prepare_data.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Prepare your custom data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Feature Preparation\n",
    "- Initial data preparation for E3 ligase and POI, PROTAC\n",
    "- The raw data format for E3 ligase and target proteins is amino acid sequences\n",
    "- The raw data format for PROTAC is SMILES"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import os.path as osp\n",
    "import pandas as pd\n",
    "\n",
    "root = 'data/custom'\n",
    "os.makedirs(root, exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Uniprot</th>\n",
       "      <th>E3 ligase Uniprot</th>\n",
       "      <th>Smiles</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Q9H8M2</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC(C2=CN(C)C(=O)C3=CN=CC=C23)=CC(OC)=C1CN...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>P03372</td>\n",
       "      <td>Q96SW2</td>\n",
       "      <td>CCN(CCCCCCC#CC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>P10275</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>P10275</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=NOC([C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)N[C@...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>P10275</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=C(C2=CC=C([C@H](CC(=O)N3CCC(N4CCC(C#CC5=CC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>O60885</td>\n",
       "      <td>Q96SW2</td>\n",
       "      <td>CC1=C(C)C2=C(S1)N1C(C)=NN=C1[C@H](CC(=O)NCCN1C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>O15264</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Q16539</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>P11474</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC(/C=C(\\C#N)C(=O)NCCCC(=O)N[C@H](C(=O)N2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>O60885</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Uniprot E3 ligase Uniprot                                             Smiles\n",
       "0  Q9H8M2            P40337  COC1=CC(C2=CN(C)C(=O)C3=CN=CC=C23)=CC(OC)=C1CN...\n",
       "1  P03372            Q96SW2  CCN(CCCCCCC#CC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=...\n",
       "2  P10275            P40337  CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...\n",
       "3  P10275            P40337  CC1=NOC([C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)N[C@...\n",
       "4  P10275            P40337  CC1=C(C2=CC=C([C@H](CC(=O)N3CCC(N4CCC(C#CC5=CC...\n",
       "5  O60885            Q96SW2  CC1=C(C)C2=C(S1)N1C(C)=NN=C1[C@H](CC(=O)NCCN1C...\n",
       "6  O15264            P40337  COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...\n",
       "7  Q16539            P40337  COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...\n",
       "8  P11474            P40337  COC1=CC(/C=C(\\C#N)C(=O)NCCCC(=O)N[C@H](C(=O)N2...\n",
       "9  O60885            P40337  CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)..."
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "raw_df = pd.read_csv(osp.join(root, 'raw.csv'))\n",
    "raw_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Prepare PROTAC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "columns = [\n",
    "    # 'Smiles',\n",
    "    'Molecular Weight',\n",
    "    'Exact Mass',\n",
    "    'XLogP3',\n",
    "    'Heavy Atom Count',\n",
    "    'Ring Count',\n",
    "    'Hydrogen Bond Acceptor Count',\n",
    "    'Hydrogen Bond Donor Count',\n",
    "    'Rotatable Bond Count',\n",
    "    'Topological Polar Surface Area'\n",
    "]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Calculate molecular properties for PROTAC\n",
    "\n",
    "> [!NOTE]\n",
    "> `XLogP3` is originally calculated via [XLogP3](http://www.sioc-ccbg.ac.cn/skins/ccbgwebsite/software/xlogp3/) software, here using `Descriptors.MolLogP()` from [RDKit](https://www.rdkit.org/)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem import Descriptors\n",
    "\n",
    "\n",
    "def calculate_molecular_descriptors(smiles):\n",
