pymol_rmsd.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! conda install -c schrodinger pymol-bundle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pymol import cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "filename_1 = 'relaxed_model_1_pred_0.pdb'\n",
    "filename_2 = 'relaxed_protein.pdb'\n",
    "\n",
    "with open(filename_1, 'r') as fp:\n",
    "    file1 = fp.read()\n",
    "\n",
    "pdb1 = cmd.read_pdbstr(file1, 'pdb1')\n",
    "\n",
    "with open(filename_2, 'r') as fp:\n",
    "    file2 = fp.read()\n",
    "\n",
    "pdb2 = cmd.read_pdbstr(file2, 'pdb2')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['pdb1', 'pdb2']"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cmd.get_names()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1.2936300039291382, 12188, 0, 1.2936300039291382, 12188, 4195.0, 779)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cmd.align('pdb1', 'pdb2', cycles=0, transform=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1.2333121299743652,\n",
       " 12131,\n",
       " 0,\n",
       " 1.2333121299743652,\n",
       " 12131,\n",
       " 3733.83642578125,\n",
       " 775)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cmd.super('pdb1', 'pdb2', cycles=0, transform=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " ExecutiveRMSPairs: RMSD =    1.295 (12189 to 12189 atoms)\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "1.2949023246765137"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cmd.pair_fit('pdb1', 'pdb2')"
   ]
  }
 ],
 "metadata": {
  "interpreter": {
   "hash": "cd30d8f35cf76d6f481890c0c669267e97b0a0370baaf98c81ab5620aceed69e"
  },
  "kernelspec": {
   "display_name": "Python 3.7.12 ('rmsd')",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.12"
  },
  "orig_nbformat": 4
 },
 "nbformat": 4,
 "nbformat_minor": 2
}