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 "cells": [
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   "cell_type": "markdown",
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   "source": [
    "# SPE calculation"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`Auto3D` is mainly designed for generating low-energy 3D structures from the SMILES. It aslo provides a wrapper function `calc_spe` to do single point energy calculation for existing 3D structures, using `ANI2x`, `AIMNET` or `ANI2xt` as the engine. \n",
    "\n",
    "Single point energy (SPE) calculation **does not** change the input geometry.\n",
    "\n",
    "The source juputer notebook can be downloaded [here](https://github.com/isayevlab/Auto3D_pkg/blob/main/example/single_point_energy.ipynb)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": "import os, sys\nroot = os.path.dirname(os.path.dirname(os.path.abspath(\"__file__\")))\nsys.path.append(root)\n\nimport Auto3D\nfrom Auto3D import Auto3DOptions, main, calc_spe"
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2.2.10\n"
     ]
    }
   ],
   "source": [
    "#Always ensure that you have the latest version\n",
    "print(Auto3D.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/jack/Auto3D_pkg/example/files/RDKIT_ANI2x_smiles/smiles_out_ANI2x_E.sdf\n"
     ]
    }
   ],
   "source": [
    "path = os.path.join(root, \"example/files/RDKIT_ANI2x_smiles/smiles_out.sdf\")\n",
    "spe = calc_spe(path, model_name=\"ANI2x\")\n",
    "print(spe)  #SPE are stored in the SDF file under the E_hartree entry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on function calc_spe in module Auto3D.SPE:\n",
      "\n",
      "calc_spe(path: str, model_name: str, gpu_idx=0)\n",
      "    Calculates single point energy.\n",
      "    \n",
      "    :param path: Input sdf file\n",
      "    :type path: str\n",
      "    :param model_name: AIMNET, ANI2x or ANI2xt\n",
      "    :type model_name: str\n",
      "    :param gpu_idx: GPU cuda index, defaults to 0\n",
      "    :type gpu_idx: int, optional\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(calc_spe)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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