docs/tutorials/io.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# The `io` module\n",
    "\n",
    "The `io` module enables loading of different input formats and conversion to different output formats.\n",
    "\n",
    "Currently the following input/output formats are supported:\n",
    "\n",
    "\n",
    "| Input | Output |\n",
    "| :--- | :--- |\n",
    "| _mol2_ (file, text) | `pandas.DataFrame` |\n",
    "| _pdb_ (file, text) | `pandas.DataFrame` |\n",
    "| _mol2_ (file, text) | `rdkit.Chem.rdchem.Mol` |\n",
    "| _pdb_ (file) | `Bio.PDB.Structure.Structure` |"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from opencadd.io.dataframe import DataFrame\n",
    "from opencadd.io.rdkit import Rdkit\n",
    "from opencadd.io.biopython import Biopython\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "DATA_PATH = Path(\"../../opencadd/tests/data/io\") "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load structural data as `DataFrame`\n",
    "\n",
    "Return data from different input formats as DataFrame with the following __default__ columns:\n",
    "\n",
    "- `atom.id`: Atom serial number.\n",
    "- `atom.name`: Atom name.\n",
    "- `atom.x`, `atom.y`, `atom.z`: Orthogonal coordinates for X, Y, Z in Angstroms.\n",
    "- `atom.charge`: Atom charge.\n",
    "- `residue.pdb_id`: Residue PDB ID.\n",
    "- `residue.name`: Residue name.\n",
    "\n",
    "It is also possible to return a DataFrame in the __verbose__ version, that contains additional columns available in the input format (but not in other input formats).\n",
    "\n",
    "Columns available from the _mol2_ format only are:\n",
    "\n",
    "- `atom.type`: SYBYL atom type set in the _mol2_ format.\n",
    "- `residue.subst_id`: ID number of the substructure containing the atom.\n",
    "- `residue.subst_name`: Name of the substructure containing the atom: Residue name + residue PDB ID.\n",
    "\n",
    "Columns available in the _pdb_ format only are:\n",
    "\n",
    "- `record.name`: Record name set in the _pdb_ format, i.e. `ATOM` or `HETATM`.\n",
    "- `atom.symbol`: Atom symbol.\n",
    "- `atom.occupancy`: Atom occupancy.\n",
    "- `atom.bfactor`: Atom B factor.\n",
    "- `atom.alternative_model`: Alternative atom positions.\n",
    "- `structure.chain`: Structure chain."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### From the _mol2_ format\n",
    "\n",
    "Check out the _mol2_ format [here](http://rasbt.github.io/biopandas/tutorials/Working_with_MOL2_Structures_in_DataFrames/#the-mol2-data-format). "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__From _mol2_ files__: Return a _mol2_ file's content as DataFrame (_mol2_ files can have 9 (default) or 10 columns)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>3.5231</td>\n",
       "      <td>35.933102</td>\n",
       "      <td>15.596400</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>H1</td>\n",
       "      <td>3.0492</td>\n",
       "      <td>36.782101</td>\n",
       "      <td>15.323000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>H2</td>\n",
       "      <td>3.1546</td>\n",
       "      <td>35.156300</td>\n",
       "      <td>15.066500</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>H3</td>\n",
       "      <td>4.5121</td>\n",
       "      <td>36.026001</td>\n",
       "      <td>15.414000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CA</td>\n",
       "      <td>3.3077</td>\n",
       "      <td>35.690701</td>\n",
       "      <td>17.044600</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4876</th>\n",
       "      <td>4877</td>\n",
       "      <td>HD2</td>\n",
       "      <td>3.5410</td>\n",
       "      <td>42.831100</td>\n",
       "      <td>42.216801</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4877</th>\n",
       "      <td>4878</td>\n",
       "      <td>HD3</td>\n",
       "      <td>1.9924</td>\n",
       "      <td>43.615398</td>\n",
       "      <td>42.610600</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4878</th>\n",
       "      <td>4879</td>\n",
       "      <td>N</td>\n",
       "      <td>3.6128</td>\n",
       "      <td>43.025902</td>\n",
       "      <td>38.110600</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4879</th>\n",
       "      <td>4880</td>\n",
       "      <td>H1</td>\n",
       "      <td>4.0174</td>\n",
       "      <td>42.840500</td>\n",
       "      <td>37.203999</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4880</th>\n",
       "      <td>4881</td>\n",
       "      <td>H2</td>\n",
       "      <td>4.1575</td>\n",
       "      <td>42.873901</td>\n",
       "      <td>38.947399</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4881 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name  atom.x     atom.y     atom.z residue.id residue.name\n",
       "0           1         N  3.5231  35.933102  15.596400        697          GLU\n",
       "1           2        H1  3.0492  36.782101  15.323000        697          GLU\n",
       "2           3        H2  3.1546  35.156300  15.066500        697          GLU\n",
       "3           4        H3  4.5121  36.026001  15.414000        697          GLU\n",
       "4           5        CA  3.3077  35.690701  17.044600        697          GLU\n",
       "...       ...       ...     ...        ...        ...        ...          ...\n",
       "4876     4877       HD2  3.5410  42.831100  42.216801       1019          PRO\n",
       "4877     4878       HD3  1.9924  43.615398  42.610600       1019          PRO\n",
       "4878     4879         N  3.6128  43.025902  38.110600       1020          GLN\n",
       "4879     4880        H1  4.0174  42.840500  37.203999       1020          GLN\n",
       "4880     4881        H2  4.1575  42.873901  38.947399       1020          GLN\n",
       "\n",
       "[4881 rows x 7 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Mol2 files with 10 columns\n",
    "DataFrame.from_file(DATA_PATH / \"2itz_chainA_protein.mol2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>C</td>\n",
       "      <td>-68.010002</td>\n",
