectory' object has no attribute 'unitcell_length'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[12], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mt\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43munitcell_length\u001b[49m[\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m]\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'Trajectory' object has no attribute 'unitcell_length'"
     ]
    }
   ],
   "source": [
    "t.unitcell_length[-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting tables\n",
      "  Downloading tables-3.10.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.2 kB)\n",
      "Requirement already satisfied: numpy>=1.20.0 in /Users/jaeohshin/miniconda3/envs/openmm/lib/python3.12/site-packages (from tables) (1.26.4)\n",
      "Collecting numexpr>=2.6.2 (from tables)\n",
      "  Downloading numexpr-2.10.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (1.2 kB)\n",
      "Requirement already satisfied: packaging in /Users/jaeohshin/miniconda3/envs/openmm/lib/python3.12/site-packages (from tables) (24.1)\n",
      "Collecting py-cpuinfo (from tables)\n",
      "  Downloading py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)\n",
      "Collecting blosc2>=2.3.0 (from tables)\n",
      "  Downloading blosc2-2.7.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (9.1 kB)\n",
      "Requirement already satisfied: typing-extensions>=4.4.0 in /Users/jaeohshin/miniconda3/envs/openmm/lib/python3.12/site-packages (from tables) (4.12.2)\n",
      "Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)\n",
      "  Downloading ndindex-1.8-py3-none-any.whl.metadata (3.4 kB)\n",
      "Collecting msgpack (from blosc2>=2.3.0->tables)\n",
      "  Downloading msgpack-1.1.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (8.4 kB)\n",
      "Downloading tables-3.10.1-cp312-cp312-macosx_11_0_arm64.whl (5.5 MB)\n",
      "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m5.5/5.5 MB\u001b[0m \u001b[31m53.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
      "\u001b[?25hDownloading blosc2-2.7.1-cp312-cp312-macosx_11_0_arm64.whl (3.3 MB)\n",
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      "\u001b[?25hDownloading numexpr-2.10.1-cp312-cp312-macosx_11_0_arm64.whl (131 kB)\n",
      "Downloading py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)\n",
      "Downloading ndindex-1.8-py3-none-any.whl (91 kB)\n",
      "Downloading msgpack-1.1.0-cp312-cp312-macosx_11_0_arm64.whl (82 kB)\n",
      "Installing collected packages: py-cpuinfo, numexpr, ndindex, msgpack, blosc2, tables\n",
      "Successfully installed blosc2-2.7.1 msgpack-1.1.0 ndindex-1.8 numexpr-2.10.1 py-cpuinfo-9.0.0 tables-3.10.1\n"
     ]
    }
   ],
   "source": [
    "!pip install tables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "t[::2].save('halftraj.h5')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "atoms_to_keep = [a.index for a in t.topology.atoms if a.name == 'CA']\n",
    "t.restrict_atoms(atoms_to_keep)\n",
    "t.save('CA-only.h5')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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