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vfscalfani/PubChem_dativeBonds.ipynb

Created February 8, 2020 21:46
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PubChem_dativeBonds.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Adding PubChem nonstandard dative bonds to a molfile"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"# See PUBCHEM_NONSTANDARDBOND\n",
"# https://pubchem.ncbi.nlm.nih.gov/upload/html/tags_substance.html\n",
"\n",
"from rdkit import Chem\n",
"from rdkit.Chem import Draw"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# define function to draw molecule with atom index (see RDKit Cookbook)\n",
"def molblock_with_atom_index(mol):\n",
" for atom in mol.GetAtoms():\n",
" # adding 1 to Idx to align with molfile atom block\n",
" atom.SetAtomMapNum(atom.GetIdx() +1) \n",
" return mol"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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GYAExBAuIIVhADMECYggWEEOwgBiCBcQQLCCGYAExBAuIIVhADMECYggWEEOwgBiCBcQQLCCGYAExBAuIIVhADMECYggWEEOwgBiCBcT4P9AFEN956BohAAAAAElFTkSuQmCC\n",
"text/plain": [
"<PIL.Image.Image image mode=RGB size=400x400 at 0x7F03C06F4E80>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Create the molecule from a molfile\n",
"# example from: Cassidy, S.J. Electron-deficient heterofluorene conjugated polymers and small molecules. \n",
"# Ph.D. Thesis, The University of Alabama, 2018.\n",
"\n",
"mol = Chem.MolFromMolBlock(\"\"\"\n",
" RDKit 2D\n",
"\n",
" 24 27 0 0 0 0 0 0 0 0999 V2000\n",
" 1.0344 -8.1310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.1491 -7.1273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.8373 -5.6601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.9520 -4.6564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.6401 -3.1891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.2135 -2.7256 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2135 -2.7256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.0000 -3.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.1568 -5.0991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.5271 -5.7092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.7406 -4.8275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.5838 -3.3357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.7548 -2.1855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.4430 -0.7182 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 4.5577 0.2855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 5.1814 -2.6490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 5.4933 -4.1162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 4.3786 -5.1199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 1 0\n",
" 2 3 1 0\n",
" 3 4 1 0\n",
" 4 5 2 0\n",
" 5 6 1 0\n",
" 6 7 1 0\n",
" 7 8 2 0\n",
" 8 9 1 0\n",
" 9 10 2 0\n",
" 10 11 1 0\n",
" 11 12 2 0\n",
" 12 13 1 0\n",
" 13 14 2 0\n",
" 14 15 1 0\n",
" 15 16 2 0\n",
" 16 17 1 0\n",
" 17 18 2 0\n",
" 5 19 1 0\n",
" 19 20 1 0\n",
" 20 21 1 0\n",
" 19 22 2 0\n",
" 22 23 1 0\n",
" 23 24 2 0\n",
" 24 4 1 0\n",
" 14 6 1 0\n",
" 12 7 1 0\n",
" 18 13 1 0\n",
"M END\"\"\")\n",
"molblock_with_atom_index(mol)\n",
"Chem.Draw.MolToImage(mol, size=(400, 400))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# We want a dative bond between Oxygen (index #2) and Boron (index #6).\n",
"# These index numbers correspond to the atom block lines (e.g., Boron is on line 6 of atom block).\n",
"\n",
"# now format the annotation: \n",
"\"\"\"\n",
"> <PUBCHEM_NONSTANDARDBOND>\n",
"2 6 5\n",
"\n",
"\"\"\"\n",
"\n",
"# This says: make a dative bond between atoms 2 and 6, with PubChem nonstandard bond 5 (which is dative)\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# final edited molfile:\n",
"\n",
"\"\"\"\n",
" RDKit 2D\n",
"\n",
" 24 27 0 0 0 0 0 0 0 0999 V2000\n",
" 1.0344 -8.1310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.1491 -7.1273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.8373 -5.6601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.9520 -4.6564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.6401 -3.1891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.2135 -2.7256 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2135 -2.7256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.0000 -3.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.1568 -5.0991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.5271 -5.7092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.7406 -4.8275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.5838 -3.3357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.7548 -2.1855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.4430 -0.7182 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 4.5577 0.2855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 5.1814 -2.6490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 5.4933 -4.1162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 4.3786 -5.1199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 1 0\n",
" 2 3 1 0\n",
" 3 4 1 0\n",
" 4 5 2 0\n",
" 5 6 1 0\n",
" 6 7 1 0\n",
" 7 8 2 0\n",
" 8 9 1 0\n",
" 9 10 2 0\n",
" 10 11 1 0\n",
" 11 12 2 0\n",
" 12 13 1 0\n",
" 13 14 2 0\n",
" 14 15 1 0\n",
" 15 16 2 0\n",
" 16 17 1 0\n",
" 17 18 2 0\n",
" 5 19 1 0\n",
" 19 20 1 0\n",
" 20 21 1 0\n",
" 19 22 2 0\n",
" 22 23 1 0\n",
" 23 24 2 0\n",
" 24 4 1 0\n",
" 14 6 1 0\n",
" 12 7 1 0\n",
" 18 13 1 0\n",
"M END\n",
"\n",
"> <PUBCHEM_NONSTANDARDBOND>\n",
"2 6 5\n",
"\n",
"$$$$\n",
"\"\"\"\n"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python [conda env:my-rdkit_2019_09_2-env] *",
"language": "python",
"name": "conda-env-my-rdkit_2019_09_2-env-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.10"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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