       "      <td>-5.498000</td>\n",
       "      <td>-49.028000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>O</td>\n",
       "      <td>-67.916000</td>\n",
       "      <td>-4.916000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>CA</td>\n",
       "      <td>-67.651001</td>\n",
       "      <td>-6.991000</td>\n",
       "      <td>-48.900002</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>N</td>\n",
       "      <td>-67.939003</td>\n",
       "      <td>-7.787000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CB</td>\n",
       "      <td>-66.192001</td>\n",
       "      <td>-7.196000</td>\n",
       "      <td>-48.494999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4878</th>\n",
       "      <td>4879</td>\n",
       "      <td>H1</td>\n",
       "      <td>-55.506401</td>\n",
       "      <td>-10.457300</td>\n",
       "      <td>-32.785599</td>\n",
       "      <td>3035</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4879</th>\n",
       "      <td>4880</td>\n",
       "      <td>H2</td>\n",
       "      <td>-55.441399</td>\n",
       "      <td>-9.182800</td>\n",
       "      <td>-31.851601</td>\n",
       "      <td>3035</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4880</th>\n",
       "      <td>4881</td>\n",
       "      <td>O</td>\n",
       "      <td>-58.311001</td>\n",
       "      <td>-15.659000</td>\n",
       "      <td>-30.250999</td>\n",
       "      <td>3045</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4881</th>\n",
       "      <td>4882</td>\n",
       "      <td>H1</td>\n",
       "      <td>-58.885601</td>\n",
       "      <td>-15.679400</td>\n",
       "      <td>-31.069201</td>\n",
       "      <td>3045</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4882</th>\n",
       "      <td>4883</td>\n",
       "      <td>H2</td>\n",
       "      <td>-57.761101</td>\n",
       "      <td>-16.492201</td>\n",
       "      <td>-30.310301</td>\n",
       "      <td>3045</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4883 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name     atom.x     atom.y     atom.z residue.id  \\\n",
       "0           1         C -68.010002  -5.498000 -49.028000        697   \n",
       "1           2         O -67.916000  -4.916000 -50.118999        697   \n",
       "2           3        CA -67.651001  -6.991000 -48.900002        697   \n",
       "3           4         N -67.939003  -7.787000 -50.118999        697   \n",
       "4           5        CB -66.192001  -7.196000 -48.494999        697   \n",
       "...       ...       ...        ...        ...        ...        ...   \n",
       "4878     4879        H1 -55.506401 -10.457300 -32.785599       3035   \n",
       "4879     4880        H2 -55.441399  -9.182800 -31.851601       3035   \n",
       "4880     4881         O -58.311001 -15.659000 -30.250999       3045   \n",
       "4881     4882        H1 -58.885601 -15.679400 -31.069201       3045   \n",
       "4882     4883        H2 -57.761101 -16.492201 -30.310301       3045   \n",
       "\n",
       "     residue.name  \n",
       "0             GLU  \n",
       "1             GLU  \n",
       "2             GLU  \n",
       "3             GLU  \n",
       "4             GLU  \n",
       "...           ...  \n",
       "4878          HOH  \n",
       "4879          HOH  \n",
       "4880          HOH  \n",
       "4881          HOH  \n",
       "4882          HOH  \n",
       "\n",
       "[4883 rows x 7 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Mol2 files with 9 columns\n",
    "DataFrame.from_file(DATA_PATH / \"2itz_protein.mol2\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In order to get all columns from the input, set `verbose=True`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "      <th>atom.type</th>\n",
       "      <th>residue.subst_id</th>\n",
       "      <th>residue.subst_name</th>\n",
       "      <th>atom.charge</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>3.5231</td>\n",
       "      <td>35.933102</td>\n",
       "      <td>15.596400</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>N.4</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>H1</td>\n",
       "      <td>3.0492</td>\n",
       "      <td>36.782101</td>\n",
       "      <td>15.323000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>H2</td>\n",
       "      <td>3.1546</td>\n",
       "      <td>35.156300</td>\n",
       "      <td>15.066500</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>H3</td>\n",
       "      <td>4.5121</td>\n",
       "      <td>36.026001</td>\n",
       "      <td>15.414000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CA</td>\n",
       "      <td>3.3077</td>\n",
       "      <td>35.690701</td>\n",
       "      <td>17.044600</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>C.3</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4876</th>\n",
       "      <td>4877</td>\n",
       "      <td>HD2</td>\n",
       "      <td>3.5410</td>\n",
       "      <td>42.831100</td>\n",
       "      <td>42.216801</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "      <td>H</td>\n",
       "      <td>302</td>\n",
       "      <td>PRO1019</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4877</th>\n",
       "      <td>4878</td>\n",
       "      <td>HD3</td>\n",
       "      <td>1.9924</td>\n",
       "      <td>43.615398</td>\n",
       "      <td>42.610600</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "      <td>H</td>\n",
       "      <td>302</td>\n",
       "      <td>PRO1019</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4878</th>\n",
       "      <td>4879</td>\n",
       "      <td>N</td>\n",
       "      <td>3.6128</td>\n",
       "      <td>43.025902</td>\n",
       "      <td>38.110600</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "      <td>N.am</td>\n",
       "      <td>303</td>\n",
       "      <td>GLN1020</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4879</th>\n",
       "      <td>4880</td>\n",
       "      <td>H1</td>\n",
       "      <td>4.0174</td>\n",
