{
"cells": [
{
"cell_type": "code",
"execution_count": 343,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"from collections import namedtuple\n",
"\n",
"from rdkit import Chem\n",
"from rdkit.Chem import rdDepictor\n",
"from rdkit.Chem.Draw import rdMolDraw2D\n",
"from rdkit.Chem.Draw import MolsToGridImage, _MolsToGridSVG\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from IPython.display import SVG"
]
},
{
"cell_type": "code",
"execution_count": 344,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"IPythonConsole.kekulizeStructures = False # Does not propagate to MolsToGridimage\n",
"Mol = namedtuple('Mol', ['RDK_mol', 'description'])"
]
},
{
"cell_type": "code",
"execution_count": 352,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [],
"source": [
"mols = []\n",
"#mols.append(Mol(Chem.MolFromSmiles('C12C3C1C23'), 'tetrahedrane'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('C12-C3-C-1-C-2-3'), 'tetrahedrane expl bonds'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*12-*3-*-1-*-2-3'), 'tetrahedrane expl bonds dummy atoms'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*12:*3:*:1-*-2-3'), 'tetrahedrane 2 ar rings dummy atoms'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*12:*3:*:1:*:2-3'), 'tetrahedrane 1 ar ring dummy atoms'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('C1CC2CCCC3C2C(C1)CCC3'), 'perhydrophenalene'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c3c1cccc2\\C=C/Cc(c12)cc3'), 'phenalene stereo'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c3c1cccc2C=CCc(c12)cc3'), 'pheyalene no stereo'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c3c1cccc2CCCc(c12)cc3'), 'dihydrophenalene 2 ar, 1 al ring'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c3:c1:c:c:c:c2-C-C-C-c(:c:1:2):c:c:3'), 'dihydrophenalene w explicit bonds'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*3:*1:*:*:*:*2-*-*-*-*(:*:1:2):*:*:3'), 'phenalene expl bonds dummy atoms, 2 ar, 1 al ring '))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*3:*1:*:*:*:*2:*:*:*:*(:*:1:2):*:*:3'), 'phenalene expl bonds dummy atoms, 3 ar ring'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*3:*1-*-*-*-*2-*-*-*-*(:*:1-2):*:*:3'), 'pheyalene expl bonds dummy atoms, 1 ar, 2 al rings'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*3:*1:*:*:*:*2:*:*:[*H]:*(:*:1:2):*:*:3'), 'phenalene expl bonds dummy atoms 3 ar ring, * and [*H]'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c3:c1:c:c:c:c2:c:c:[nH]:c(:c:1:2):c:c:3'), 'phenalene expl bonds, c [nH], 3 ar rings'))\n",
"mols.append(Mol(Chem.MolFromSmiles('c1c[C+]1'), 'c1c[C+]1 cyclopropenium'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c1:c:[C+]:1'), 'cyclopropenium, explicit ar bonds'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('c1c[BH]1'), 'c1c[BH]1 borirene with [BH]'))\n",
"#mols.append(Mol(Chem.MolFromSmiles('*1:*:*:1'), '*1:*:*:1 cyclopropane skeleton, dummy atoms, explicit ar bonds'))\n"
]
},
{
"cell_type": "code",
"execution_count": 353,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 353,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"my_mols = [mol.RDK_mol for mol in mols]\n",
"my_descriptions = [mol.description for mol in mols]\n",
"type(gridImage)\n",
"gridImage = MolsToGridImage(my_mols, molsPerRow=2, subImgSize=(350, 250), legends=my_descriptions, useSVG=True, kekulize=False)\n",
"gridImage"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [conda env:rdk0]",
"language": "python",
"name": "conda-env-rdk0-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.12"
}
},
"nbformat": 4,
"nbformat_minor": 1
}