    "    mol = Chem.MolFromSmiles(smiles)\n",
    "    return [\n",
    "        Descriptors.MolWt(mol),\n",
    "        Descriptors.ExactMolWt(mol),\n",
    "        Descriptors.MolLogP(mol), # XLogP3 to LogP\n",
    "        Descriptors.HeavyAtomCount(mol),\n",
    "        Descriptors.RingCount(mol),\n",
    "        Descriptors.NumHAcceptors(mol),\n",
    "        Descriptors.NumHDonors(mol),\n",
    "        Descriptors.NumRotatableBonds(mol),\n",
    "        Descriptors.TPSA(mol)\n",
    "    ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Uniprot</th>\n",
       "      <th>E3 ligase Uniprot</th>\n",
       "      <th>Smiles</th>\n",
       "      <th>Molecular Weight</th>\n",
       "      <th>Exact Mass</th>\n",
       "      <th>XLogP3</th>\n",
       "      <th>Heavy Atom Count</th>\n",
       "      <th>Ring Count</th>\n",
       "      <th>Hydrogen Bond Acceptor Count</th>\n",
       "      <th>Hydrogen Bond Donor Count</th>\n",
       "      <th>Rotatable Bond Count</th>\n",
       "      <th>Topological Polar Surface Area</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Q9H8M2</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC(C2=CN(C)C(=O)C3=CN=CC=C23)=CC(OC)=C1CN...</td>\n",
       "      <td>1041.257</td>\n",
       "      <td>1040.484140</td>\n",
       "      <td>4.89042</td>\n",
       "      <td>74.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>199.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>P03372</td>\n",
       "      <td>Q96SW2</td>\n",
       "      <td>CCN(CCCCCCC#CC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=...</td>\n",
       "      <td>783.947</td>\n",
       "      <td>783.297822</td>\n",
       "      <td>7.67440</td>\n",
       "      <td>57.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>136.48</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>P10275</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...</td>\n",
       "      <td>1047.255</td>\n",
       "      <td>1046.416987</td>\n",
       "      <td>9.11460</td>\n",
       "      <td>73.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>188.07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>P10275</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=NOC([C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)N[C@...</td>\n",
       "      <td>1114.302</td>\n",
       "      <td>1113.422800</td>\n",
       "      <td>9.58712</td>\n",
       "      <td>78.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>214.10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>P10275</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=C(C2=CC=C([C@H](CC(=O)N3CCC(N4CCC(C#CC5=CC...</td>\n",
       "      <td>1136.861</td>\n",
       "      <td>1135.512044</td>\n",
       "      <td>8.35418</td>\n",
       "      <td>81.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>221.09</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>O60885</td>\n",
       "      <td>Q96SW2</td>\n",
       "      <td>CC1=C(C)C2=C(S1)N1C(C)=NN=C1[C@H](CC(=O)NCCN1C...</td>\n",
       "      <td>913.414</td>\n",
       "      <td>912.278022</td>\n",
       "      <td>3.62756</td>\n",
       "      <td>64.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>223.35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>O15264</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...</td>\n",
       "      <td>1078.205</td>\n",
       "      <td>1077.411783</td>\n",
       "      <td>7.71442</td>\n",
       "      <td>77.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>228.87</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Q16539</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...</td>\n",
       "      <td>1180.341</td>\n",
       "      <td>1179.458733</td>\n",
       "      <td>10.39662</td>\n",
       "      <td>85.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>26.0</td>\n",
       "      <td>220.08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>P11474</td>\n",
       "      <td>P40337</td>\n",
       "      <td>COC1=CC(/C=C(\\C#N)C(=O)NCCCC(=O)N[C@H](C(=O)N2...</td>\n",