       "      <td>42.840500</td>\n",
       "      <td>37.203999</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "      <td>H</td>\n",
       "      <td>303</td>\n",
       "      <td>GLN1020</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4880</th>\n",
       "      <td>4881</td>\n",
       "      <td>H2</td>\n",
       "      <td>4.1575</td>\n",
       "      <td>42.873901</td>\n",
       "      <td>38.947399</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "      <td>H</td>\n",
       "      <td>303</td>\n",
       "      <td>GLN1020</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4881 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name  atom.x     atom.y     atom.z residue.id residue.name  \\\n",
       "0           1         N  3.5231  35.933102  15.596400        697          GLU   \n",
       "1           2        H1  3.0492  36.782101  15.323000        697          GLU   \n",
       "2           3        H2  3.1546  35.156300  15.066500        697          GLU   \n",
       "3           4        H3  4.5121  36.026001  15.414000        697          GLU   \n",
       "4           5        CA  3.3077  35.690701  17.044600        697          GLU   \n",
       "...       ...       ...     ...        ...        ...        ...          ...   \n",
       "4876     4877       HD2  3.5410  42.831100  42.216801       1019          PRO   \n",
       "4877     4878       HD3  1.9924  43.615398  42.610600       1019          PRO   \n",
       "4878     4879         N  3.6128  43.025902  38.110600       1020          GLN   \n",
       "4879     4880        H1  4.0174  42.840500  37.203999       1020          GLN   \n",
       "4880     4881        H2  4.1575  42.873901  38.947399       1020          GLN   \n",
       "\n",
       "     atom.type  residue.subst_id residue.subst_name  atom.charge  \n",
       "0          N.4                 1             GLU697          1.0  \n",
       "1            H                 1             GLU697          0.0  \n",
       "2            H                 1             GLU697          0.0  \n",
       "3            H                 1             GLU697          0.0  \n",
       "4          C.3                 1             GLU697          0.0  \n",
       "...        ...               ...                ...          ...  \n",
       "4876         H               302            PRO1019          0.0  \n",
       "4877         H               302            PRO1019          0.0  \n",
       "4878      N.am               303            GLN1020          0.0  \n",
       "4879         H               303            GLN1020          0.0  \n",
       "4880         H               303            GLN1020          0.0  \n",
       "\n",
       "[4881 rows x 11 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_file(DATA_PATH / \"2itz_chainA_protein.mol2\", verbose=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__From _mol2_ text__: Return a _mol2_ string (text) as DataFrame. This functionality is useful if you are fetching data directly from a website like [PDB](https://www.rcsb.org/) or [KLIFS](https://klifs.vu-compmedchem.nl/)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Let's load a file's content as string (text) to simulate example input data\n",
    "with open(DATA_PATH / \"2itz_chainA_protein.mol2\", \"r\") as f:\n",
    "    text = f.read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>3.5231</td>\n",
       "      <td>35.933102</td>\n",
       "      <td>15.596400</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>H1</td>\n",
       "      <td>3.0492</td>\n",
       "      <td>36.782101</td>\n",
       "      <td>15.323000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>H2</td>\n",
       "      <td>3.1546</td>\n",
       "      <td>35.156300</td>\n",
       "      <td>15.066500</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>H3</td>\n",
       "      <td>4.5121</td>\n",
       "      <td>36.026001</td>\n",
       "      <td>15.414000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CA</td>\n",
       "      <td>3.3077</td>\n",
       "      <td>35.690701</td>\n",
       "      <td>17.044600</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4876</th>\n",
       "      <td>4877</td>\n",
       "      <td>HD2</td>\n",
       "      <td>3.5410</td>\n",
       "      <td>42.831100</td>\n",
       "      <td>42.216801</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4877</th>\n",
       "      <td>4878</td>\n",
       "      <td>HD3</td>\n",
       "      <td>1.9924</td>\n",
       "      <td>43.615398</td>\n",
       "      <td>42.610600</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4878</th>\n",
       "      <td>4879</td>\n",
       "      <td>N</td>\n",
       "      <td>3.6128</td>\n",
       "      <td>43.025902</td>\n",
       "      <td>38.110600</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4879</th>\n",
       "      <td>4880</td>\n",
       "      <td>H1</td>\n",
       "      <td>4.0174</td>\n",
       "      <td>42.840500</td>\n",
       "      <td>37.203999</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4880</th>\n",
       "      <td>4881</td>\n",
       "      <td>H2</td>\n",
       "      <td>4.1575</td>\n",
       "      <td>42.873901</td>\n",
       "      <td>38.947399</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4881 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name  atom.x     atom.y     atom.z residue.id residue.name\n",
       "0           1         N  3.5231  35.933102  15.596400        697          GLU\n",
       "1           2        H1  3.0492  36.782101  15.323000        697          GLU\n",
       "2           3        H2  3.1546  35.156300  15.066500        697          GLU\n",
       "3           4        H3  4.5121  36.026001  15.414000        697          GLU\n",
       "4           5        CA  3.3077  35.690701  17.044600        697          GLU\n",
       "...       ...       ...     ...        ...        ...        ...          ...\n",
       "4876     4877       HD2  3.5410  42.831100  42.216801       1019          PRO\n",
