{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem import rdChemReactions\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from rdkit.Chem import Draw\n",
"IPythonConsole.ipython_useSVG=True"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"intra_rxn = AllChem.ReactionFromSmarts('([C:1][C:2](=[O:6])[O:3].[N:4][C:5])>>[C:1][C:2](=[O:6])[N:4][C:5]')\n",
"inter_rxn = AllChem.ReactionFromSmarts('[C:1][C:2](=[O:6])[O:3].[N:4][C:5]>>[C:1][C:2](=[O:6])[N:4][C:5]')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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ggQcAuLq6RkREVJaXq7xrRMplZ2fv2bPH/OdmGsTSHSLSZINER0f/9a9/NRqNNtuTu/vf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\n+X+hqYmJtbTrGwAAAABJRU5ErkJggg==\n",
"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"intra_rxn"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"inter_rxn"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"acid = Chem.MolFromSmiles('CC(=O)O')\n",
"amine = Chem.MolFromSmiles('NC')\n",
"aminoacid = Chem.MolFromSmiles('N(C)CCC(O)CC(=O)O')\n",
"combmol = Chem.MolFromSmiles(\"CC(=O)O.N1CCC(C)1\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAABmJLR0QA/wD/AP+gvaeTAAANU0lE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\nAElFTkSuQmCC\n",
"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"inter_rxn.RunReactants([acid, amine])[0][0]"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ps = intra_rxn.RunReactants([aminoacid])\n",
"Draw.MolsToGridImage([ aminoacid, ps[0][0]])"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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Zt28fgF/84hcOjtmwYQOAt956y21Veb7q6urk5GQ/Pz8A/fv3//TTT/U7WECG6upqk8mk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\nRK5CYII=\n",
"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Intra reaction can not represent with inter molecular reactoin query\n",
"inter_rxn.RunReactant(aminoacid,0)[0][0]"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"#inra moleclar query works fine\n",
"intra_rxn.RunReactant(aminoacid,0)[0][0]"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# paired molecular object also works but get two molecules as one object\n",
"intra_rxn.RunReactant(combmol,0)[0][0]"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"def sepMol(mol):\n",
" smi_list = Chem.MolToSmiles(mol).split('.')\n",
" mols = [ Chem.MolFromSmiles(smi) for smi in smi_list]\n",
" return mols"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2\n"
]
}
],
"source": [
"ms = sepMol(combmol)\n",
"print(len(ms))\n",
"ms.append(intra_rxn.RunReactant(combmol,0)[0][0])"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Draw.MolsToGridImage(ms, molsPerRow=1)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [default]",
"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": "3.5.4"
}
},
"nbformat": 4,
"nbformat_minor": 1
}