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Upload accessing_the_data.ipynb
Browse files- accessing_the_data.ipynb +8 -1014
accessing_the_data.ipynb
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@@ -17,7 +17,7 @@
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},
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{
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"cell_type": "code",
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"execution_count":
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"metadata": {},
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"outputs": [],
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"source": [
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@@ -35,7 +35,7 @@
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},
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{
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"cell_type": "code",
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"execution_count":
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"metadata": {},
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"outputs": [],
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"source": [
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@@ -63,23 +63,9 @@
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},
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{
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"cell_type": "code",
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"execution_count":
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"IterableDataset({\n",
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" 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",
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" n_shards: 430\n",
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"})"
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]
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},
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"# load the dataset\n",
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"hub_dataset = load_dataset(path=path,\n",
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@@ -135,59 +121,9 @@
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},
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{
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"cell_type": "code",
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"execution_count":
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"['cid',\n",
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" 'state',\n",
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" 'pubchem-inchi',\n",
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" 'pubchem-charge',\n",
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" 'pubchem-version',\n",
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" 'name',\n",
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" 'coordinates',\n",
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" 'atomic-numbers',\n",
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" 'atom-count',\n",
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" 'heavy-atom-count',\n",
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" 'core-electrons',\n",
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" 'bond-order',\n",
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" 'connection-indices',\n",
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" 'formula',\n",
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" 'version',\n",
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" 'obabel-inchi',\n",
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" 'pm6-obabel-canonical-smiles',\n",
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" 'charge',\n",
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" 'energy-beta-gap',\n",
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" 'energy-beta-homo',\n",
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" 'energy-beta-lumo',\n",
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" 'energy-alpha-gap',\n",
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" 'energy-alpha-homo',\n",
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" 'energy-alpha-lumo',\n",
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" 'total-energy',\n",
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" 'homos',\n",
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" 'orbital-energies',\n",
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" 'mo-count',\n",
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" 'basis-count',\n",
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" 'multiplicity',\n",
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" 'molecular-mass',\n",
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" 'number-of-atoms',\n",
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" 'lowdin-partial-charges',\n",
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" 'mulliken-partial-charges',\n",
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" 'dipole-moment',\n",
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" 'pubchem-multiplicity',\n",
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" 'pubchem-obabel-canonical-smiles',\n",
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" 'pubchem-isomeric-smiles',\n",
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" 'pubchem-molecular-weight',\n",
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" 'pubchem-molecular-formula']"
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]
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},
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"execution_count": 13,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"# print the column names\n",
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"hub_dataset.column_names"
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@@ -205,951 +141,9 @@
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},
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{
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"cell_type": "code",
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"execution_count":
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"[{'cid': 1,\n",
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" 'state': 'S0',\n",
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" '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",
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" 'pubchem-charge': 0,\n",
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" 'pubchem-version': '20160829',\n",
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" 'name': '[email protected]',\n",
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" 'coordinates': [4.543149670829423,\n",
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" -2.8411897941733857,\n",
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| 222 |
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" -1.6418598810432616,\n",
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" 5.164339625816055,\n",
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" -1.776079871333543,\n",
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" -0.8127099411272803,\n",
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" 6.303009543349172,\n",
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" -1.3517299020731781,\n",
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" -0.8573999378940053,\n",
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" 4.255369691704345,\n",
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" -1.2926799063382324,\n",
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" 0.08501999385276329,\n",
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" 4.60962966603199,\n",
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" -0.12267999112548451,\n",
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" 0.9209899332554315,\n",
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" 3.2824497621808693,\n",
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" 0.5602999593942104,\n",
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" 1.1527099164801087,\n",
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" 3.3767697553673353,\n",
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" 3.9935697106646764,\n",
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" 1.3808998999270228,\n",
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" 2.881229791246801,\n",