       "4877     4878       HD3  1.9924  43.615398  42.610600       1019          PRO\n",
       "4878     4879         N  3.6128  43.025902  38.110600       1020          GLN\n",
       "4879     4880        H1  4.0174  42.840500  37.203999       1020          GLN\n",
       "4880     4881        H2  4.1575  42.873901  38.947399       1020          GLN\n",
       "\n",
       "[4881 rows x 7 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_text(text, \"mol2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "      <th>atom.type</th>\n",
       "      <th>residue.subst_id</th>\n",
       "      <th>residue.subst_name</th>\n",
       "      <th>atom.charge</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>3.5231</td>\n",
       "      <td>35.933102</td>\n",
       "      <td>15.596400</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>N.4</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>H1</td>\n",
       "      <td>3.0492</td>\n",
       "      <td>36.782101</td>\n",
       "      <td>15.323000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>H2</td>\n",
       "      <td>3.1546</td>\n",
       "      <td>35.156300</td>\n",
       "      <td>15.066500</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>H3</td>\n",
       "      <td>4.5121</td>\n",
       "      <td>36.026001</td>\n",
       "      <td>15.414000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>H</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CA</td>\n",
       "      <td>3.3077</td>\n",
       "      <td>35.690701</td>\n",
       "      <td>17.044600</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>C.3</td>\n",
       "      <td>1</td>\n",
       "      <td>GLU697</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4876</th>\n",
       "      <td>4877</td>\n",
       "      <td>HD2</td>\n",
       "      <td>3.5410</td>\n",
       "      <td>42.831100</td>\n",
       "      <td>42.216801</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "      <td>H</td>\n",
       "      <td>302</td>\n",
       "      <td>PRO1019</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4877</th>\n",
       "      <td>4878</td>\n",
       "      <td>HD3</td>\n",
       "      <td>1.9924</td>\n",
       "      <td>43.615398</td>\n",
       "      <td>42.610600</td>\n",
       "      <td>1019</td>\n",
       "      <td>PRO</td>\n",
       "      <td>H</td>\n",
       "      <td>302</td>\n",
       "      <td>PRO1019</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4878</th>\n",
       "      <td>4879</td>\n",
       "      <td>N</td>\n",
       "      <td>3.6128</td>\n",
       "      <td>43.025902</td>\n",
       "      <td>38.110600</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "      <td>N.am</td>\n",
       "      <td>303</td>\n",
       "      <td>GLN1020</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4879</th>\n",
       "      <td>4880</td>\n",
       "      <td>H1</td>\n",
       "      <td>4.0174</td>\n",
       "      <td>42.840500</td>\n",
       "      <td>37.203999</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "      <td>H</td>\n",
       "      <td>303</td>\n",
       "      <td>GLN1020</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4880</th>\n",
       "      <td>4881</td>\n",
       "      <td>H2</td>\n",
       "      <td>4.1575</td>\n",
       "      <td>42.873901</td>\n",
       "      <td>38.947399</td>\n",
       "      <td>1020</td>\n",
       "      <td>GLN</td>\n",
       "      <td>H</td>\n",
       "      <td>303</td>\n",
       "      <td>GLN1020</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4881 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name  atom.x     atom.y     atom.z residue.id residue.name  \\\n",
       "0           1         N  3.5231  35.933102  15.596400        697          GLU   \n",
       "1           2        H1  3.0492  36.782101  15.323000        697          GLU   \n",
       "2           3        H2  3.1546  35.156300  15.066500        697          GLU   \n",
       "3           4        H3  4.5121  36.026001  15.414000        697          GLU   \n",
       "4           5        CA  3.3077  35.690701  17.044600        697          GLU   \n",
       "...       ...       ...     ...        ...        ...        ...          ...   \n",
       "4876     4877       HD2  3.5410  42.831100  42.216801       1019          PRO   \n",
       "4877     4878       HD3  1.9924  43.615398  42.610600       1019          PRO   \n",
       "4878     4879         N  3.6128  43.025902  38.110600       1020          GLN   \n",
       "4879     4880        H1  4.0174  42.840500  37.203999       1020          GLN   \n",
       "4880     4881        H2  4.1575  42.873901  38.947399       1020          GLN   \n",
       "\n",
       "     atom.type  residue.subst_id residue.subst_name  atom.charge  \n",
       "0          N.4                 1             GLU697          1.0  \n",
       "1            H                 1             GLU697          0.0  \n",
       "2            H                 1             GLU697          0.0  \n",
       "3            H                 1             GLU697          0.0  \n",
       "4          C.3                 1             GLU697          0.0  \n",
       "...        ...               ...                ...          ...  \n",
       "4876         H               302            PRO1019          0.0  \n",
       "4877         H               302            PRO1019          0.0  \n",
       "4878      N.am               303            GLN1020          0.0  \n",
       "4879         H               303            GLN1020          0.0  \n",
       "4880         H               303            GLN1020          0.0  \n",
       "\n",
       "[4881 rows x 11 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_text(text, \"mol2\", verbose=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### From the _pdb_ format\n",
    "\n",
    "Check out the _pdb_ format [here](https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__From _pdb_ file__:  Return a _pdb_ file's content as DataFrame (`ATOM` and `HETATM` entries only). "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>-67.939003</td>\n",
