{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ac25f0ce-5583-4663-864c-65abd7eb0886",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "from pymol import cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "173a1278-3198-492b-8ccd-78518aac858d",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0a6c2235-fdbf-4f7f-bfb8-7b9795d3275c",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "df = pd.read_excel(\"TCR-pHMC4.xlsx\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "36e1d2e3-d63e-482a-93ae-71587ccecfbe",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "215"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df[\"pdb_id\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "bf7825ab-2691-4cfd-9237-0c7c59a15426",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "173"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df[\"pdb_id\"].drop_duplicates())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c0a2e052-e54e-43b0-8d12-fddc94f69e99",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "pdb_id = df[\"pdb_id\"].drop_duplicates().to_list()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "21adf583-9374-4bdd-9f95-a333dad57e51",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "pdb_id = [i for i in pdb_id if type(i) == str]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "fdd7b621-6005-4494-9cc5-aaaaeca087c8",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['1ao7',\n",
       " '1mi5',\n",
       " '1oga',\n",
       " '2ypl',\n",
       " '3gsn',\n",
       " '3mv7',\n",
       " '3o4l',\n",
       " '3vxs',\n",
       " '4g9f',\n",
       " '4mji',\n",
       " '5d2l',\n",
       " '5d2n',\n",
       " '5e6i',\n",
       " '5isz',\n",
       " '5jhd',\n",
       " '5nht',\n",
       " '5tez',\n",
       " '6cql',\n",
       " '6dfs',\n",
       " '6dfw',\n",
       " '6dfx',\n",
       " '6l9l',\n",
       " '6mtm',\n",
       " '6px6',\n",
       " '6py2',\n",
       " '6rp9',\n",
       " '6rpa',\n",
       " '6rpb',\n",
       " '6rsy',\n",
       " '6tro',\n",
       " '6u3n',\n",
       " '6vmx',\n",
       " '6vrm',\n",
       " '6vrn',\n",
       " '7n1e',\n",
       " '7n1f',\n",
       " '7n6e',\n",
       " '2nx5',\n",
       " '2vlj',\n",
       " '2vlk',\n",
       " '2vlr',\n",
       " '3mv8',\n",
       " '3mv9',\n",
       " '4ftv',\n",
       " '4pri',\n",
       " '5euo',\n",
       " '5nqk',\n",
       " '7rtr',\n",
       " '5bs0',\n",
       " '5brz',\n",
       " '4eup',\n",
       " '3utt',\n",
       " '3qdg',\n",
       " '3hg1',\n",
       " '5e9d',\n",
       " '3qdm',\n",
       " '6vqo',\n",
       " '5men',\n",
       " '5yxn',\n",
       " '3pwp',\n",
       " '1bd2',\n",
       " '3h9s',\n",
       " '6amu',\n",
       " '5c0a',\n",
       " '5c0b',\n",
       " '5c0c',\n",
       " '5c08',\n",
       " '5nmg',\n",
       " '2bnr',\n",
       " '5nme',\n",
       " '6am5',\n",
       " '5eu6',\n",
       " '5c09',\n",
       " '5c07',\n",
       " '5wkh',\n",
       " '3vxm',\n",
       " '6avg',\n",
       " '6avf',\n",
       " '3ffc',\n",
       " '3sjv',\n",
       " '4qrp',\n",
       " '6bj2',\n",
       " '4jrx',\n",
       " '3dxa',\n",
       " '3kpr',\n",
       " '3kps',\n",
       " '6uon',\n",
       " '4p4k',\n",
       " '4grl',\n",
       " '4may',\n",
       " '3pl6',\n",
       " '5ks9',\n",
       " '4gg6',\n",
       " '4z7u',\n",
       " '4z7v',\n",
       " '4z7w',\n",
       " '4ozf',\n",
       " '4ozi',\n",
       " '6u3o',\n",
       " '5ksb',\n",
       " '5ksa',\n",
       " '2iam',\n",
       " '4e41',\n",
       " '1j8h',\n",
