Upload accessing_the_data.ipynb

accessing_the_data.ipynb

@@ -0,0 +1,1179 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Accessing the Data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In order to be able to access the data on Hugging Face Hub, we must import the\n",
+    "necessary libraries"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datasets import load_dataset           # Loading datasets from Hugging Face Hub\n",
+    "from pprint import pprint                   # Pretty print"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "After importing the modules, we set a few variables that will be used throughout\n",
+    "this demo."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# path to the dataset repository on the Hugging Face Hub\n",
+    "path = \"molssiai-hub/pubchemqc-b3lyp\"\n",
+    "\n",
+    "# set the dataset configuration/subset name\n",
+    "name = \"b3lyp_pm6\"\n",
+    "\n",
+    "# set the dataset split\n",
+    "split = \"train\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In this tutorial, we are going to work with the\n",
+    "[PubChemQC-B3LYP/6-31G*//PM6\n",
+    "Dataset](https://huggingface.co/datasets/molssiai-hub/pubchemqc-b3lyp)\n",
+    "(PubChemQC-B3LYP for short) from the [PubChemQC dataset\n",
+    "collection](https://huggingface.co/collections/molssiai-hub/pubchemqc-datasets-669e5482260861ba7cce3d1c).\n",
+    "Let us load the dataset as shown below"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "IterableDataset({\n",
+       "    features: ['cid', 'state', 'pubchem-inchi', 'pubchem-charge', 'pubchem-version', 'name', 'coordinates', 'atomic-numbers', 'atom-count', 'heavy-atom-count', 'core-electrons', 'bond-order', 'connection-indices', 'formula', 'version', 'obabel-inchi', 'pm6-obabel-canonical-smiles', 'charge', 'energy-beta-gap', 'energy-beta-homo', 'energy-beta-lumo', 'energy-alpha-gap', 'energy-alpha-homo', 'energy-alpha-lumo', 'total-energy', 'homos', 'orbital-energies', 'mo-count', 'basis-count', 'multiplicity', 'molecular-mass', 'number-of-atoms', 'lowdin-partial-charges', 'mulliken-partial-charges', 'dipole-moment', 'pubchem-multiplicity', 'pubchem-obabel-canonical-smiles', 'pubchem-isomeric-smiles', 'pubchem-molecular-weight', 'pubchem-molecular-formula'],\n",
+       "    n_shards: 430\n",
+       "})"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# load the dataset\n",
+    "hub_dataset = load_dataset(path=path,\n",
+    "                           name=name,\n",
+    "                           split=split,\n",
+    "                           streaming=True,\n",
+    "                           trust_remote_code=True)\n",
+    "\n",
+    "hub_dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "PubChemQC datasets are very large and downloading them on your local machine can\n",
+    "be a heavy lift for your internet network and disk storage. Therefore, we set\n",
+    "the `streaming` parameter to `True` to avoid downloading the dataset on disk and\n",
+    "ensure streaming the data from the hub. In this mode, the `load_dataset`\n",
+    "function returns an `IterableDataset` object that can be iterated over to access\n",
+    "the data. The `trust_remote_code` argument is also set to `True` to allow the\n",
+    "usage of a custom [load\n",
+    "script](https://huggingface.co/datasets/molssiai-hub/pubchemqc-b3lyp/blob/main/pubchemqc-b3lyp.py)\n",
+    "for the data.\n",
+    "\n",
+    "The PubChemQC-B3LYP dataset is made of several files called `shards` that enable\n",
+    "multiprocessing and parallelization of the data loading process. Multiprocessing\n",
+    "can speed up the loading process significantly if you are absolutely sure that\n",
+    "you have enough CPU cores to handle the load and enough memory and storage space\n",
+    "to download and store the data.\n",
+    "\n",
+    "You can choose the number of processes to use for loading the data by setting\n",
+    "the `num_proc` parameter in the `load_dataset` function.\n",
+    "\n",
+    "```python\n",
+    "\n",
+    "    >>> dataset = load_dataset(path=path,\n",
+    "                               split=split,\n",
+    "                               streaming=True,\n",
+    "                               trust_remote_code=True,\n",
+    "                               num_proc=4)\n",
