rmsd_calculation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "import glob\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [],
   "source": [
    "files = []\n",
    "with open(\"/Users/dshrestha/Desktop/Daniel/testSet/vinaposes_testSet.txt\", 'r') as f:\n",
    "    content = f.readlines()\n",
    "    for line in content:\n",
    "        files.append(line[3:].split('\\n')[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "crystal_pose_dir = \"/Users/dshrestha/Desktop/Daniel/testSet/crystal_poses\"\n",
    "test_poses_dir = \"/Users/dshrestha/Downloads/screening/testSetposes\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2131"
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pose_files = glob.glob(os.path.join(test_poses_dir, \"*.pdb\"))\n",
    "len(pose_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "216\n"
     ]
    }
   ],
   "source": [
    "rmsd_dict = {}\n",
    "error_ids = []\n",
    "\n",
    "# Loop through the files found in list of files in the text\n",
    "for _file in files:\n",
    "    # Get the id\n",
    "    _, f = os.path.split(_file)\n",
    "    _id = f[:4]\n",
    "    posefile = os.path.join(test_poses_dir, _file)\n",
    "    crystalfile = os.path.join(crystal_pose_dir, _id + \"_crystal.pdb\")\n",
    "    \n",
    "    # Get the molecules using RDKit\n",
    "    poseMol = Chem.MolFromPDBFile(posefile)\n",
    "    crystalMol = Chem.MolFromPDBFile(crystalfile)\n",
    "    \n",
    "    # Get the distance\n",
    "    try:\n",
    "        rmsd = AllChem.GetBestRMS(poseMol, crystalMol)\n",
    "    except:\n",
    "        error_ids.append(_id)\n",
    "        continue\n",
    "        \n",
    "    # Save it in the dictionary\n",
    "    rmsd_dict[_id] = float(rmsd)\n",
    "\n",
    "#print \"ERRORS FOUND IN: \", error_ids\n",
    "print len(rmsd_dict)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "('4q7p', 0.00048342414909596955)\n",
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      "('4r73', 0.15485541242485476)\n",
      "('3pxf', 0.5759285851955126)\n",
      "('5aoi', 1.154949570750373)\n",
      "('3uil', 1.4987299423051528)\n",
      "('4eo8', 0.2801980306782703)\n",
      "('2qbs', 0.3980028514718265)\n",
      "('4h7q', 0.9360528625632956)\n",
      "('1df8', 0.1782034774019207)\n",
      "('2cle', 1.3148307197487332)\n",
      "('4cd4', 0.36256513497507004)\n",
      "('3k97', 0.049125003268589956)\n"
     ]
    }
   ],
   "source": [
    "dlscore = open('/Users/dshrestha/Desktop/Daniel/testSet/vinascore_rmsd.csv','w')\n",
    "dlscore.write('ligand,rmsd\\n')\n",
    "for key, value in rmsd_dict.iteritems():\n",
    "        print(key, value)\n",
    "        dlscore.write(key+','+str(value)+'\\n')\n",
    "dlscore.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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