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iwatobipen/jazzy_demo.ipynb

Created February 4, 2023 11:25
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jazzy_demo.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "f85dcda3",
"metadata": {},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from rdkit.Chem import Draw\n",
"#import jazzy!\n",
"from jazzy.api import molecular_vector_from_smiles\n",
"from jazzy.api import atomic_map_from_smiles\n",
"from jazzy.api import atomic_tuples_from_smiles\n",
"from jazzy.api import deltag_from_smiles\n",
"from jazzy.api import atomic_strength_vis_from_smiles\n",
"from jazzy.visualisation import depict_strengths\n",
"\n",
"import pandas as pd\n",
"from IPython.display import SVG"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "0b18839a",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f75f17e4a60>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# ref https://drughunter.com/wp-content/uploads/2023/01/DH-MOTM-Poster-December-2022-R4.pdf\n",
"smi = 'CC(C)C1=CC(=NNC1=O)OC2=C(C=C(C=C2Cl)N3C(=O)NC(=O)C(=N3)C#N)Cl'\n",
"mol = Chem.MolFromSmiles(smi)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "5319eea1",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'sdc': 6.5481,\n",
" 'sdx': 2.4184,\n",
" 'sa': 5.544,\n",
" 'dga': -14.7676,\n",
" 'dgp': -108.2574,\n",
" 'dgtot': -107.0211}"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol_vec = molecular_vector_from_smiles(smi)\n",
"mol_vec"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "6772b671",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"-107.0211"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Gibbs Free Energy of Hydration (kJ/mol)\n",
"deltag_from_smiles(smi)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "57d1c7ff",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[(('z', 6),\n",
" ('q', 0),\n",
" ('eeq', -0.2051),\n",
" ('alp', 7.6489),\n",
" ('hyb', 'sp3'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', -0.0689),\n",
" ('alp', 7.1388),\n",
" ('hyb', 'sp3'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', -0.216),\n",
" ('alp', 7.6677),\n",
" ('hyb', 'sp3'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.0062),\n",
" ('alp', 8.8627),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', -0.0637),\n",
" ('alp', 9.1222),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.2412),\n",
" ('alp', 8.0256),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 7),\n",
" ('q', 0),\n",
" ('eeq', -0.2203),\n",
" ('alp', 7.6447),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 1),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.507)),\n",
" (('z', 7),\n",
" ('q', 0),\n",
" ('eeq', -0.3088),\n",
" ('alp', 7.6528),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 1),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.5246)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.2956),\n",
" ('alp', 7.8563),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 8),\n",
" ('q', 0),\n",
" ('eeq', -0.3888),\n",
" ('alp', 6.205),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 2),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.7416)),\n",
" (('z', 8),\n",
" ('q', 0),\n",
" ('eeq', -0.3129),\n",
" ('alp', 5.9074),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 2),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.5128)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.1446),\n",
" ('alp', 8.3619),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.0426),\n",
" ('alp', 8.7168),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', -0.0348),\n",
" ('alp', 9.0154),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.1067),\n",
" ('alp', 8.4922),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', -0.0497),\n",
" ('alp', 9.0724),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.0396),\n",
" ('alp', 8.7274),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 17),\n",
" ('q', 0),\n",
" ('eeq', -0.0607),\n",
" ('alp', 15.2166),\n",
" ('hyb', 'sp3'),\n",
" ('num_lp', 3),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0952)),\n",
" (('z', 7),\n",
" ('q', 0),\n",
" ('eeq', -0.1814),\n",
" ('alp', 7.2287),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 1),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.321)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.3956),\n",
" ('alp', 7.551),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 8),\n",
" ('q', 0),\n",
" ('eeq', -0.3793),\n",
" ('alp', 6.1781),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 2),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.689)),\n",
" (('z', 7),\n",
" ('q', 0),\n",
" ('eeq', -0.4492),\n",
" ('alp', 8.1615),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 1),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.5083)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.3131),\n",
" ('alp', 7.8046),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 8),\n",
" ('q', 0),\n",
" ('eeq', -0.3331),\n",
" ('alp', 6.0488),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 2),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.5697)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.1737),\n",
" ('alp', 8.2605),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 7),\n",
" ('q', 0),\n",
" ('eeq', -0.2542),\n",
" ('alp', 7.7591),\n",
" ('hyb', 'sp2'),\n",
" ('num_lp', 1),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.4759)),\n",
" (('z', 6),\n",
" ('q', 0),\n",
" ('eeq', 0.1843),\n",
" ('alp', 8.3997),\n",