+    "```\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Once we create our `Dataset` or `IterableDataset` instance, we can access its\n",
+    "features or column names using the `features` or `column_names` attributes of\n",
+    "the dataset object.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['cid',\n",
+       " 'state',\n",
+       " 'pubchem-inchi',\n",
+       " 'pubchem-charge',\n",
+       " 'pubchem-version',\n",
+       " 'name',\n",
+       " 'coordinates',\n",
+       " 'atomic-numbers',\n",
+       " 'atom-count',\n",
+       " 'heavy-atom-count',\n",
+       " 'core-electrons',\n",
+       " 'bond-order',\n",
+       " 'connection-indices',\n",
+       " 'formula',\n",
+       " 'version',\n",
+       " 'obabel-inchi',\n",
+       " 'pm6-obabel-canonical-smiles',\n",
+       " 'charge',\n",
+       " 'energy-beta-gap',\n",
+       " 'energy-beta-homo',\n",
+       " 'energy-beta-lumo',\n",
+       " 'energy-alpha-gap',\n",
+       " 'energy-alpha-homo',\n",
+       " 'energy-alpha-lumo',\n",
+       " 'total-energy',\n",
+       " 'homos',\n",
+       " 'orbital-energies',\n",
+       " 'mo-count',\n",
+       " 'basis-count',\n",
+       " 'multiplicity',\n",
+       " 'molecular-mass',\n",
+       " 'number-of-atoms',\n",
+       " 'lowdin-partial-charges',\n",
+       " 'mulliken-partial-charges',\n",
+       " 'dipole-moment',\n",
+       " 'pubchem-multiplicity',\n",
+       " 'pubchem-obabel-canonical-smiles',\n",
+       " 'pubchem-isomeric-smiles',\n",
+       " 'pubchem-molecular-weight',\n",
+       " 'pubchem-molecular-formula']"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# print the column names\n",
+    "hub_dataset.column_names"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can use `take(n)` to fetch the first $n$ examples from the dataset.\n",
+    "For demonstration purposes, we set $n$ to 2 which yields a list of\n",
+    "two dictionaries, each containing the features of the corresponding\n",
+    "data point."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[{'cid': 1,\n",
+       "  'state': 'S0',\n",
+       "  'pubchem-inchi': 'InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3',\n",
+       "  'pubchem-charge': 0,\n",
+       "  'pubchem-version': '20160829',\n",
+       "  'name': '[email protected]',\n",
+       "  'coordinates': [4.543149670829423,\n",
+       "   -2.8411897941733857,\n",
+       "   -1.6418598810432616,\n",
+       "   5.164339625816055,\n",
+       "   -1.776079871333543,\n",
+       "   -0.8127099411272803,\n",
+       "   6.303009543349172,\n",
+       "   -1.3517299020731781,\n",
+       "   -0.8573999378940053,\n",
+       "   4.255369691704345,\n",
+       "   -1.2926799063382324,\n",
+       "   0.08501999385276329,\n",
+       "   4.60962966603199,\n",
+       "   -0.12267999112548451,\n",
+       "   0.9209899332554315,\n",
+       "   3.2824497621808693,\n",
+       "   0.5602999593942104,\n",
+       "   1.1527099164801087,\n",
+       "   3.3767697553673353,\n",
+       "   1.7012998767313179,\n",
+       "   2.2331298382255156,\n",
+       "   3.9935697106646764,\n",
+       "   1.3808998999270228,\n",
+       "   3.2894897616953807,\n",
+       "   2.881229791246801,\n",
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+       "   1.9378698595831967,\n",
+       "   5.234679620732287,\n",
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+       "   2.561759814391751,\n",
+       "   7.676599443790074,\n",
+       "   -0.7797299435035565,\n",
+       "   1.7129698758981244,\n",
+       "   6.666809516973522,\n",
+       "   1.3677999008968658,\n",
+       "   2.3902798268023666,\n",
+       "   6.871359502159529,\n",
+       "   -0.444549967769325,\n",
+       "   4.023889708442672,\n",
+       "   4.4186396798669705,\n",
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+       "   0.6238299547913445,\n",
+       "   7.7404594391760275,\n",
+       "   -1.8650498648728673,\n",
+       "   1.890259863072561,\n",
+       "   8.670379371800149,\n",
+       "   -0.34142997526909646,\n",
+       "   1.891069862987387,\n",
+       "   6.552169525296595,\n",
+       "   1.671489878887934,\n",
+       "   1.3366699031511258,\n",
+       "   7.59468944975336,\n",
+       "   1.8007598695576095,\n",
