{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"from rdkit import Chem\n",
"from rdkit.Chem import rdBase\n",
"from rdkit.Chem import RDConfig\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem import Draw\n",
"from rdkit.Chem.Draw import rdMolDraw2D\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from rdkit.Chem import rdDepictor\n",
"import rdkit\n",
"from IPython.display import SVG\n",
"\n",
"from rdkit.Chem import ChemicalFeatures\n",
"fdef = os.path.join(RDConfig.RDContribDir, 'M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef')\n",
"ffact = ChemicalFeatures.BuildFeatureFactory(fdef)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'2020.03.1'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"rdDepictor.SetPreferCoordGen(True)\n",
"rdkit.__version__"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"sdf = os.path.join(RDConfig.RDDocsDir, 'Book/data/cdk2.sdf')\n",
"mols = [m for m in Chem.SDMolSupplier(sdf)]\n",
"for m in mols:\n",
" AllChem.Compute2DCoords(m)\n",
"mol1 = mols[1]"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"# the code is bollowed from following url.\n",
"# https://bit.ly/3aTUBCU\n",
"class HorizontalDisplay:\n",
" def __init__(self, *args):\n",
" self.args = args\n",
"\n",
" def _repr_html_(self):\n",
" template = '{0}
'\n",
" return \"\\n\".join(template.format(arg)\n",
" for arg in self.args)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"d2d = rdMolDraw2D.MolDraw2DSVG(250, 200)\n",
"d2d.DrawMolecule(mol1)\n",
"d2d.FinishDrawing()\n",
"text1 = d2d.GetDrawingText()\n",
"SVG(d2d.GetDrawingText())"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"d2d = rdMolDraw2D.MolDraw2DSVG(250, 200)\n",
"d2d.drawOptions().addAtomIndices = True\n",
"d2d.DrawMolecule(mol1)\n",
"d2d.FinishDrawing()\n",
"text2 = d2d.GetDrawingText()\n",
"SVG(d2d.GetDrawingText())"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"from collections import defaultdict\n",
"feats = ffact.GetFeaturesForMol(mol1)\n",
"colors = {'SingleAtomDonor':(1,0.5,0.5),\n",
" 'SingleAtomAcceptor':(0.5,0.5,1),\n",
" 'BasicGroup':(0,1,1),\n",
" 'Arom6':(1,0.8,0.5),\n",
" 'Hphobe':(0.7,0.7,0.3)}"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"atomHighlighs = defaultdict(list)\n",
"highlightRads = {}\n",
"for feat in feats:\n",
" if feat.GetType() in colors:\n",
" clr = colors[feat.GetType()]\n",
" for aid in feat.GetAtomIds():\n",
" atomHighlighs[aid].append(clr)\n",
" highlightRads[aid] = 0.4"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"d2d = rdMolDraw2D.MolDraw2DSVG(250, 200)\n",
"d2d.DrawMoleculeWithHighlights(mol1, '', dict(atomHighlighs), {}, highlightRads, {})\n",
"d2d.drawOptions().addAtomIndices = True\n",
"d2d.FinishDrawing()\n",
"text3 = d2d.GetDrawingText()\n",
"SVG(d2d.GetDrawingText())"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"d2d = rdMolDraw2D.MolDraw2DSVG(250, 200)\n",
"dos = d2d.drawOptions()\n",
"dos.atomHighlightsAreCricle = True\n",
"dos.fillHighlights = False\n",
"d2d.DrawMoleculeWithHighlights(mol1, '', dict(atomHighlighs), {}, highlightRads, {})\n",
"d2d.drawOptions().addAtomIndices = True\n",
"d2d.FinishDrawing()\n",
"text4 = d2d.GetDrawingText()\n",
"SVG(d2d.GetDrawingText())"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"
\n",
"
\n",
"
\n",
"
\n",
"
\n",
"
\n",
"
\n",
"