       "      <td>-7.787000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>CA</td>\n",
       "      <td>-67.651001</td>\n",
       "      <td>-6.991000</td>\n",
       "      <td>-48.900002</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>C</td>\n",
       "      <td>-68.010002</td>\n",
       "      <td>-5.498000</td>\n",
       "      <td>-49.028000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>O</td>\n",
       "      <td>-67.916000</td>\n",
       "      <td>-4.916000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CB</td>\n",
       "      <td>-66.192001</td>\n",
       "      <td>-7.196000</td>\n",
       "      <td>-48.494999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2507</th>\n",
       "      <td>2509</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.306000</td>\n",
       "      <td>6.613000</td>\n",
       "      <td>-8.937000</td>\n",
       "      <td>3061</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2508</th>\n",
       "      <td>2510</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.908001</td>\n",
       "      <td>17.349001</td>\n",
       "      <td>-15.693000</td>\n",
       "      <td>3062</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2509</th>\n",
       "      <td>2511</td>\n",
       "      <td>O</td>\n",
       "      <td>-61.183998</td>\n",
       "      <td>-5.126000</td>\n",
       "      <td>-41.009998</td>\n",
       "      <td>3063</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2510</th>\n",
       "      <td>2512</td>\n",
       "      <td>O</td>\n",
       "      <td>-60.660999</td>\n",
       "      <td>8.159000</td>\n",
       "      <td>-21.872000</td>\n",
       "      <td>3064</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2511</th>\n",
       "      <td>2513</td>\n",
       "      <td>O</td>\n",
       "      <td>-69.189003</td>\n",
       "      <td>8.275000</td>\n",
       "      <td>-36.944000</td>\n",
       "      <td>3065</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2512 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name     atom.x     atom.y     atom.z residue.id  \\\n",
       "0           1         N -67.939003  -7.787000 -50.118999        697   \n",
       "1           2        CA -67.651001  -6.991000 -48.900002        697   \n",
       "2           3         C -68.010002  -5.498000 -49.028000        697   \n",
       "3           4         O -67.916000  -4.916000 -50.118999        697   \n",
       "4           5        CB -66.192001  -7.196000 -48.494999        697   \n",
       "...       ...       ...        ...        ...        ...        ...   \n",
       "2507     2509         O -54.306000   6.613000  -8.937000       3061   \n",
       "2508     2510         O -54.908001  17.349001 -15.693000       3062   \n",
       "2509     2511         O -61.183998  -5.126000 -41.009998       3063   \n",
       "2510     2512         O -60.660999   8.159000 -21.872000       3064   \n",
       "2511     2513         O -69.189003   8.275000 -36.944000       3065   \n",
       "\n",
       "     residue.name  \n",
       "0             GLU  \n",
       "1             GLU  \n",
       "2             GLU  \n",
       "3             GLU  \n",
       "4             GLU  \n",
       "...           ...  \n",
       "2507          HOH  \n",
       "2508          HOH  \n",
       "2509          HOH  \n",
       "2510          HOH  \n",
       "2511          HOH  \n",
       "\n",
       "[2512 rows x 7 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_file(DATA_PATH / \"2itz.pdb\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In order to get all columns from the input, set `verbose=True`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "      <th>record.name</th>\n",
       "      <th>atom.symbol</th>\n",
       "      <th>atom.occupancy</th>\n",
       "      <th>atom.bfactor</th>\n",
       "      <th>atom.alternative_model</th>\n",
       "      <th>structure.chain</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>-67.939003</td>\n",
       "      <td>-7.787000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>N</td>\n",
       "      <td>1.0</td>\n",
       "      <td>62.040001</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>CA</td>\n",
       "      <td>-67.651001</td>\n",
       "      <td>-6.991000</td>\n",
       "      <td>-48.900002</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>C</td>\n",
       "      <td>1.0</td>\n",
       "      <td>61.730000</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>C</td>\n",
       "      <td>-68.010002</td>\n",
       "      <td>-5.498000</td>\n",
       "      <td>-49.028000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>C</td>\n",
       "      <td>1.0</td>\n",
       "      <td>60.290001</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>O</td>\n",
       "      <td>-67.916000</td>\n",
       "      <td>-4.916000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>61.189999</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CB</td>\n",
       "      <td>-66.192001</td>\n",
       "      <td>-7.196000</td>\n",
       "      <td>-48.494999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>C</td>\n",
       "      <td>1.0</td>\n",
       "      <td>62.389999</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2507</th>\n",
       "      <td>2509</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.306000</td>\n",
       "      <td>6.613000</td>\n",
       "      <td>-8.937000</td>\n",
       "      <td>3061</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>66.239998</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2508</th>\n",
       "      <td>2510</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.908001</td>\n",
       "      <td>17.349001</td>\n",
       "      <td>-15.693000</td>\n",
       "      <td>3062</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>58.820000</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2509</th>\n",
       "      <td>2511</td>\n",
       "      <td>O</td>\n",
       "      <td>-61.183998</td>\n",
