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ptosco/BondStereo.ipynb

Created September 9, 2016 22:37
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BondStereo.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import sys\n",
"import os\n",
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"m = Chem.MolFromSmiles('[C@H](Cl)(Br)(F)')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAJ/UlEQVR4nO3df0zV9R7H8ddBIyGg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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x1c3945de8f0>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"m"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"AllChem.Compute2DCoords(m)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"mb = Chem.MolToMolBlock(m, includeStereo = True)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
" RDKit 2D\n",
"\n",
" 4 3 0 0 0 0 0 0 0 0999 V2000\n",
" -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2990 0.7500 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.0000 -1.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.2990 0.7500 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 1 0\n",
" 1 3 1 0\n",
" 1 4 1 6\n",
"M END\n",
"\n"
]
}
],
"source": [
"print(mb)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAKA0lEQVR4nO3df0zV9R7H8ddBI1Gg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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x1c394848670>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.MolFromMolBlock(mb)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"mbWithParity = mb.replace('C 0 0 0', 'C 0 0 1')"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAKA0lEQVR4nO3df0zV9R7H8ddBI1Gg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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x1c3948488a0>"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.MolFromMolBlock(mbWithParity)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"mbWithParityWithoutBondStereo = mbWithParity.replace('1 4 1 6', '1 4 1 0')"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAYAAABNcIgQAAAHyElEQVR4nO3df6jV9R3H8dfJLC23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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x1c394848e90>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.MolFromMolBlock(mbWithParityWithoutBondStereo)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"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": "3.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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