{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import qcportal as ptl\n",
"client = ptl.FractalClient()\n",
"ds = client.get_collection(\"Dataset\", \"COMP6 DrugBank\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"mols = ds.get_molecules()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(13379, 1)"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mols.shape"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['ωB97x', 'b3lyp', 'b3lyp-d3m(bj)', 'hf', 'pbe', 'pbe-d3m(bj)',\n",
" 'svwn', 'wb97m', 'wb97m-d3(bj)'], dtype=object)"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.list_values().reset_index()['method'].unique()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['6-31g*', 'def2-tzvp'], dtype=object)"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.list_values().reset_index()['basis'].unique()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"
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"\n",
"
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" | \n",
" method | \n",
" basis | \n",
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" def2-tzvp | \n",
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" hf | \n",
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" 5 | \n",
" svwn | \n",
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" \n",
" 6 | \n",
" wb97m | \n",
" def2-tzvp | \n",
" 1 | \n",
"
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" \n",
" 7 | \n",
" wb97m-d3(bj) | \n",
" def2-tzvp | \n",
" 1 | \n",
"
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" \n",
" 8 | \n",
" ωB97x | \n",
" 6-31g* | \n",
" 6 | \n",
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"
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"
"
],
"text/plain": [
" method basis 0\n",
"0 b3lyp def2-tzvp 1\n",
"1 b3lyp-d3m(bj) def2-tzvp 1\n",
"2 hf def2-tzvp 1\n",
"3 pbe def2-tzvp 1\n",
"4 pbe-d3m(bj) def2-tzvp 1\n",
"5 svwn def2-tzvp 1\n",
"6 wb97m def2-tzvp 1\n",
"7 wb97m-d3(bj) def2-tzvp 1\n",
"8 ωB97x 6-31g* 6"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.list_values().reset_index().groupby(['method','basis']).size().reset_index()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
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" \n",
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" | \n",
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" | \n",
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\n",
" \n",
" \n",
" \n",
" False | \n",
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" Unknown | \n",
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" \n",
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" Unknown | \n",
" Hirshfeld Charges | \n",
"
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" \n",
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" 6-31g* | \n",
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" Energy | \n",
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" \n",
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" gaussian | \n",
" ωB97x | \n",
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" Hirshfeld Dipole | \n",
"
\n",
" \n",
" spin_density | \n",
" gaussian | \n",
" ωB97x | \n",
" 6-31g* | \n",
" Unknown | \n",
" Spin Density | \n",
"
\n",
" \n",
" True | \n",
" energy | \n",
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" def2-tzvp | \n",
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"
\n",
" \n",
" b3lyp-d3m(bj) | \n",
" def2-tzvp | \n",
" scf_default | \n",
" B3LYP-D3M(BJ)/def2-tzvp | \n",
"
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" \n",
" hf | \n",
" def2-tzvp | \n",
" scf_default | \n",
" HF/def2-tzvp | \n",
"
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" \n",
" pbe | \n",
" def2-tzvp | \n",
" scf_default | \n",
" PBE/def2-tzvp | \n",
"
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" \n",
" pbe-d3m(bj) | \n",
" def2-tzvp | \n",
" scf_default | \n",
" PBE-D3M(BJ)/def2-tzvp | \n",
"
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" \n",
" svwn | \n",
" def2-tzvp | \n",
" scf_default | \n",
" SVWN/def2-tzvp | \n",
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" wb97m | \n",
" def2-tzvp | \n",
" scf_default | \n",
" WB97M/def2-tzvp | \n",
"
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" \n",
" wb97m-d3(bj) | \n",
" def2-tzvp | \n",
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" WB97M-D3(BJ)/def2-tzvp | \n",
"
\n",
" \n",
"
\n",
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"
],
"text/plain": [
" keywords \\\n",
"native driver program method basis \n",
"False charge gaussian ωB97x 6-31g* Unknown \n",
" 6-31g* Unknown \n",
" energy gaussian ωB97x 6-31g* Unknown \n",
" gradient gaussian ωB97x 6-31g* Unknown \n",
" hirshfeld_dipole gaussian ωB97x 6-31g* Unknown \n",
" spin_density gaussian ωB97x 6-31g* Unknown \n",
"True energy psi4 b3lyp def2-tzvp scf_default \n",
" b3lyp-d3m(bj) def2-tzvp scf_default \n",
" hf def2-tzvp scf_default \n",
" pbe def2-tzvp scf_default \n",
" pbe-d3m(bj) def2-tzvp scf_default \n",
" svwn def2-tzvp scf_default \n",
" wb97m def2-tzvp scf_default \n",
" wb97m-d3(bj) def2-tzvp scf_default \n",
"\n",
" name \n",
"native driver program method basis \n",
"False charge gaussian ωB97x 6-31g* CM5 Charges \n",
" 6-31g* Hirshfeld Charges \n",
" energy gaussian ωB97x 6-31g* Energy \n",
" gradient gaussian ωB97x 6-31g* Gradient \n",
" hirshfeld_dipole gaussian ωB97x 6-31g* Hirshfeld Dipole \n",
" spin_density gaussian ωB97x 6-31g* Spin Density \n",
"True energy psi4 b3lyp def2-tzvp B3LYP/def2-tzvp \n",
" b3lyp-d3m(bj) def2-tzvp B3LYP-D3M(BJ)/def2-tzvp \n",
" hf def2-tzvp HF/def2-tzvp \n",
" pbe def2-tzvp PBE/def2-tzvp \n",
" pbe-d3m(bj) def2-tzvp PBE-D3M(BJ)/def2-tzvp \n",
" svwn def2-tzvp SVWN/def2-tzvp \n",
" wb97m def2-tzvp WB97M/def2-tzvp \n",
" wb97m-d3(bj) def2-tzvp WB97M-D3(BJ)/def2-tzvp "
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.list_values()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"val = ds.get_values(method='ωB97x')"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Index(['CM5 Charges', 'Hirshfeld Charges', 'Energy', 'Gradient',\n",
" 'Hirshfeld Dipole', 'Spin Density'],\n",
" dtype='object')"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"val.columns"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"energy = val['Energy']"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "4408b4a9174c4b598fbb4f0b73caa893",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"_ColormakerRegistry()"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "4d4eb20bc7e1422b8f06fdb0b07d96d7",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"mols['molecule'][0].show()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-636107.9519541461"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"energy[0]"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "ae99865052b94841bc4053b0ac9718fb",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"mols['molecule'][1].show()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-558044.7290289854"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"energy[1]"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
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\n",
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" energy | \n",
" psi4 | \n",
" wb97m-d3(bj) | \n",
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"0 energy psi4 hf def2-tzvp scf_default \n",
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"9 energy psi4 b3lyp-d3m(bj) def2-tzvp scf_default \n",
"10 energy psi4 wb97m-d3(bj) def2-tzvp scf_default \n",
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]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ds.list_records()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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