       " '3o6f',\n",
       " '4h1l',\n",
       " '1zgl',\n",
       " '7jwj',\n",
       " '5m02',\n",
       " '6g9q',\n",
       " '5wlg',\n",
       " '3pqy',\n",
       " '5ivx',\n",
       " '1mwa',\n",
       " '1fo0',\n",
       " '1kj2',\n",
       " '1nam',\n",
       " '1g6r',\n",
       " '2ol3',\n",
       " '3tpu',\n",
       " '4n0c',\n",
       " '3tfk',\n",
       " '2oi9',\n",
       " '3tf7',\n",
       " '4mvb',\n",
       " '4mxq',\n",
       " '4n5e',\n",
       " '3c60',\n",
       " '3c5z',\n",
       " '3rdt',\n",
       " '6mnn',\n",
       " '3mbe',\n",
       " '1d9k',\n",
       " '1u3h',\n",
       " '2z31',\n",
       " '4p2q',\n",
       " '4p2r',\n",
       " '3qiu',\n",
       " '3qib',\n",
       " '4p2o',\n",
       " '6bga',\n",
       " '6r2l',\n",
       " '6uk4',\n",
       " '6uln',\n",
       " '6vm8',\n",
       " '6zkw',\n",
       " '7dzm',\n",
       " '7ndq',\n",
       " '7l1d',\n",
       " '7rrg',\n",
       " '7na5',\n",
       " '7ow5',\n",
       " '7qpj',\n",
       " '7phr',\n",
       " '7nme',\n",
       " '8d5q',\n",
       " '8gvb',\n",
       " '7rk7',\n",
       " '7n2n',\n",
       " '8gom',\n",
       " '6r0e',\n",
       " '6xc9',\n",
       " '6xco',\n",
       " '7rdv',\n",
       " '7sg0',\n",
       " '7sg1',\n",
       " '7z50',\n",
       " '7t2c',\n",
       " '7t2b',\n",
       " '3gjf',\n",
       " '2p5e',\n",
       " '2g9h']"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pdb_id"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "76562368-942c-47ec-ba62-8fdd991fba36",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " Error-fetch: unable to load '5ksb'.\n",
      " Error-fetch: unable to load '7ndq'.\n",
      " Error-fetch: unable to load '6r0e'.\n"
     ]
    }
   ],
   "source": [
    "for i, j in enumerate(pdb_id):\n",
    "    cmd.fetch(j, type=\"pdb\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ccd5db18-1c40-4f71-af4d-d379e3812420",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "a9fcaf92-957f-43bf-b3ab-374d5aa9a531",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "!mkdir -p data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "64ad88c8-0332-4744-9713-669a05948f2d",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "!mv *.pdb data/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "c62b4e2b-9d2b-4d29-8382-eaa532f60e2e",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data/\n",
      "data/1ao7.pdb\n",
      "data/1bd2.pdb\n",
      "data/1d9k.pdb\n",
      "data/1fo0.pdb\n",
      "data/1g6r.pdb\n",
      "data/1j8h.pdb\n",
      "data/1kj2.pdb\n",
      "data/1mi5.pdb\n",
      "data/1mwa.pdb\n",
      "data/1nam.pdb\n",
      "data/1oga.pdb\n",
      "data/1u3h.pdb\n",
      "data/1zgl.pdb\n",
      "data/2bnr.pdb\n",
      "data/2g9h.pdb\n",
      "data/2iam.pdb\n",
      "data/2nx5.pdb\n",
      "data/2oi9.pdb\n",
      "data/2ol3.pdb\n",
      "data/2p5e.pdb\n",
      "data/2vlj.pdb\n",
      "data/2vlk.pdb\n",
      "data/2vlr.pdb\n",
      "data/2ypl.pdb\n",
      "data/2z31.pdb\n",
      "data/3c5z.pdb\n",
      "data/3c60.pdb\n",
      "data/3dxa.pdb\n",
      "data/3ffc.pdb\n",
      "data/3gjf.pdb\n",
      "data/3gsn.pdb\n",
      "data/3h9s.pdb\n",
      "data/3hg1.pdb\n",
      "data/3kpr.pdb\n",
      "data/3kps.pdb\n",
      "data/3mbe.pdb\n",
      "data/3mv7.pdb\n",
      "data/3mv8.pdb\n",
      "data/3mv9.pdb\n",
      "data/3o4l.pdb\n",
      "data/3o6f.pdb\n",
      "data/3pl6.pdb\n",
      "data/3pqy.pdb\n",
      "data/3pwp.pdb\n",
      "data/3qdg.pdb\n",
      "data/3qdm.pdb\n",
