{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import numpy as np"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from IPython.display import SVG"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import rdkit\n",
"from rdkit import Chem, Geometry\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem.Draw import IPythonConsole, rdMolDraw2D"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"def draw_in_scale(mol):\n",
" \"\"\"Draw molecules with fixed bond length\"\"\"\n",
" mc = Chem.Mol(mol.ToBinary())\n",
" AllChem.Compute2DCoords(mc)\n",
" \n",
" coords = mc.GetConformer(-1).GetPositions()\n",
" \n",
" # if the margin +/-1 is removed linear molecules are broken\n",
" min_p = Geometry.Point2D(*coords.min(0)[:2] - 1)\n",
" max_p = Geometry.Point2D(*coords.max(0)[:2] + 1)\n",
" \n",
" dpa = 50\n",
" # try to catch 0's with max()\n",
" w = int(dpa * (max_p.x - min_p.x)) + 1\n",
" h = int(dpa * (max_p.y - min_p.y)) + 1\n",
" #print(w, h)\n",
" \n",
" drawer = rdMolDraw2D.MolDraw2DSVG(max(w, dpa), max(h, dpa))\n",
" \n",
" drawer.SetScale(w, h, min_p, max_p)\n",
" \n",
" \n",
" drawer.DrawMolecule(mc)\n",
" drawer.FinishDrawing()\n",
" img = drawer.GetDrawingText()\n",
" return SVG(img.replace('svg:', '')) "
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": false
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('C(CC(C(=O)O-*)N-*)CN=C(N)N'))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('C(=O)O'))"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('C(N)(N)=N'))"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O'))"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('NC1=NC=NC2=C1N=C[NH]2'))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('C(=O)'))"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"draw_in_scale(Chem.MolFromSmiles('C-C#C-C'))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [conda root]",
"language": "python",
"name": "conda-root-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": "3.5.2"
}
},
"nbformat": 4,
"nbformat_minor": 1
}