       "      <td>942.980</td>\n",
       "      <td>942.320938</td>\n",
       "      <td>7.35620</td>\n",
       "      <td>66.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>182.98</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>O60885</td>\n",
       "      <td>P40337</td>\n",
       "      <td>CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...</td>\n",
       "      <td>1092.786</td>\n",
       "      <td>1091.416430</td>\n",
       "      <td>8.65168</td>\n",
       "      <td>76.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>211.49</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Uniprot E3 ligase Uniprot  \\\n",
       "0  Q9H8M2            P40337   \n",
       "1  P03372            Q96SW2   \n",
       "2  P10275            P40337   \n",
       "3  P10275            P40337   \n",
       "4  P10275            P40337   \n",
       "5  O60885            Q96SW2   \n",
       "6  O15264            P40337   \n",
       "7  Q16539            P40337   \n",
       "8  P11474            P40337   \n",
       "9  O60885            P40337   \n",
       "\n",
       "                                              Smiles  Molecular Weight  \\\n",
       "0  COC1=CC(C2=CN(C)C(=O)C3=CN=CC=C23)=CC(OC)=C1CN...          1041.257   \n",
       "1  CCN(CCCCCCC#CC1=CC=CC2=C1CN(C1CCC(=O)NC1=O)C2=...           783.947   \n",
       "2  CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...          1047.255   \n",
       "3  CC1=NOC([C@H](C(=O)N2C[C@H](O)C[C@H]2C(=O)N[C@...          1114.302   \n",
       "4  CC1=C(C2=CC=C([C@H](CC(=O)N3CCC(N4CCC(C#CC5=CC...          1136.861   \n",
       "5  CC1=C(C)C2=C(S1)N1C(C)=NN=C1[C@H](CC(=O)NCCN1C...           913.414   \n",
       "6  COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...          1078.205   \n",
       "7  COC1=CC2=C(OC3=CC=C(NC(=O)C4(C(=O)NC5=CC=C(F)C...          1180.341   \n",
       "8  COC1=CC(/C=C(\\C#N)C(=O)NCCCC(=O)N[C@H](C(=O)N2...           942.980   \n",
       "9  CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)...          1092.786   \n",
       "\n",
       "    Exact Mass    XLogP3  Heavy Atom Count  Ring Count  \\\n",
       "0  1040.484140   4.89042              74.0         8.0   \n",
       "1   783.297822   7.67440              57.0         7.0   \n",
       "2  1046.416987   9.11460              73.0         6.0   \n",
       "3  1113.422800   9.58712              78.0         7.0   \n",
       "4  1135.512044   8.35418              81.0         9.0   \n",
       "5   912.278022   3.62756              64.0         8.0   \n",
       "6  1077.411783   7.71442              77.0         8.0   \n",
       "7  1179.458733  10.39662              85.0        10.0   \n",
       "8   942.320938   7.35620              66.0         5.0   \n",
       "9  1091.416430   8.65168              76.0         8.0   \n",
       "\n",
       "   Hydrogen Bond Acceptor Count  Hydrogen Bond Donor Count  \\\n",
       "0                          16.0                        3.0   \n",
       "1                           9.0                        3.0   \n",
       "2                          10.0                        4.0   \n",
       "3                          12.0                        4.0   \n",
       "4                          12.0                        4.0   \n",
       "5                          17.0                        2.0   \n",
       "6                          14.0                        5.0   \n",
       "7                          14.0                        4.0   \n",
       "8                          10.0                        4.0   \n",
       "9                          15.0                        4.0   \n",
       "\n",
       "   Rotatable Bond Count  Topological Polar Surface Area  \n",
       "0                  22.0                          199.15  \n",
       "1                  15.0                          136.48  \n",
       "2                  20.0                          188.07  \n",
       "3                  22.0                          214.10  \n",
