AA_Score.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Extract Binding Pocket"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "!run scripts/get_pocket_by_schrodinger.py data/5otc/Rec.pdb data/5otc/Lig.sdf pocket.pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pocket.pdb\n"
     ]
    }
   ],
   "source": [
    "!ls pocket*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Run AA_Score"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from AA_Score import predict_dG\n",
    "from rdkit import Chem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "ligand_file = \"data/5vsd/Lig.sdf\"\n",
    "protein_file = \"data/5vsd/pocket.pdb\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol_lig = next(Chem.SDMolSupplier(ligand_file, removeHs=False))\n",
    "mol_prot = Chem.MolFromPDBFile(protein_file, removeHs=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol_name, score = predict_dG(mol_prot, mol_lig, output_file=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "name: LIG, energy: -9.53 kcal/mol\n"
     ]
    }
   ],
   "source": [
    "print(\"name: {}, energy: {} kcal/mol\".format(mol_name, round(score, 2)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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