       "      <td>-5.126000</td>\n",
       "      <td>-41.009998</td>\n",
       "      <td>3063</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>37.119999</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2510</th>\n",
       "      <td>2512</td>\n",
       "      <td>O</td>\n",
       "      <td>-60.660999</td>\n",
       "      <td>8.159000</td>\n",
       "      <td>-21.872000</td>\n",
       "      <td>3064</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>48.790001</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2511</th>\n",
       "      <td>2513</td>\n",
       "      <td>O</td>\n",
       "      <td>-69.189003</td>\n",
       "      <td>8.275000</td>\n",
       "      <td>-36.944000</td>\n",
       "      <td>3065</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>44.000000</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2512 rows × 13 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name     atom.x     atom.y     atom.z residue.id  \\\n",
       "0           1         N -67.939003  -7.787000 -50.118999        697   \n",
       "1           2        CA -67.651001  -6.991000 -48.900002        697   \n",
       "2           3         C -68.010002  -5.498000 -49.028000        697   \n",
       "3           4         O -67.916000  -4.916000 -50.118999        697   \n",
       "4           5        CB -66.192001  -7.196000 -48.494999        697   \n",
       "...       ...       ...        ...        ...        ...        ...   \n",
       "2507     2509         O -54.306000   6.613000  -8.937000       3061   \n",
       "2508     2510         O -54.908001  17.349001 -15.693000       3062   \n",
       "2509     2511         O -61.183998  -5.126000 -41.009998       3063   \n",
       "2510     2512         O -60.660999   8.159000 -21.872000       3064   \n",
       "2511     2513         O -69.189003   8.275000 -36.944000       3065   \n",
       "\n",
       "     residue.name record.name atom.symbol  atom.occupancy  atom.bfactor  \\\n",
       "0             GLU        ATOM           N             1.0     62.040001   \n",
       "1             GLU        ATOM           C             1.0     61.730000   \n",
       "2             GLU        ATOM           C             1.0     60.290001   \n",
       "3             GLU        ATOM           O             1.0     61.189999   \n",
       "4             GLU        ATOM           C             1.0     62.389999   \n",
       "...           ...         ...         ...             ...           ...   \n",
       "2507          HOH      HETATM           O             1.0     66.239998   \n",
       "2508          HOH      HETATM           O             1.0     58.820000   \n",
       "2509          HOH      HETATM           O             1.0     37.119999   \n",
       "2510          HOH      HETATM           O             1.0     48.790001   \n",
       "2511          HOH      HETATM           O             1.0     44.000000   \n",
       "\n",
       "     atom.alternative_model structure.chain  \n",
       "0                                         A  \n",
       "1                                         A  \n",
       "2                                         A  \n",
       "3                                         A  \n",
       "4                                         A  \n",
       "...                     ...             ...  \n",
       "2507                                      A  \n",
       "2508                                      A  \n",
       "2509                                      A  \n",
       "2510                                      A  \n",
       "2511                                      A  \n",
       "\n",
       "[2512 rows x 13 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_file(DATA_PATH / \"2itz.pdb\", verbose=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__From _pdb_ text__: Return a _pdb_ string (text) as DataFrame (`ATOM` and `HETATM` entries only). "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Let's load a file's content as string (text) to simulate example input data\n",
    "with open(DATA_PATH / \"2itz.pdb\", \"r\") as f:\n",
    "    text = f.read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>-67.939003</td>\n",
       "      <td>-7.787000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>CA</td>\n",
       "      <td>-67.651001</td>\n",
       "      <td>-6.991000</td>\n",
       "      <td>-48.900002</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>C</td>\n",
       "      <td>-68.010002</td>\n",
       "      <td>-5.498000</td>\n",
       "      <td>-49.028000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>O</td>\n",
       "      <td>-67.916000</td>\n",
       "      <td>-4.916000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CB</td>\n",
       "      <td>-66.192001</td>\n",
       "      <td>-7.196000</td>\n",
       "      <td>-48.494999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2507</th>\n",
       "      <td>2509</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.306000</td>\n",
       "      <td>6.613000</td>\n",
       "      <td>-8.937000</td>\n",
       "      <td>3061</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2508</th>\n",
       "      <td>2510</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.908001</td>\n",
       "      <td>17.349001</td>\n",
       "      <td>-15.693000</td>\n",
       "      <td>3062</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2509</th>\n",
       "      <td>2511</td>\n",
       "      <td>O</td>\n",
       "      <td>-61.183998</td>\n",
       "      <td>-5.126000</td>\n",
       "      <td>-41.009998</td>\n",
       "      <td>3063</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2510</th>\n",
       "      <td>2512</td>\n",
       "      <td>O</td>\n",
       "      <td>-60.660999</td>\n",
       "      <td>8.159000</td>\n",
       "      <td>-21.872000</td>\n",
       "      <td>3064</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2511</th>\n",
       "      <td>2513</td>\n",
       "      <td>O</td>\n",
       "      <td>-69.189003</td>\n",
