{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Highlight atoms with a specific color using transparency"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import rdBase\n",
    "from rdkit import Chem\n",
    "# display molecules\n",
    "from rdkit.Chem import Draw\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from IPython.display import SVG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2018.09.1'"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdBase.rdkitVersion"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create an example molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "m = Chem.MolFromSmiles(\"O1CCCC1\") # tetrahydrofuran\n",
    "highlight=[0] # oxygen"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Use default colors for highlighting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7FC13E55B4A8>"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Draw.MolsToGridImage( [m],highlightAtomLists=[highlight])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Use user-defined color"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7FC13E571048>"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Draw.MolsToGridImage( [m],highlightAtomLists=[highlight], highlightAtomColors=[{0:(255,0,0)}]) # same result with RGB=(1,0,0)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The highlight masks the oxygen."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Try to apply some transparency"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7FC13E571550>"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Draw.MolsToGridImage( [m],highlightAtomLists=[highlight], highlightAtomColors=[{0:(255,0,0,50)}]) # same result with RGBA=(1,0,0,0.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The alpha setting is set by default, but I can't set it when defining my own atom color map.  \n",
    "What am I missing?"
   ]
  }
 ],
 "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": "3.6.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}