draw_grid_with_drawOptions.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit.Chem import Draw, AllChem as Chem  # 面倒なのでAllChem\n",
    "from IPython.display import SVG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "data = [\n",
    "    ('c1ccccc1', [(1, 'X')]),\n",
    "    ('c1cnccc1', [(4, 'V')]),\n",
    "    ('c1cnccc1CCC', [(4, 'X'), (6, 'Y')]),\n",
    "    ('c1cnccc1NCC', [(4, 'Y'), (6, 'Z')]),\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def preprocess(smi):\n",
    "    mol = Chem.MolFromSmiles(smi)\n",
    "    Chem.Compute2DCoords(mol)\n",
    "    return mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "mols = [(preprocess(smi), hl) for smi, hl in data]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def ClearIntStringMap(m):\n",
    "    '''IntStringMapの中身を消す関数\n",
    "    drawer.drawOptions()が使い回されるので。'''\n",
    "    for kv in list(m):\n",
    "        del m[kv.key()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 前から2つでキャンバス全体のサイズを、残り2つで1つの分子のサイズを指定する。\n",
    "# 分子サイズの認識が甘いのでサイズを微調整する必要があり、多少つらい。\n",
    "drawer = Draw.MolDraw2DSVG(400, 200, 100, 100)\n",
    "\n",
    "# optをとり出しておく\n",
    "opt = drawer.drawOptions()\n",
    "\n",
    "for (mol, hl), (x, y) in zip(mols, [(0,0), (0,100), (150, 0), (150,100)]):\n",
    "    # SetOffsetで左上の座標を指定できる\n",
    "    drawer.SetOffset(x, y)\n",
    "    \n",
    "    # いったん消してから\n",
    "    ClearIntStringMap(opt.atomLabels)\n",
    "    \n",
    "    # 書く\n",
    "    for (i, v) in hl:\n",
    "        opt.atomLabels[i] = v\n",
    "\n",
    "    # 分子をSVGに書く\n",
    "    drawer.DrawMolecule(mol)\n",
    "    \n",
    "\n",
    "# </svg> 書く\n",
    "drawer.FinishDrawing()\n",
    "\n",
    "# 表示\n",
    "SVG(drawer.GetDrawingText())"
   ]
  }
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