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310 changes: 310 additions & 0 deletions jupyter/06_pandas_integration_examples.ipynb
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"source": "# __Pandas examples with ChemAxon molecules__",
"id": "b70058148a1f011b"
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{
"metadata": {},
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"source": "You can see simpler examples of using pandas.DataGrame.read_table with ChemAxon molecules in the [Calculators](02_calculators.ipynb) and [Molecular similiarity notebook](03_molecular_similarity.ipynb). But here are some additional examples showing how to work with ChemAxon molecules in pandas DataFrames.",
"id": "74aa29c7fecce4b7"
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{
"metadata": {},
"cell_type": "markdown",
"source": "By default, molecules are printed in the _cxsmiles_ format. In case of issues with that, it is written in the _cxsmarts_ format. If none of them are possible for some reason, representation falls back to use the original format, which was recognized during the import process.",
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"source": [
"import pandas as pd\n",
"from chemaxon import import_mol, open_for_import\n",
"\n",
"mol = import_mol('CC(=O)NC1=CC=C(O)C=C1')\n",
"\n",
"mol_lst = []\n",
"with open_for_import('/home/lnagy/IdeaProjects/python-api/chemaxon/resources/test.sdf') as mol_importer:\n",
" for m in mol_importer:\n",
" mol_lst.append(m)\n",
"\n",
"d = {'molecule': [mol] + mol_lst }\n",
"df_mols = pd.DataFrame(data=d)\n",
"\n",
"df_mols"
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"text/plain": [
" molecule\n",
"0 CC(=O)NC1=CC=C(O)C=C1 |c:9,t:4,6|\n",
"1 [Li]C1=C(I)C(Br)=C(F)C2=C1C(Cl)=C(N)C(O)=C2S |..."
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"<div>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>molecule</th>\n",
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" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CC(=O)NC1=CC=C(O)C=C1 |c:9,t:4,6|</td>\n",
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" <tr>\n",
" <th>1</th>\n",
" <td>[Li]C1=C(I)C(Br)=C(F)C2=C1C(Cl)=C(N)C(O)=C2S |...</td>\n",
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"source": "In case of creating HTML output from pandas.DataFrame, you can use the helper function _mol_to_svg_formatter_ to visualize the molecules as SVG images.",
"id": "7d771f74cf01d2f6"
},
{
"metadata": {
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"end_time": "2025-12-01T14:44:23.122745Z",
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},
"cell_type": "code",
"source": [
"from chemaxon import mol_to_svg_formatter\n",
"\n",
"df_mols.to_html('web_view.html', escape=False, formatters=dict(molecule=mol_to_svg_formatter))"
],
"id": "27bf252df19e4e0f",
"outputs": [],
"execution_count": 3
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Since the __Molecule__ objects are being stored in the __DataFrame__, not just their representation, you can easily calculate properties for them and store the results in new columns.",
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"source": [
"from chemaxon import logp\n",
"\n",
"df_mols['LogP'] = df_mols['molecule'].apply(lambda m: logp(m))\n",
"df_mols"
],
"id": "d4877596d4d17c61",
"outputs": [
{
"data": {
"text/plain": [
" molecule LogP\n",
"0 CC(=O)NC1=CC=C(O)C=C1 |c:9,t:4,6| 0.92\n",
"1 [Li]C1=C(I)C(Br)=C(F)C2=C1C(Cl)=C(N)C(O)=C2S |... 4.06"
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" <th></th>\n",
" <th>molecule</th>\n",
" <th>LogP</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
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" <td>0.92</td>\n",
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" <tr>\n",
" <th>1</th>\n",
" <td>[Li]C1=C(I)C(Br)=C(F)C2=C1C(Cl)=C(N)C(O)=C2S |...</td>\n",
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"</table>\n",
"</div>"
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"metadata": {},
"cell_type": "markdown",
"source": "You can also easily create new molecule columns based on existing columns, that contain molecules in any supported format.",
"id": "754df0780b6944f8"
},
{
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"ExecuteTime": {
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},
"cell_type": "code",
"source": [
"d = {'SMILES': ['CN1C=NC2=C1C(=O)N(C)C(=O)N2C'], 'name': ['coffein'] }\n",
"df = pd.DataFrame(data=d)\n",
"\n",
"df = pd.concat([df, pd.DataFrame.from_records([{'SMILES' : 'CC[C@H](C)[C@@H]1NC(=O)[C@H](CC2=CC=C(O)C=C2)NC(=O)[C@@H](N)CSSC[C@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(C)C)C(=O)NCC(N)=O', 'name' : 'oxytocin'}])])\n",
"\n",
"df['molecule'] = df['SMILES'].apply(lambda s: import_mol(s))\n",
"df\n"
],
"id": "7cf77defedadb058",
"outputs": [
{
"data": {
"text/plain": [
" SMILES name \\\n",
"0 CN1C=NC2=C1C(=O)N(C)C(=O)N2C coffein \n",
"0 CC[C@H](C)[C@@H]1NC(=O)[C@H](CC2=CC=C(O)C=C2)N... oxytocin \n",
"\n",
" molecule \n",
"0 CN1C=NC2=C1C(=O)N(C)C(=O)N2C |c:2,4| \n",
"0 CC[C@H](C)[C@@H]1NC(=O)[C@H](CC2=CC=C(O)C=C2)N... "
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" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>SMILES</th>\n",
" <th>name</th>\n",
" <th>molecule</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CN1C=NC2=C1C(=O)N(C)C(=O)N2C</td>\n",
" <td>coffein</td>\n",
" <td>CN1C=NC2=C1C(=O)N(C)C(=O)N2C |c:2,4|</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>CC[C@H](C)[C@@H]1NC(=O)[C@H](CC2=CC=C(O)C=C2)N...</td>\n",
" <td>oxytocin</td>\n",
" <td>CC[C@H](C)[C@@H]1NC(=O)[C@H](CC2=CC=C(O)C=C2)N...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
]
},
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