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+       "   5.791549580395056,\n",
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+       "   0.06863999502835459,\n",
+       "   4.660949662319101,\n",
+       "   7.864189430232259,\n",
+       "   -0.0930299932397971,\n",
+       "   4.345629685137421],\n",
+       "  'atomic-numbers': [6,\n",
+       "   6,\n",
+       "   8,\n",
+       "   8,\n",
+       "   6,\n",
+       "   6,\n",
+       "   6,\n",
+       "   8,\n",
+       "   8,\n",
+       "   6,\n",
+       "   7,\n",
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+       "   1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   1],\n",
+       "  'atom-count': 31,\n",
+       "  'heavy-atom-count': 14,\n",
+       "  'core-electrons': [0,\n",
+       "   0,\n",
+       "   0,\n",
+       "   0,\n",
+       "   0,\n",
+       "   0,\n",
+       "   0,\n",
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+       "   0,\n",
+       "   0,\n",
+       "   0,\n",
+       "   0,\n",
+       "   0],\n",
+       "  'bond-order': [1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   2,\n",
+       "   1,\n",
+       "   1,\n",
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+       "   1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   1,\n",
+       "   1],\n",
+       "  'connection-indices': [15,\n",
+       "   1,\n",
+       "   17,\n",
+       "   1,\n",
+       "   1,\n",
+       "   16,\n",
+       "   1,\n",
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+       "   31,\n",
+       "   14,\n",
+       "   30],\n",
+       "  'formula': 'C9H17NO4',\n",
+       "  'version': '1.0',\n",
+       "  'obabel-inchi': 'InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3/t8-/m0/s1',\n",
+       "  'pm6-obabel-canonical-smiles': '[O]C(=O)C[C@@H](C[N](C)(C)C)OC(=O)C',\n",
+       "  'charge': 0,\n",
+       "  'energy-beta-gap': 4.34837933099,\n",
+       "  'energy-beta-homo': -4.60960862747,\n",
+       "  'energy-beta-lumo': -0.2612292964799998,\n",
+       "  'energy-alpha-gap': 4.34837933099,\n",
+       "  'energy-alpha-homo': -4.60960862747,\n",
+       "  'energy-alpha-lumo': -0.2612292964799998,\n",
+       "  'total-energy': -19286.973573267132,\n",
+       "  'homos': [54],\n",
+       "  'orbital-energies': [[-522.303488065215,\n",
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+       "    127.37105114203999]],\n",
+       "  'mo-count': 244,\n",
+       "  'basis-count': 244,\n",
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+       "  'number-of-atoms': 31,\n",
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+       "   0.241415,\n",
+       "   0.185706],\n",
+       "  'dipole-moment': 11.419443262233626,\n",
+       "  'pubchem-multiplicity': 1,\n",
+       "  'pubchem-obabel-canonical-smiles': '[O-]C(=O)CC(C[N+](C)(C)C)OC(=O)C',\n",
+       "  'pubchem-isomeric-smiles': 'CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C',\n",
+       "  'pubchem-molecular-weight': 203.23558,\n",
+       "  'pubchem-molecular-formula': 'C9H17NO4'},\n",
+       " {'cid': 3,\n",
+       "  'state': 'S0',\n",
+       "  'pubchem-inchi': 'InChI=1S/C7H8O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,5-6,8-9H,(H,10,11)',\n",
+       "  'pubchem-charge': 0,\n",
+       "  'pubchem-version': '20160829',\n",
+       "  'name': '[email protected]',\n",
+       "  'coordinates': [1.040909924594702,\n",
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+       "   0.5780199581090726,\n",
+       "   -1.4850598923904088,\n",
+       "   -2.077949849455232],\n",
+       "  'atomic-numbers': [6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1],\n",
+       "  'atom-count': 19,\n",
+       "  'heavy-atom-count': 11,\n",
+       "  'core-electrons': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n",
+       "  'bond-order': [1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1],\n",
+       "  'connection-indices': [19,\n",
+       "   11,\n",
+       "   11,\n",
+       "   3,\n",
+       "   15,\n",
+       "   4,\n",
+       "   8,\n",
+       "   7,\n",
+       "   7,\n",
+       "   5,\n",
+       "   7,\n",
+       "   9,\n",
+       "   16,\n",
+       "   6,\n",
+       "   3,\n",
+       "   4,\n",
+       "   3,\n",
+       "   2,\n",
+       "   3,\n",