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" 'atomic-numbers': [6,\n",
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" 8,\n",
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" 'bond-order': [1,\n",
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" 'connection-indices': [15,\n",
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" 31,\n",
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" 30],\n",
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| 467 |
-
" 'formula': 'C9H17NO4',\n",
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-
" 'version': '1.0',\n",
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| 469 |
-
" '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",
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| 470 |
-
" 'pm6-obabel-canonical-smiles': '[O]C(=O)C[C@@H](C[N](C)(C)C)OC(=O)C',\n",
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| 471 |
-
" 'charge': 0,\n",
|
| 472 |
-
" 'energy-beta-gap': 4.34837933099,\n",
|
| 473 |
-
" 'energy-beta-homo': -4.60960862747,\n",
|
| 474 |
-
" 'energy-beta-lumo': -0.2612292964799998,\n",
|
| 475 |
-
" 'energy-alpha-gap': 4.34837933099,\n",
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| 476 |
-
" 'energy-alpha-homo': -4.60960862747,\n",
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| 860 |
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|
| 861 |
-
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|
| 862 |
-
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|
| 863 |
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| 864 |
-
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|
| 865 |
-
" 'connection-indices': [19,\n",
|
| 866 |
-
" 11,\n",
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" 11,\n",
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" 3,\n",
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" 15,\n",
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" 4,\n",
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" 8,\n",
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" 7,\n",
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" 5,\n",
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" 7,\n",
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" 16,\n",
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" 6,\n",
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" 3,\n",
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" 3,\n",
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-
" 2,\n",
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| 883 |
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" 3,\n",
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| 884 |
-
" 14,\n",
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| 885 |
-
" 5,\n",
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| 886 |
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" 6,\n",
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-
" 5,\n",
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| 888 |
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" 4,\n",
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" 1,\n",
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" 4,\n",
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| 892 |
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" 10,\n",
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| 893 |
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" 2,\n",
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" 1,\n",
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" 2,\n",
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" 13,\n",
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" 1,\n",
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" 9,\n",
|
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" 17,\n",
|
| 901 |
-
" 10,\n",
|
| 902 |
-
" 18],\n",
|
| 903 |
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" 'formula': 'C7H8O4',\n",
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| 904 |
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" 'version': '1.0',\n",
|
| 905 |
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" '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",
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| 906 |
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| 999 |
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| 1000 |
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| 1024 |
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| 1063 |
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| 1071 |
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| 1080 |
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| 1082 |
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| 1084 |
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| 1085 |
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| 1086 |
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| 1087 |
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| 1089 |
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| 1090 |
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" 116.195335302005,\n",
|
| 1093 |
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|
| 1094 |
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" 120.57364715655001,\n",
|
| 1095 |
-
" 122.5056554951,\n",
|
| 1096 |
-
" 128.723456979025]],\n",
|
| 1097 |
-
" 'mo-count': 181,\n",
|
| 1098 |
-
" 'basis-count': 181,\n",
|
| 1099 |
-
" 'multiplicity': 1,\n",
|
| 1100 |
-
" 'molecular-mass': 156.13601999999992,\n",
|
| 1101 |
-
" 'number-of-atoms': 19,\n",
|
| 1102 |
-
" 'lowdin-partial-charges': [-0.165834,\n",
|
| 1103 |
-
" -0.166217,\n",
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| 1104 |
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" -0.00709,\n",
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| 1105 |
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" 0.167807,\n",
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| 1118 |
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|
| 1119 |
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" 0.351181,\n",
|
| 1120 |
-
" 0.346156],\n",
|
| 1121 |
-
" 'mulliken-partial-charges': [-0.122757,\n",
|
| 1122 |
-
" -0.14337,\n",
|
| 1123 |
-
" 0.076825,\n",
|
| 1124 |
-
" 0.022155,\n",
|
| 1125 |
-
" 0.032184,\n",
|
| 1126 |
-
" -0.158536,\n",
|
| 1127 |
-
" 0.54755,\n",
|
| 1128 |
-
" -0.448879,\n",
|
| 1129 |
-
" -0.6056,\n",
|
| 1130 |
-
" -0.631763,\n",
|
| 1131 |
-
" -0.61658,\n",
|
| 1132 |
-
" 0.149995,\n",
|
| 1133 |
-
" 0.155257,\n",
|
| 1134 |
-
" 0.162402,\n",
|
| 1135 |
-
" 0.184383,\n",
|
| 1136 |
-
" 0.175571,\n",
|
| 1137 |
-
" 0.426152,\n",
|
| 1138 |
-
" 0.402121,\n",
|
| 1139 |
-
" 0.392891],\n",
|
| 1140 |
-
" 'dipole-moment': 5.099240805823648,\n",
|
| 1141 |
-
" 'pubchem-multiplicity': 1,\n",
|
| 1142 |
-
" 'pubchem-obabel-canonical-smiles': 'OC1C=CC=C(C1O)C(=O)O',\n",
|
| 1143 |
-
" 'pubchem-isomeric-smiles': 'C1=CC(C(C(=C1)C(=O)O)O)O',\n",
|
| 1144 |
-
" 'pubchem-molecular-weight': 156.13602,\n",
|
| 1145 |
-
" 'pubchem-molecular-formula': 'C7H8O4'}]"
|
| 1146 |
-
]
|
| 1147 |
-
},
|
| 1148 |
-
"execution_count": 15,
|
| 1149 |
-
"metadata": {},
|
| 1150 |
-
"output_type": "execute_result"
|
| 1151 |
-
}
|
| 1152 |
-
],
|
| 1153 |
"source": [
|
| 1154 |
"list(hub_dataset.take(2))"
|
| 1155 |
]
|
|
|
|
| 17 |
},
|
| 18 |
{
|
| 19 |
"cell_type": "code",
|
| 20 |
+
"execution_count": null,
|
| 21 |
"metadata": {},
|
| 22 |
"outputs": [],
|
| 23 |
"source": [
|
|
|
|
| 35 |
},
|
| 36 |
{
|
| 37 |
"cell_type": "code",
|
| 38 |
+
"execution_count": null,
|
| 39 |
"metadata": {},
|
| 40 |
"outputs": [],
|
| 41 |
"source": [
|
|
|
|
| 63 |
},
|
| 64 |
{
|
| 65 |
"cell_type": "code",
|
| 66 |
+
"execution_count": null,
|
| 67 |
"metadata": {},
|
| 68 |
+
"outputs": [],
|
|
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|
| 69 |
"source": [
|
| 70 |
"# load the dataset\n",
|
| 71 |
"hub_dataset = load_dataset(path=path,\n",
|
|
|
|
| 121 |
},
|
| 122 |
{
|
| 123 |
"cell_type": "code",
|
| 124 |
+
"execution_count": null,
|
| 125 |
"metadata": {},
|
| 126 |
+
"outputs": [],
|
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|
| 127 |
"source": [
|
| 128 |
"# print the column names\n",
|
| 129 |
"hub_dataset.column_names"
|
|
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|
| 141 |
},
|
| 142 |
{
|
| 143 |
"cell_type": "code",
|
| 144 |
+
"execution_count": null,
|
| 145 |
"metadata": {},
|
| 146 |
+
"outputs": [],
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| 147 |
"source": [
|
| 148 |
"list(hub_dataset.take(2))"
|
| 149 |
]
|