       "      <td>8.275000</td>\n",
       "      <td>-36.944000</td>\n",
       "      <td>3065</td>\n",
       "      <td>HOH</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2512 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name     atom.x     atom.y     atom.z residue.id  \\\n",
       "0           1         N -67.939003  -7.787000 -50.118999        697   \n",
       "1           2        CA -67.651001  -6.991000 -48.900002        697   \n",
       "2           3         C -68.010002  -5.498000 -49.028000        697   \n",
       "3           4         O -67.916000  -4.916000 -50.118999        697   \n",
       "4           5        CB -66.192001  -7.196000 -48.494999        697   \n",
       "...       ...       ...        ...        ...        ...        ...   \n",
       "2507     2509         O -54.306000   6.613000  -8.937000       3061   \n",
       "2508     2510         O -54.908001  17.349001 -15.693000       3062   \n",
       "2509     2511         O -61.183998  -5.126000 -41.009998       3063   \n",
       "2510     2512         O -60.660999   8.159000 -21.872000       3064   \n",
       "2511     2513         O -69.189003   8.275000 -36.944000       3065   \n",
       "\n",
       "     residue.name  \n",
       "0             GLU  \n",
       "1             GLU  \n",
       "2             GLU  \n",
       "3             GLU  \n",
       "4             GLU  \n",
       "...           ...  \n",
       "2507          HOH  \n",
       "2508          HOH  \n",
       "2509          HOH  \n",
       "2510          HOH  \n",
       "2511          HOH  \n",
       "\n",
       "[2512 rows x 7 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_text(text, \"pdb\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>atom.id</th>\n",
       "      <th>atom.name</th>\n",
       "      <th>atom.x</th>\n",
       "      <th>atom.y</th>\n",
       "      <th>atom.z</th>\n",
       "      <th>residue.id</th>\n",
       "      <th>residue.name</th>\n",
       "      <th>record.name</th>\n",
       "      <th>atom.symbol</th>\n",
       "      <th>atom.occupancy</th>\n",
       "      <th>atom.bfactor</th>\n",
       "      <th>atom.alternative_model</th>\n",
       "      <th>structure.chain</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>N</td>\n",
       "      <td>-67.939003</td>\n",
       "      <td>-7.787000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>N</td>\n",
       "      <td>1.0</td>\n",
       "      <td>62.040001</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>CA</td>\n",
       "      <td>-67.651001</td>\n",
       "      <td>-6.991000</td>\n",
       "      <td>-48.900002</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>C</td>\n",
       "      <td>1.0</td>\n",
       "      <td>61.730000</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>C</td>\n",
       "      <td>-68.010002</td>\n",
       "      <td>-5.498000</td>\n",
       "      <td>-49.028000</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>C</td>\n",
       "      <td>1.0</td>\n",
       "      <td>60.290001</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>O</td>\n",
       "      <td>-67.916000</td>\n",
       "      <td>-4.916000</td>\n",
       "      <td>-50.118999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>61.189999</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>CB</td>\n",
       "      <td>-66.192001</td>\n",
       "      <td>-7.196000</td>\n",
       "      <td>-48.494999</td>\n",
       "      <td>697</td>\n",
       "      <td>GLU</td>\n",
       "      <td>ATOM</td>\n",
       "      <td>C</td>\n",
       "      <td>1.0</td>\n",
       "      <td>62.389999</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2507</th>\n",
       "      <td>2509</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.306000</td>\n",
       "      <td>6.613000</td>\n",
       "      <td>-8.937000</td>\n",
       "      <td>3061</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>66.239998</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2508</th>\n",
       "      <td>2510</td>\n",
       "      <td>O</td>\n",
       "      <td>-54.908001</td>\n",
       "      <td>17.349001</td>\n",
       "      <td>-15.693000</td>\n",
       "      <td>3062</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>58.820000</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2509</th>\n",
       "      <td>2511</td>\n",
       "      <td>O</td>\n",
       "      <td>-61.183998</td>\n",
       "      <td>-5.126000</td>\n",
       "      <td>-41.009998</td>\n",
       "      <td>3063</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>37.119999</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2510</th>\n",
       "      <td>2512</td>\n",
       "      <td>O</td>\n",
       "      <td>-60.660999</td>\n",
       "      <td>8.159000</td>\n",
       "      <td>-21.872000</td>\n",
       "      <td>3064</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>48.790001</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2511</th>\n",
       "      <td>2513</td>\n",
       "      <td>O</td>\n",
       "      <td>-69.189003</td>\n",
       "      <td>8.275000</td>\n",
       "      <td>-36.944000</td>\n",
       "      <td>3065</td>\n",
       "      <td>HOH</td>\n",
       "      <td>HETATM</td>\n",
       "      <td>O</td>\n",
       "      <td>1.0</td>\n",
       "      <td>44.000000</td>\n",
       "      <td></td>\n",
       "      <td>A</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2512 rows × 13 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      atom.id atom.name     atom.x     atom.y     atom.z residue.id  \\\n",
       "0           1         N -67.939003  -7.787000 -50.118999        697   \n",
       "1           2        CA -67.651001  -6.991000 -48.900002        697   \n",
       "2           3         C -68.010002  -5.498000 -49.028000        697   \n",
       "3           4         O -67.916000  -4.916000 -50.118999        697   \n",
       "4           5        CB -66.192001  -7.196000 -48.494999        697   \n",
       "...       ...       ...        ...        ...        ...        ...   \n",