+       "   14,\n",
+       "   5,\n",
+       "   6,\n",
+       "   5,\n",
+       "   4,\n",
+       "   6,\n",
+       "   1,\n",
+       "   4,\n",
+       "   10,\n",
+       "   2,\n",
+       "   1,\n",
+       "   2,\n",
+       "   13,\n",
+       "   1,\n",
+       "   12,\n",
+       "   9,\n",
+       "   17,\n",
+       "   10,\n",
+       "   18],\n",
+       "  'formula': 'C7H8O4',\n",
+       "  'version': '1.0',\n",
+       "  'obabel-inchi': 'InChI=1S/C7H8O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,5-6,8-9H,(H,10,11)/t5-,6-/m0/s1',\n",
+       "  'pm6-obabel-canonical-smiles': 'O[C@H]1C=CC=C([C@@H]1O)C(=O)O',\n",
+       "  'charge': 0,\n",
+       "  'energy-beta-gap': 4.58783951943,\n",
+       "  'energy-beta-homo': -6.72121210735,\n",
+       "  'energy-beta-lumo': -2.1333725879200003,\n",
+       "  'energy-alpha-gap': 4.58783951943,\n",
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+       "  'energy-alpha-lumo': -2.1333725879200003,\n",
+       "  'total-energy': -15575.751067250567,\n",
+       "  'homos': [40],\n",
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+       "    58.882716109695,\n",
+       "    59.742595877275,\n",
+       "    60.22423739266,\n",
+       "    61.85147821865,\n",
+       "    62.877347435035006,\n",
+       "    63.394363750985,\n",
+       "    63.987571945075004,\n",
+       "    64.38213702830001,\n",
+       "    65.571274554985,\n",
+       "    66.46380798462499,\n",
+       "    67.13592919536,\n",
+       "    68.07472197958501,\n",
+       "    68.40670087719501,\n",
+       "    69.08970664195,\n",
+       "    70.104691304315,\n",
+       "    71.23124264538501,\n",
+       "    71.70199960675,\n",
+       "    72.88297371792,\n",
+       "    73.11699162935,\n",
+       "    73.593190867725,\n",
+       "    76.11568626186,\n",
+       "    76.92114325934,\n",
+       "    77.664014071205,\n",
+       "    78.45586537616,\n",
+       "    81.000129878335,\n",
+       "    83.051868311105,\n",
+       "    84.559379042875,\n",
+       "    88.62475996934499,\n",
+       "    101.659013408295,\n",
+       "    103.759732334155,\n",
+       "    105.58561627101,\n",
+       "    110.20066717549001,\n",
+       "    112.26873243929,\n",
+       "    114.1245488997,\n",
+       "    116.195335302005,\n",
+       "    119.86070886824,\n",
+       "    120.57364715655001,\n",
+       "    122.5056554951,\n",
+       "    128.723456979025]],\n",
+       "  'mo-count': 181,\n",
+       "  'basis-count': 181,\n",
+       "  'multiplicity': 1,\n",
+       "  'molecular-mass': 156.13601999999992,\n",
+       "  'number-of-atoms': 19,\n",
+       "  'lowdin-partial-charges': [-0.165834,\n",
+       "   -0.166217,\n",
+       "   -0.00709,\n",
+       "   -0.013209,\n",
+       "   -0.079093,\n",
+       "   -0.123254,\n",
+       "   0.188072,\n",
+       "   -0.245033,\n",
+       "   -0.385089,\n",
+       "   -0.452317,\n",
+       "   -0.452864,\n",
+       "   0.167807,\n",
+       "   0.16777,\n",
+       "   0.161347,\n",
+       "   0.170277,\n",
+       "   0.178644,\n",
+       "   0.358744,\n",
+       "   0.351181,\n",
+       "   0.346156],\n",
+       "  'mulliken-partial-charges': [-0.122757,\n",
+       "   -0.14337,\n",
+       "   0.076825,\n",
+       "   0.022155,\n",
+       "   0.032184,\n",
+       "   -0.158536,\n",
+       "   0.54755,\n",
+       "   -0.448879,\n",
+       "   -0.6056,\n",
+       "   -0.631763,\n",
+       "   -0.61658,\n",
+       "   0.149995,\n",
+       "   0.155257,\n",
+       "   0.162402,\n",
+       "   0.184383,\n",
+       "   0.175571,\n",
+       "   0.426152,\n",
+       "   0.402121,\n",
+       "   0.392891],\n",
+       "  'dipole-moment': 5.099240805823648,\n",
+       "  'pubchem-multiplicity': 1,\n",
+       "  'pubchem-obabel-canonical-smiles': 'OC1C=CC=C(C1O)C(=O)O',\n",
+       "  'pubchem-isomeric-smiles': 'C1=CC(C(C(=C1)C(=O)O)O)O',\n",
+       "  'pubchem-molecular-weight': 156.13602,\n",
+       "  'pubchem-molecular-formula': 'C7H8O4'}]"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "list(hub_dataset.take(2))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "hugface",
+   "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": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}