{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[16:48:05] Explicit valence for atom # 79 C, 7, is greater than permitted\n"
     ]
    },
    {
     "ename": "ValueError",
     "evalue": "Failed to load protein from ../generate/2p16/7.pdb",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[12], line 6\u001b[0m\n\u001b[1;32m      4\u001b[0m protein \u001b[38;5;241m=\u001b[39m Chem\u001b[38;5;241m.\u001b[39mMolFromPDBFile(pdb_file)\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m protein \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m----> 6\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFailed to load protein from \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpdb_file\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n",
      "\u001b[0;31mValueError\u001b[0m: Failed to load protein from ../generate/2p16/7.pdb"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import Draw\n",
    "pdb_file=\"../generate/2p16/7h.pdb\"\n",
    "protein = Chem.MolFromPDBFile(pdb_file)\n",
    "if protein is None:\n",
    "    raise ValueError(f\"Failed to load protein from {pdb_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "pdb_file = \"../generate/2p16/7.pdb\"\n",
    "protein = Chem.MolFromPDBFile(pdb_file, sanitize=False)\n",
    "if protein is None:\n",
    "    raise ValueError(f\"Failed to load protein from {pdb_file}\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "module 'plip' has no attribute 'Plip'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[11], line 10\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28mcomplex\u001b[39m\u001b[38;5;241m.\u001b[39mload_pdb(pdb_file)\n\u001b[1;32m      9\u001b[0m \u001b[38;5;66;03m# 初始化PLIP分析器\u001b[39;00m\n\u001b[0;32m---> 10\u001b[0m plip_analyzer \u001b[38;5;241m=\u001b[39m \u001b[43mplip\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mPlip\u001b[49m()\n\u001b[1;32m     11\u001b[0m plip_analyzer\u001b[38;5;241m.\u001b[39manalyze(\u001b[38;5;28mcomplex\u001b[39m)\n\u001b[1;32m     13\u001b[0m \u001b[38;5;66;03m# 获取相互作用信息\u001b[39;00m\n",
      "\u001b[0;31mAttributeError\u001b[0m: module 'plip' has no attribute 'Plip'"
     ]
    }
   ],
   "source": [
    "import plip\n",
    "from plip.structure.preparation import PDBComplex\n",
    "\n",
    "# 加载PDB文件\n",
    "pdb_file = '../generate/2p16/merged.pdb'\n",
    "complex = PDBComplex()\n",
    "complex.load_pdb(pdb_file)\n",
    "\n",
    "# 初始化PLIP分析器\n",
    "plip_analyzer = plip.Plip()\n",
    "plip_analyzer.analyze(complex)\n",
    "\n",
    "# 获取相互作用信息\n",
    "interactions = plip_analyzer.interaction_sets\n",
    "for interaction in interactions:\n",
    "    print(interaction)\n"
   ]
  }
 ],
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