       "2507     2509         O -54.306000   6.613000  -8.937000       3061   \n",
       "2508     2510         O -54.908001  17.349001 -15.693000       3062   \n",
       "2509     2511         O -61.183998  -5.126000 -41.009998       3063   \n",
       "2510     2512         O -60.660999   8.159000 -21.872000       3064   \n",
       "2511     2513         O -69.189003   8.275000 -36.944000       3065   \n",
       "\n",
       "     residue.name record.name atom.symbol  atom.occupancy  atom.bfactor  \\\n",
       "0             GLU        ATOM           N             1.0     62.040001   \n",
       "1             GLU        ATOM           C             1.0     61.730000   \n",
       "2             GLU        ATOM           C             1.0     60.290001   \n",
       "3             GLU        ATOM           O             1.0     61.189999   \n",
       "4             GLU        ATOM           C             1.0     62.389999   \n",
       "...           ...         ...         ...             ...           ...   \n",
       "2507          HOH      HETATM           O             1.0     66.239998   \n",
       "2508          HOH      HETATM           O             1.0     58.820000   \n",
       "2509          HOH      HETATM           O             1.0     37.119999   \n",
       "2510          HOH      HETATM           O             1.0     48.790001   \n",
       "2511          HOH      HETATM           O             1.0     44.000000   \n",
       "\n",
       "     atom.alternative_model structure.chain  \n",
       "0                                         A  \n",
       "1                                         A  \n",
       "2                                         A  \n",
       "3                                         A  \n",
       "4                                         A  \n",
       "...                     ...             ...  \n",
       "2507                                      A  \n",
       "2508                                      A  \n",
       "2509                                      A  \n",
       "2510                                      A  \n",
       "2511                                      A  \n",
       "\n",
       "[2512 rows x 13 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_text(text, \"pdb\", verbose=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Column types:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "atom.id                 int32\n",
       "atom.name              string\n",
       "atom.x                float32\n",
       "atom.y                float32\n",
       "atom.z                float32\n",
       "residue.id             string\n",
       "residue.name           string\n",
       "atom.type              string\n",
       "residue.subst_id        Int64\n",
       "residue.subst_name     string\n",
       "atom.charge           float32\n",
       "dtype: object"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_file(DATA_PATH / \"2itz_chainA_protein.mol2\", verbose=True).dtypes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "atom.id                     int32\n",
       "atom.name                  string\n",
       "atom.x                    float32\n",
       "atom.y                    float32\n",
       "atom.z                    float32\n",
       "residue.id                 string\n",
       "residue.name               string\n",
       "record.name                string\n",
       "atom.symbol                string\n",
       "atom.occupancy            float32\n",
       "atom.bfactor              float32\n",
       "atom.alternative_model     string\n",
       "structure.chain            string\n",
       "dtype: object"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DataFrame.from_file(DATA_PATH / \"2itz.pdb\", verbose=True).dtypes"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load structural data as `rdkit` molecule\n",
    "\n",
    "__Note__: `rdkit` is a cheminformatics toolkit that focuses on working with small molecules. Technically you can load protein structures as `rdkit` molecule, however we recommend to use this data structure for small molecules only."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### From the _mol2_ format"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__From _mol2_ files__: Return a _mol2_ file's content as DataFrame (_mol2_ files can have 9 (default) or 10 columns)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f78214d3620>"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Rdkit.from_file(DATA_PATH / \"2itz_chainA_ligand.mol2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f78216bf7b0>"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Rdkit.from_file(DATA_PATH / \"2itz_chainA_ligand.mol2\", compute2d=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__From _mol2_ text__: Return a _mol2_ string (text) as DataFrame. This functionality is useful if you are fetching data directly from a website like [KLIFS](https://klifs.net/)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Let's load a file's content as string (text) to simulate example input data\n",
    "with open(DATA_PATH / \"2itz_chainA_ligand.mol2\", \"r\") as f:\n",
    "    text = f.read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f78211c7d00>"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Rdkit.from_text(text, \"mol2\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load structural data as `biopython`'s `Structure` objects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Structure id=>"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structure = Biopython.from_file(DATA_PATH / \"2itz.pdb\")\n",
    "structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Bio.PDB.Structure.Structure"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(structure)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of residues: 370\n"
     ]
    }
   ],
   "source": [
    "print(f\"Number of residues: {len(list(structure.get_residues()))}\")"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.8.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}