       "4                  14.0                          221.09  \n",
       "5                  19.0                          223.35  \n",
       "6                  23.0                          228.87  \n",
       "7                  26.0                          220.08  \n",
       "8                  16.0                          182.98  \n",
       "9                  22.0                          211.49  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "property_df = raw_df['Smiles'].apply(calculate_molecular_descriptors).apply(pd.Series)\n",
    "property_df.columns = columns\n",
    "custom_df = pd.concat([raw_df, property_df], axis=1)\n",
    "custom_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "custom_df.to_csv(osp.join(root, 'custom.csv'), index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Prepare E3 ligase and target"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'Q96SW2', 'O15264', 'P10275', 'P11474', 'P40337', 'Q9H8M2', 'Q16539', 'O60885', 'P03372'}\n"
     ]
    }
   ],
   "source": [
    "# collect all uniprot ids\n",
    "uniprot_ids = set(custom_df['Uniprot'].tolist() + custom_df['E3 ligase Uniprot'].tolist())\n",
    "print(uniprot_ids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pickle\n",
    "import time\n",
    "from io import StringIO\n",
    "\n",
    "import requests\n",
    "from Bio import SeqIO\n",
    "from requests.exceptions import HTTPError, RequestException\n",
    "\n",
    "try: \n",
    "    seq_cache = pickle.load(open(osp.join(root, 'seq_cache.pkl'), 'rb'))\n",
    "except:\n",
    "    seq_cache = {}\n",
    "\n",
    "def get_aa_seq(uniprot_id):\n",
    "    \"\"\"\n",
    "    Download fasta file from Uniprot and extract amino acid sequence\n",
    "    \n",
    "    Parameters:\n",
    "        uniprot_id (str): UniProt ID of the protein.\n",
    "        \n",
    "    Returns:\n",
    "        str: Amino acid sequence of the protein.\n",
    "        \n",
    "    Example:\n",
    "        get_aa_seq('P04637')\n",
    "        >>> 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD'\n",
    "    \"\"\"\n",
    "    try:\n",
    "        if uniprot_id in seq_cache:\n",
    "            return seq_cache[uniprot_id]\n",
    "        \n",
    "        url = f'https://www.uniprot.org/uniprot/{uniprot_id}.fasta'\n",
    "        r = requests.get(url)\n",
    "        r.raise_for_status()\n",
    "        fasta = r.text\n",
    "        fasta_io = StringIO(fasta)\n",
    "        seq_record = SeqIO.read(fasta_io, 'fasta')\n",
    "        time.sleep(1)\n",
    "        seq = str(seq_record.seq)\n",
    "        seq_cache[uniprot_id] = seq\n",
    "        pickle.dump(seq_cache, open(osp.join(root, 'seq_cache.pkl'), 'wb'))\n",
    "        return seq\n",
    "    except HTTPError as http_err:\n",
    "        print(f'发生HTTP错误: {http_err}')\n",
    "    except RequestException as req_err:\n",
    "        print(f'发生请求错误: {req_err}')\n",
    "    except Exception as e:\n",
    "        print(f'发生意外错误: {e}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Q96SW2 MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL\n",
      "O15264 MSLIRKKGFYKQDVNKTAWELPKTYVSPTHVGSGAYGSVCSAIDKRSGEKVAIKKLSRPFQSEIFAKRAYRELLLLKHMQHENVIGLLDVFTPASSLRNFYDFYLVMPFMQTDLQKIMGMEFSEEKIQYLVYQMLKGLKYIHSAGVVHRDLKPGNLAVNEDCELKILDFGLARHADAEMTGYVVTRWYRAPEVILSWMHYNQTVDIWSVGCIMAEMLTGKTLFKGKDYLDQLTQILKVTGVPGTEFVQKLNDKAAKSYIQSLPQTPRKDFTQLFPRASPQAADLLEKMLELDVDKRLTAAQALTHPFFEPFRDPEEETEAQQPFDDSLEHEKLTVDEWKQHIYKEIVNFSPIARKDSRRRSGMKL\n",
      "P10275 MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPGAAVAASKGLPQQLPAPPDEDDSAAPSTLSLLGPTFPGLSSCSADLKDILSEASTMQLLQQQQQEAVSEGSSSGRAREASGAPTSSKDNYLGGTSTISDNAKELCKAVSVSMGLGVEALEHLSPGEQLRGDCMYAPLLGVPPAVRPTPCAPLAECKGSLLDDSAGKSTEDTAEYSPFKGGYTKGLEGESLGCSGSAAAGSSGTLELPSTLSLYKSGALDEAAAYQSRDYYNFPLALAGPPPPPPPPHPHARIKLENPLDYGSAWAAAAAQCRYGDLASLHGAGAAGPGSGSPSAAASSSWHTLFTAEEGQLYGPCGGGGGGGGGGGGGGGGGGGGGGGEAGAVAPYGYTRPPQGLAGQESDFTAPDVWYPGGMVSRVPYPSPTCVKSEMGPWMDSYSGPYGDMRLETARDHVLPIDYYFPPQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGNLKLQEEGEASSTTSPTEETTQKLTVSHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGKVKPIYFHTQ\n",
