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iwatobipen/datamol_example.ipynb

Created October 8, 2022 12:58
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datamol_example.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "incoming-liquid",
"metadata": {},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"import datamol as dm"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "supreme-highlight",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'rdkit.Chem.rdchem.Mol'>\n"
]
}
],
"source": [
"mols = dm.read_sdf('cdk2.sdf')\n",
"print(type(mols[0]))"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "seasonal-journalism",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"maccs\n",
"ecfp\n",
"topological\n",
"atompair\n",
"rdkit\n",
"pattern\n",
"layered\n",
"erg\n",
"estate\n",
"avalon-count\n",
"rdkit-count\n",
"ecfp-count\n",
"fcfp-count\n",
"topological-count\n",
"atompair-count\n"
]
}
],
"source": [
"for fp in dm.list_supported_fingerprints():\n",
" print(fp)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "charged-matter",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'numpy.ndarray'> 2048\n",
"<class 'numpy.ndarray'> 512\n"
]
}
],
"source": [
"#ecfp\n",
"fp = dm.to_fp(mols[0], fp_type='ecfp')\n",
"print(type(fp), len(fp))\n",
"#ecfp 4 nBits=512\n",
"fp = dm.to_fp(mols[0], 2,fp_type='ecfp', nBits=512)\n",
"print(type(fp), len(fp))"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "present-apparel",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f565d7c73f0>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mcs = dm.find_mcs(mols[:10])\n",
"Chem.MolFromSmarts(mcs)\n"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "retired-genetics",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f565d7c7850>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mcs = dm.find_mcs(mols[:10], threshold=0.8)\n",
"Chem.MolFromSmarts(mcs)\n"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "caroline-triangle",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"\\ndm.find_mcs(\\n mols: List[rdkit.Chem.rdchem.Mol],\\n maximize_bonds: bool = True,\\n threshold: float = 0.0,\\n timeout: int = 5,\\n verbose: bool = False,\\n match_valences: bool = False,\\n ring_matches_ring_only: bool = True,\\n complete_rings_only: bool = False,\\n match_chiral_tag: bool = False,\\n seed_smarts: str = '',\\n atom_compare: str = 'CompareElements',\\n bond_compare: str = 'CompareOrder',\\n ring_compare: str = 'IgnoreRingFusion',\\n with_details: bool = False,\\n **kwargs: Any,\\n)\\n\""
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"'''\n",
"dm.find_mcs(\n",
" mols: List[rdkit.Chem.rdchem.Mol],\n",
" maximize_bonds: bool = True,\n",
" threshold: float = 0.0,\n",
" timeout: int = 5,\n",
" verbose: bool = False,\n",
" match_valences: bool = False,\n",
" ring_matches_ring_only: bool = True,\n",
" complete_rings_only: bool = False,\n",
" match_chiral_tag: bool = False,\n",
" seed_smarts: str = '',\n",
" atom_compare: str = 'CompareElements',\n",
" bond_compare: str = 'CompareOrder',\n",
" ring_compare: str = 'IgnoreRingFusion',\n",
" with_details: bool = False,\n",
" **kwargs: Any,\n",
")\n",
"'''"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "regulated-iraqi",
"metadata": {},
"outputs": [
{
"data": {
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"<!-- END OF HEADER -->\n",
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dm.viz.to_image(mols[:5], mol_size=(200,200))"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "female-pregnancy",
"metadata": {},
"outputs": [],
"source": [
"dm.log.disable_rdkit_log()\n",
"Chem.MolFromSmiles('c1cccc1')"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "worth-flexibility",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[21:56:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4\n"
]
}
],
"source": [
"dm.log.enable_rdkit_log()\n",
"Chem.MolFromSmiles('c1cccc1')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "invalid-northwest",
"metadata": {},
"outputs": [
{
"data": {
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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f565d6845d0>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = Chem.MolFromSmiles('N#CCC1(CN(C1)S(=O)(=O)CC)n1ncc(c1)c1ncnc2c1cc[nH]2')\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "hundred-timer",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol.GetNumConformers()"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "alone-timeline",
"metadata": {},
"outputs": [],
"source": [
"mol3d = dm.conformers.generate(mol)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "liberal-roman",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"50"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol3d.GetNumConformers()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "numerous-firewall",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.7.9"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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