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   "execution_count": null,
   "metadata": {
    "scrolled": true,
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "outputs": [],
   "source": [
    "from IPython.display import HTML\n",
    "HTML('<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/zV949buXdSg?autoplay=1&loop=1\" frameborder=\"0\" allowfullscreen></iframe>')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
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   "source": [
    "### Structures like these are encoded in \"PDB\" files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "![pdb_atoms](https://raw.githubusercontent.com/harmsm/pythonic-science/master/chapters/03_dealing-with-files/data/pdb_header.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "![pdb_atoms](https://raw.githubusercontent.com/harmsm/pythonic-science/master/chapters/03_dealing-with-files/data/pdb_atoms.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "Entries are determined by columns in the file, not by spaces between the columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "#record   atom_name chain           x       y       z   occupancy        atom_type\n",
    "#  |          |       |             |       |       |      |                  |\n",
    "#ATOM   1086  CG  LYS A 141      -4.812   9.683   2.584  1.00 26.78           N0\n",
    "#         |        |      |                                     |\n",
    "#    atom_num amino_acid  resid_num                           bfactor"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Predict what the following will do"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
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   "outputs": [],
   "source": [
    "line_frompdb = \"ATOM   1086  N   SER A 141      -4.812   9.683   2.584  1.00 26.78           N0\"\n",
    "print(line_frompdb[2:4])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "Write a program that: \n",
    "+ Reads a pdb file (download 1stn.pdb)\n",
    "+ Grabs all \"ATOM\" lines whose atom type is \"CA\" \n",
    "+ Shifts the position of the molecule in x by +10 angstroms\n",
    "+ Writes out a new pdb file containing these shifted atoms\n",
    "+ If you want to check your work, download PyMOL and open up the files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "#record   atom_name chain           x       y       z   occupancy        atom_type\n",
    "#  |          |       |             |       |       |      |                  |\n",
    "#ATOM   1086  CG  LYS A 141      -4.812   9.683   2.584  1.00 26.78           N0\n",
    "#         |        |      |                                     |\n",
    "#    atom_num amino_acid  resid_num                           bfactor"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "f = open(\"data/1stn.pdb\")\n",
    "g = open(\"1stn_shifted.pdb\",\"w\")\n",
    "\n",
    "for line in f.readlines():\n",
    "    if line[0:4] == \"ATOM\" and line[13:16] == \"CA \":\n",
    "\n",
    "        first_chunk = line[:30]\n",
    "        x = line[30:38]\n",
    "        last_chunk = line[38:]\n",
    "        \n",
    "        new_x = float(x) + 10\n",
    "        \n",
    "        g.write(\"{:}{:8.3f}{:}\".format(first_chunk,new_x,last_chunk))\n",
    "\n",
    "f.close()\n",
    "g.close()"
   ]
  }
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