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    "# Getting Started\n",
    "\n",
    "QMzyme is a Python toolkit aimed at facilitating QM-based calculations. To begin with the QM calculation setup, we need to first set the structure file. Currently, QMzyme supports `PDB`, `prmtop`, `RST`, `PQR`, and `DCD` file formats.\n",
    "\n",
    "In this example, you will see how you can initialize the QMzyme GenerateModel module in various ways, using the pre-packaged QMzyme data and how these loaded structure files can be used!\n",
    "\n",
    "## Classes used in this example\n",
    "\n",
    "- [GenerateModel](https://qmzyme.readthedocs.io/en/latest/API/QMzyme.GenerateModel.html)"
   ]
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  {
   "cell_type": "code",
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   "source": [
    "# To start with, we'll import the necesary packages.\n",
    "import QMzyme\n",
    "import os"
   ]
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   "source": [
    "## Initialize Model\n",
    "After importing QMzyme, we need to initialize `QMzymeModel` by providing a structure file. The GenerateModel class can be initialized in any way that an MDAnalysis Universe can be initialized. Here are some ways to initialize QMzymeModel!"
   ]
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     "text": [
      "File:  1oh0.pdb\n",
      "\n",
      "Charge information not present. QMzyme will try to guess region charges based on residue names consistent with AMBER naming conventions (i.e., aspartate: ASP --> Charge: -1, aspartic acid: ASH --> Charge: 0.). See QMzyme.data.residue_charges for the full set.\n",
      "\n",
      "\tNonconventional Residues Found\n",
      "\t------------------------------\n",
      "\tEQU --> Charge: UNK, defaulting to 0\n",
      "\n",
      "You can update charge information for nonconventional residues by running \n",
      "\t>>>QMzyme.data.residue_charges.update({'3LETTER_RESNAME':INTEGER_CHARGE}). \n",
      "Note your changes will not be stored after you exit your session. It is recommended to only alter the residue_charges dictionary. If you alter the protein_residues dictionary instead that could cause unintended bugs in other modules (TruncationSchemes).\n",
      "\n",
      "GenerateModel instance:  <QMzymeModel built from <Universe with 4258 atoms> contains 0 region(s)>\n"
     ]
    }
   ],
   "source": [
    "#1. With a PDB file:\n",
    "\n",
    "from QMzyme.data import PDB\n",
    "print(\"File: \", os.path.basename(PDB))\n",
    "pdb_model = QMzyme.GenerateModel(PDB)\n",
    "print(\"GenerateModel instance: \", pdb_model)"
   ]
  },
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   "execution_count": 4,
   "id": "88a45a1d-6137-4e6f-ac9d-73d1dea23a38",
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     "text": [
      "Files:  1oh0_equ.prmtop 1oh0_equ.rst7\n",
      "GenerateModel instance:  <QMzymeModel built from <Universe with 58553 atoms> contains 0 region(s)>\n"
     ]
    }
   ],
   "source": [
    "#2. With a topology file (.prmtop) and a restart file (.rst7) used in an AMBER MM simulation setup.\n",
    "#   The contained structure inclues the water box, so there are many atoms!\n",
    "\n",
    "from QMzyme.data import TOP, RST\n",
    "print(\"Files: \", os.path.basename(TOP), os.path.basename(RST))\n",
    "top_rst_model = QMzyme.GenerateModel(TOP, RST, format='RESTRT')\n",
    "print(\"GenerateModel instance: \", top_rst_model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "297ba1ef-987a-4460-9c75-d45d8cad8854",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Files:  1oh0_equ.prod_1.stripped.pqr 1oh0_equ.prod_1.stripped.dcd\n",
      "GenerateModel instance:  <QMzymeModel built from <Universe with 4258 atoms> contains 0 region(s)>\n"
     ]
    }
   ],
   "source": [
    "#3. With a PQR file, containing charge information, and a trajectory DCD file:\n",
    "\n",
    "from QMzyme.data import PQR, DCD\n",
    "print(\"Files: \", os.path.basename(PQR), os.path.basename(DCD))\n",
    "pqr_dcd = QMzyme.GenerateModel(PQR, DCD)\n",
    "print(\"GenerateModel instance: \", pqr_dcd)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9175ebc5-ea73-45a2-a01c-64cf050e88fb",
   "metadata": {},
   "source": [
    "Congratulations, you have successfully made your first QMzymeModel! The next workflows will walk through how to use QMzyme to generate QM input files for ORCA and Gaussian."
   ]
  }
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