notebooks/quickstart.ipynb

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   "source": [
    "# rcsbsearch quickstart\n",
    "\n",
    "This notebook contains examples from the rcsbsearch [quickstart](https://rcsbsearch.readthedocs.io/en/latest/quickstart.html)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "african-monthly",
   "metadata": {},
   "outputs": [],
   "source": [
    "from rcsbsearch import TextQuery\n",
    "from rcsbsearch import rcsb_attributes as attrs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "sublime-karen",
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   "source": [
    "## Operator syntax\n",
    "\n",
    "Here is an example from the RCSB Search API page, using the operator syntax. This query finds symmetric dimers having a twofold rotation with the DNA-binding domain of a heat-shock transcription factor.\n",
    "\n",
    "Note the use of standard comparison operators (`==`, `>` etc) for rcsb attributes and set operators for combining queries."
   ]
  },
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   "cell_type": "code",
   "execution_count": 2,
   "id": "enabling-america",
   "metadata": {},
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     "text": [
      "1FYL-2\n",
      "1FYL-1\n",
      "1FYM-1\n",
      "1FYK-1\n",
      "3HTS-1\n",
      "5D8K-1\n",
      "5D8L-2\n",
      "5D8L-1\n",
      "5D5W-1\n",
      "5D5X-1\n",
      "5HDN-2\n",
      "5HDN-1\n",
      "5D5V-1\n",
      "5D5U-1\n"
     ]
    }
   ],
   "source": [
    "# Create terminals for each query\n",
    "q1 = TextQuery('\"heat-shock transcription factor\"')\n",
    "q2 = attrs.rcsb_struct_symmetry.symbol == \"C2\"\n",
    "q3 = attrs.rcsb_struct_symmetry.kind == \"Global Symmetry\"\n",
    "q4 = attrs.rcsb_entry_info.polymer_entity_count_DNA >= 1\n",
    "\n",
    "# combined using bitwise operators (&, |, ~, etc)\n",
    "query = q1 & q2 & q3 & q4  # AND of all queries\n",
    "\n",
    "# Call the query to execute it\n",
    "for assemblyid in query(\"assembly\"):\n",
    "    print(assemblyid)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "accomplished-passion",
   "metadata": {},
   "source": [
    "Attribute names can be found in the [RCSB schema](http://search.rcsb.org/rcsbsearch/v1/metadata/schema). They can also be found via tab completion, or by iterating:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "supported-observer",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['citation.rcsb_authors',\n",
       " 'pdbx_nmr_software.authors',\n",
       " 'rcsb_primary_citation.rcsb_authors',\n",
       " 'rcsb_bird_citation.rcsb_authors']"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[a.attribute for a in attrs if \"authors\" in a.attribute]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "other-grant",
   "metadata": {},
   "source": [
    "## Fluent syntax\n",
    "\n",
    "Here is the same example using the fluent syntax:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "polish-indonesia",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1FYL-2\n",
      "1FYL-1\n",
      "1FYM-1\n",
      "1FYK-1\n",
      "3HTS-1\n",
      "5D8K-1\n",
      "5D8L-2\n",
      "5D8L-1\n",
      "5D5W-1\n",
      "5D5X-1\n",
      "5HDN-2\n",
      "5HDN-1\n",
      "5D5V-1\n",
      "5D5U-1\n"
     ]
    }
   ],
   "source": [
    "# Start with a Attr or TextQuery, then add terms\n",
    "results = TextQuery('\"heat-shock transcription factor\"') \\\n",
    "    .and_(\"rcsb_struct_symmetry.symbol\").exact_match(\"C2\") \\\n",
    "    .and_(\"rcsb_struct_symmetry.kind\").exact_match(\"Global Symmetry\") \\\n",
    "    .and_(\"rcsb_entry_info.polymer_entity_count_DNA\").greater_or_equal(1) \\\n",
    "    .exec(\"assembly\")\n",
    "\n",
    "# Exec produces an iterator of IDs\n",
    "for assemblyid in results:\n",
    "    print(assemblyid)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "adopted-gnome",
   "metadata": {},
   "source": [
    "For a more practical example, see the [Covid-19 notebook](covid.ipynb)"
   ]
  }
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