      "P11474 MSSQVVGIEPLYIKAEPASPDSPKGSSETETEPPVALAPGPAPTRCLPGHKEEEDGEGAGPGEQGGGKLVLSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEAMMD\n",
      "P40337 MPRRAENWDEAEVGAEEAGVEEYGPEEDGGEESGAEESGPEESGPEELGAEEEMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD\n",
      "Q9H8M2 MGKKHKKHKAEWRSSYEDYADKPLEKPLKLVLKVGGSEVTELSGSGHDSSYYDDRSDHERERHKEKKKKKKKKSEKEKHLDDEERRKRKEEKKRKREREHCDTEGEADDFDPGKKVEVEPPPDRPVRACRTQPAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKQAALLGNEDTAVEEPVPEVVPVQVETAKKSKKPSREVISCMFEPEGNACSLTDSTAEEHVLALVEHAADEARDRINRFLPGGKMGYLKRNGDGSLLYSVVNTAEPDADEEETHPVDLSSLSSKLLPGFTTLGFKDERRNKVTFLSSATTALSMQNNSVFGDLKSDEMELLYSAYGDETGVQCALSLQEFVKDAGSYSKKVVDDLLDQITGGDHSRTLFQLKQRRNVPMKPPDEAKVGDTLGDSSSSVLEFMSMKSYPDVSVDISMLSSLGKVKKELDPDDSHLNLDETTKLLQDLHEAQAERGGSRPSSNLSSLSNASERDQHHLGSPSRLSVGEQPDVTHDPYEFLQSPEPAASAKT\n",
      "Q16539 MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES\n",
      "O60885 MSAESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAASTNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRGRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMTVVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTIDPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVAVSSPAVPPPTKVVAPPSSSDSSSDSSSDSDSSTDDSEEERAQRLAELQEQLKAVHEQLAALSQPQQNKPKKKEKDKKEKKKEKHKRKEEVEENKKSKAKEPPPKKTKKNNSSNSNVSKKEPAPMKSKPPPTYESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRKKRKPQAEKVDVIAGSSKMKGFSSSESESSSESSSSDSEDSETEMAPKSKKKGHPGREQKKHHHHHHQQMQQAPAPVPQQPPPPPQQPPPPPPPQQQQQPPPPPPPPSMPQQAAPAMKSSPPPFIATQVPVLEPQLPGSVFDPIGHFTQPILHLPQPELPPHLPQPPEHSTPPHLNQHAVVSPPALHNALPQQPSRPSNRAAALPPKPARPPAVSPALTQTPLLPQPPMAQPPQVLLEDEEPPAPPLTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPLPPPPHPSVQQQLQQQPPPPPPPQPQPPPQQQHQPPPRPVHLQPMQFSTHIQQPPPPQGQQPPHPPPGQQPPPPQPAKPQQVIQHHHSPRHHKSDPYSTGHLREAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPKKQELRAASVVQPQPLVVVKEEKIHSPIIRSEPFSPSLRPEPPKHPESIKAPVHLPQRPEMKPVDVGRPVIRPPEQNAPPPGAPDKDKQKQEPKTPVAPKKDLKIKNMGSWASLVQKHPTTPSSTAKSSSDSFEQFRRAAREKEEREKALKAQAEHAEKEKERLRQERMRSREDEDALEQARRAHEEARRRQEQQQQQRQEQQQQQQQQAAAVAAAATPQAQSSQPQSMLDQQRELARKREQERRRREAMAATIDMNFQSDLLSIFEENLF\n",
      "P03372 MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYTVREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEVGSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV\n"
     ]
    }
   ],
   "source": [
    "p_map = {uniprot_id: get_aa_seq(uniprot_id) for uniprot_id in uniprot_ids}\n",
    "for k, v in p_map.items():\n",
    "    print(k, v)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data/custom\n"
     ]
    }
   ],
   "source": [
    "print(root)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(osp.join(root, 'p_map.pkl'), 'wb') as f:\n",
    "    pickle.dump(p_map, f)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Processing protein sequence features into implicit structural representations\n",
    "- Protein sequence hash table: `p_map`\n",
    "- Protein structural representation hash table: `esm_s_map`\n",
    "\n",
    "> ![NOTE] \n",
    "> This part needs to be prepared separately, taking into account the large GPU resources required for the Protein Language Model as well as persistent data to improve training efficiency. \n",
    "```shell\n",
    "$ conda activate ems+\n",
    "$ python get_embed_s.py\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Ready for PROTAC-STAN inference\n",
    "\n",
    "- Your ready custom data: `customed.csv` and `esm_s_map.pkl`, keep them in the same directory, such as: `./data/custom`\n",
    "- Using `inference.py`, usage: `python inference.py [-h] [--root ROOT] [--name NAME] [--save_att]`\n",
    "  - for example:\n",
    "    ```shell\n",
    "    $ conda activate protac-stan\n",
    "    $ python inference.py --root 'data/custom' --name 'custom'\n",
    "    ```"
   ]
  }
 ],
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    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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