      "data/3qib.pdb\n",
      "data/3qiu.pdb\n",
      "data/3rdt.pdb\n",
      "data/3sjv.pdb\n",
      "data/3tf7.pdb\n",
      "data/3tfk.pdb\n",
      "data/3tpu.pdb\n",
      "data/3utt.pdb\n",
      "data/3vxm.pdb\n",
      "data/3vxs.pdb\n",
      "data/4e41.pdb\n",
      "data/4eup.pdb\n",
      "data/4ftv.pdb\n",
      "data/4g9f.pdb\n",
      "data/4gg6.pdb\n",
      "data/4grl.pdb\n",
      "data/4h1l.pdb\n",
      "data/4jrx.pdb\n",
      "data/4may.pdb\n",
      "data/4mji.pdb\n",
      "data/4mvb.pdb\n",
      "data/4mxq.pdb\n",
      "data/4n0c.pdb\n",
      "data/4n5e.pdb\n",
      "data/4ozf.pdb\n",
      "data/4ozi.pdb\n",
      "data/4p2o.pdb\n",
      "data/4p2q.pdb\n",
      "data/4p2r.pdb\n",
      "data/4p4k.pdb\n",
      "data/4pri.pdb\n",
      "data/4qrp.pdb\n",
      "data/4z7u.pdb\n",
      "data/4z7v.pdb\n",
      "data/4z7w.pdb\n",
      "data/5brz.pdb\n",
      "data/5bs0.pdb\n",
      "data/5c07.pdb\n",
      "data/5c08.pdb\n",
      "data/5c09.pdb\n",
      "data/5c0a.pdb\n",
      "data/5c0b.pdb\n",
      "data/5c0c.pdb\n",
      "data/5d2l.pdb\n",
      "data/5d2n.pdb\n",
      "data/5e6i.pdb\n",
      "data/5e9d.pdb\n",
      "data/5eu6.pdb\n",
      "data/5euo.pdb\n",
      "data/5isz.pdb\n",
      "data/5ivx.pdb\n",
      "data/5jhd.pdb\n",
      "data/5ks9.pdb\n",
      "data/5ksa.pdb\n",
      "data/5m02.pdb\n",
      "data/5men.pdb\n",
      "data/5nht.pdb\n",
      "data/5nme.pdb\n",
      "data/5nmg.pdb\n",
      "data/5nqk.pdb\n",
      "data/5tez.pdb\n",
      "data/5wkh.pdb\n",
      "data/5wlg.pdb\n",
      "data/5yxn.pdb\n",
      "data/6am5.pdb\n",
      "data/6amu.pdb\n",
      "data/6avf.pdb\n",
      "data/6avg.pdb\n",
      "data/6bga.pdb\n",
      "data/6bj2.pdb\n",
      "data/6cql.pdb\n",
      "data/6dfs.pdb\n",
      "data/6dfw.pdb\n",
      "data/6dfx.pdb\n",
      "data/6g9q.pdb\n",
      "data/6l9l.pdb\n",
      "data/6mnn.pdb\n",
      "data/6mtm.pdb\n",
      "data/6px6.pdb\n",
      "data/6py2.pdb\n",
      "data/6r2l.pdb\n",
      "data/6rp9.pdb\n",
      "data/6rpa.pdb\n",
      "data/6rpb.pdb\n",
      "data/6rsy.pdb\n",
      "data/6tro.pdb\n",
      "data/6u3n.pdb\n",
      "data/6u3o.pdb\n",
      "data/6uk4.pdb\n",
      "data/6uln.pdb\n",
      "data/6uon.pdb\n",
      "data/6vm8.pdb\n",
      "data/6vmx.pdb\n",
      "data/6vqo.pdb\n",
      "data/6vrm.pdb\n",
      "data/6vrn.pdb\n",
      "data/6xc9.pdb\n",
      "data/6xco.pdb\n",
      "data/6zkw.pdb\n",
      "data/7dzm.pdb\n",
      "data/7jwj.pdb\n",
      "data/7l1d.pdb\n",
      "data/7n1e.pdb\n",
      "data/7n1f.pdb\n",
      "data/7n2n.pdb\n",
      "data/7n6e.pdb\n",
      "data/7na5.pdb\n",
      "data/7nme.pdb\n",
      "data/7ow5.pdb\n",
      "data/7phr.pdb\n",
      "data/7qpj.pdb\n",
      "data/7rdv.pdb\n",
      "data/7rk7.pdb\n",
      "data/7rrg.pdb\n",
      "data/7rtr.pdb\n",
      "data/7sg0.pdb\n",
      "data/7sg1.pdb\n",
      "data/7t2b.pdb\n",
      "data/7t2c.pdb\n",
      "data/7z50.pdb\n",
      "data/8d5q.pdb\n",
      "data/8gom.pdb\n",
      "data/8gvb.pdb\n",
      "data/5ksb.pdb\n",
      "data/7ndq.cif\n",
      "data/6r0e.cif\n"
     ]
    }
   ],
   "source": [
    "!tar zcvf data.tar.gz data/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d20fd480-1950-4e3b-af62-d11a15fef650",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "PDBfixer Environment",
   "language": "python",
   "name": "pdbfixer"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.7"
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 },
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}