" ('hyb', 'sp'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 7),\n",
" ('q', 0),\n",
" ('eeq', -0.3112),\n",
" ('alp', 7.5932),\n",
" ('hyb', 'sp'),\n",
" ('num_lp', 1),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.55)),\n",
" (('z', 17),\n",
" ('q', 0),\n",
" ('eeq', -0.0421),\n",
" ('alp', 15.1743),\n",
" ('hyb', 'sp3'),\n",
" ('num_lp', 3),\n",
" ('sdc', 0.0),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0489)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1275),\n",
" ('alp', 1.9494),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.5124),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1303),\n",
" ('alp', 1.9384),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.5288),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1155),\n",
" ('alp', 2.0093),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.4442),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1509),\n",
" ('alp', 1.8405),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.7447),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1173),\n",
" ('alp', 1.9999),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.4412),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1384),\n",
" ('alp', 1.898),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.5607),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.125),\n",
" ('alp', 1.9616),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.4847),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1263),\n",
" ('alp', 1.9563),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.7445),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.2661),\n",
" ('alp', 1.4222),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 1.1324),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.1798),\n",
" ('alp', 1.7182),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 1.0994),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.166),\n",
" ('alp', 1.7753),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.9875),\n",
" ('sdx', 0.0),\n",
" ('sa', 0.0)),\n",
" (('z', 1),\n",
" ('q', 0),\n",
" ('eeq', 0.2939),\n",
" ('alp', 1.3403),\n",
" ('hyb', 'unspecified'),\n",
" ('num_lp', 0),\n",
" ('sdc', 0.0),\n",
" ('sdx', 1.286),\n",
" ('sa', 0.0))]"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"#Atomic Features\n",
"\"\"\"\n",
"e atomic number (z), \n",
"formal charge (q), \n",
"partial charge (eeq), \n",
"atomic-charge dependent dynamic atomic polarizabilities (alp),\n",
"hybridisation (hyb),\n",
"number of lone pairs (num_lp), C-H donor strength (sdc),\n",
"X-H donor strength (sdx) where X includes any non-carbon atoms,\n",
"acceptor strength (sda)\n",
"\"\"\"\n",
"atomic_tuples_from_smiles(smi)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "6b512b95",
"metadata": {},
"outputs": [
{
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],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"#Hydrogen-bond Strength Depiction\n",
"\n",
"svg = atomic_strength_vis_from_smiles(smi,\n",
" flatten_molecule=True,\n",
" )\n",
"SVG(svg)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "0bf411ad",
"metadata": {},
"outputs": [
{
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"\n",
"svg = atomic_strength_vis_from_smiles(smi,\n",
" flatten_molecule=True,\n",
" highlight_atoms=True,\n",
" ignore_sa=False,\n",
" ignore_sdc=False,\n",
" ignore_sdx=False,\n",
" rounding_digits=2,\n",
" sdc_threshold=0.7,\n",
" sdx_threshold=0.7\n",
" )\n",
"SVG(svg)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "ef58d6e6",
"metadata": {},
"outputs": [
{
"data": {
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" 27: {'z': 7,\n",
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" 28: {'z': 17,\n",
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" 'hyb': 'unspecified',\n",
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" 'hyb': 'unspecified',\n",
" 'num_lp': 0,\n",
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" 'num_lp': 0,\n",
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" 'num_lp': 0,\n",
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" 'sdx': 1.1596,\n",
" 'sa': 0.0},\n",
" 38: {'z': 1,\n",
" 'q': 0,\n",
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" 'hyb': 'unspecified',\n",
" 'num_lp': 0,\n",
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" 'sa': 0.0},\n",
" 39: {'z': 1,\n",
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" 'sdx': 0.0,\n",
" 'sa': 0.0},\n",
" 40: {'z': 1,\n",
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" 'sdc': 0.0,\n",
" 'sdx': 1.3163,\n",
" 'sa': 0.0}}"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from jazzy.core import rdkit_molecule_from_smiles, kallisto_molecule_from_rdkit_molecule\n",
"from jazzy.core import get_covalent_atom_idxs, get_charges_from_kallisto_molecule, calculate_polar_strength_map\n",
"rdkit_mol = rdkit_molecule_from_smiles(smi, minimisation_method=\"MMFF94\")\n",
"kallisto_mol = kallisto_molecule_from_rdkit_molecule(rdkit_mol)\n",
"atoms_and_nbrs = get_covalent_atom_idxs(rdkit_mol)\n",
"kallisto_charges = get_charges_from_kallisto_molecule(kallisto_mol, charge=0)\n",
"calculate_polar_strength_map(rdkit_mol, kallisto_mol, atoms_and_nbrs, kallisto_charges)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "593a4eaf",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"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": "3.9.15"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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