rdMolDraw2D_for_png_svg.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 一、绘制png：MolDraw2DCairo\n",
    "* 首先，创建一个Cairo drawer：Chem.Draw.rdMolDraw2D.MolDraw2DCairo(arg1, arg2)，同Chem.Draw.MolDraw2DCairo(arg1, arg2)\n",
    "arg1和arg2分别是绘制图像的长和宽\n",
    "* 接着，准备待绘制的分子：PrepareMolForDrawing(mol, kekulize=True ,addChiralHs=True, wedgeBonds=True, forceCoords=False)\n",
    "为了画出更好看的分子，需要进行一些预处理。可以处理的选项有：计算凯库勒式、手性中心补氢、手性中心添加楔形键、生成2D坐标\n",
    "* 开始绘制：DrawMolecule()\n",
    "* 结束绘制：FinishDrawing()\n",
    "* 输出结果：WriteDrawingText(file_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import rdMolDraw2D\n",
    "from IPython.display import Image"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles('[H][C@](C)(O)F')\n",
    "d = rdMolDraw2D.MolDraw2DCairo(400, 200)\n",
    "tmp = rdMolDraw2D.PrepareMolForDrawing(mol)\n",
    "d.DrawMolecule(mol)\n",
    "d.FinishDrawing()\n",
    "d.WriteDrawingText('data/rdMolDraw2D_1.png')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "execution_count": 3,
     "metadata": {
      "image/png": {
       "width": 250
      }
     },
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Image(filename = 'data/rdMolDraw2D_1.png', width=250)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 二、绘制svg：MolDraw2DSVG\n",
    "* 首先，创建一个svg drawer：Chem.Draw.rdMolDraw2D.MolDraw2DSVG(arg1, arg2)，同Chem.Draw.MolDraw2DSVG(arg1, arg2)\n",
    "arg1和arg2分别是绘制图像的长和宽\n",
    "* 接着，准备并绘制分子，两个步骤合二为一：PrepareAndDrawMolecule(drawer, mol, ...)\n",
    "* 结束绘制：FinishDrawing()\n",
    "* 获取结果：GetDrawingText(file_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles('c1ccccc1')\n",
    "d = rdMolDraw2D.MolDraw2DSVG(150, 150)\n",
    "rdMolDraw2D.PrepareAndDrawMolecule(d, mol)\n",
    "d.FinishDrawing()\n",
    "svg = d.GetDrawingText()\n",
    "with open('data/rdMolDraw2D_2.svg', 'w') as f:\n",
    "    f.write(svg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![title](data/rdMolDraw2D_2.svg)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 三、绘制设置(svg设置类似)\n",
    "* 实例化一个参数器：do = rdMolDraw2D.MolDrawOptions()\n",
    "* 将分子键的宽度设置为4：do.bondLineWidth = 4\n",
    "* 将分子键的长度设置为30：do.fixedBondLength = 30\n",
    "* 将分子顺时针旋转30度：do.rotate = 30\n",
    "* 修改原子标签：do.atomLabels[2] = 'OH group'\n",
    "* 应用设置：SetDrawOptions(do)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "execution_count": 5,
     "metadata": {
      "image/png": {
       "width": 250
      }
     },
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = Chem.MolFromSmiles('[H][C@](C)(O)F')\n",
    "d = rdMolDraw2D.MolDraw2DCairo(150, 150)\n",
    "do = rdMolDraw2D.MolDrawOptions()\n",
    "do.bondLineWidth = 4\n",
    "do.fixedBondLength = 30\n",
    "do.rotate = 30\n",
    "do.atomLabels[2] = 'OH group'\n",
    "d.SetDrawOptions(do)\n",
    "rdMolDraw2D.PrepareAndDrawMolecule(d, m)\n",
    "d.FinishDrawing()\n",
    "d.WriteDrawingText('data/rdMolDraw2D_3.png')\n",
    "Image(filename='data/rdMolDraw2D_3.png', width=250)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 参考：\n",
    "https://github.com/Yosuyo/canvas_server/blob/master/structure.py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def createImage(smiles):\n",
    "    from rdkit import Chem\n",
    "    from rdkit.Chem import rdDepictor\n",
    "    from rdkit.Chem.Draw import rdMolDraw2D\n",
    "    from rdkit.Chem.Draw.MolDrawing import DrawingOptions\n",
    "\n",
    "    mol = Chem.MolFromSmiles(smiles)  # Penicillin\n",
    "    rdDepictor.Compute2DCoords(mol)  # for generating conformer ID\n",
    "    # create a drawer container\n",
    "    drawer = rdMolDraw2D.MolDraw2DSVG(300, 300)\n",
    "    # define drawer options\n",
    "    drawer.drawOptions().updateAtomPalette({k: (0, 0, 0) for k in DrawingOptions.elemDict.keys()})\n",
    "    drawer.SetLineWidth(2)\n",
    "    drawer.SetFontSize(1.0)\n",
    "    #\n",
    "    drawer.DrawMolecule(mol)\n",
    "    drawer.FinishDrawing()\n",
    "    # generate and write the svg strings\n",
    "    svg = drawer.GetDrawingText().replace('svg:', '')\n",
    "    with open(\"static/images/svgs/\"+smiles+\".svg\", \"w\") as f:\n",
    "        f.write(svg)\n",
    "\n",
    "def createImageHighlight(smiles, smarts):\n",
    "    from rdkit import Chem\n",
    "    from rdkit.Chem import AllChem\n",
    "    from rdkit.Chem import rdDepictor\n",
    "    from rdkit.Chem.Draw import rdMolDraw2D\n",
    "    from rdkit.Chem.Draw.MolDrawing import DrawingOptions\n",
    "\n",
    "    mol = Chem.MolFromSmiles(smiles)\n",
    "    patt = Chem.MolFromSmarts(smarts)\n",
    "    hitatoms = mol.GetSubstructMatches(patt) #反応部位のアトムインデックス\n",
    "    hitatomslist = []\n",
    "    for x in hitatoms:\n",
    "        hitatomslist += x\n",
    "    hitatomsSum = tuple(hitatomslist)\n",
    "    tm = rdMolDraw2D.PrepareMolForDrawing(mol)\n",
    "    rdDepictor.Compute2DCoords(mol)  # for generating conformer ID\n",
    "    # create a drawer container\n",
    "    drawer = rdMolDraw2D.MolDraw2DSVG(300, 300)\n",
    "    # define drawer options\n",
    "    drawer.drawOptions().updateAtomPalette({k: (0, 0, 0) for k in DrawingOptions.elemDict.keys()})\n",
    "    drawer.SetLineWidth(2)\n",
    "    drawer.SetFontSize(1.0)\n",
    "    drawer.drawOptions().setHighlightColour((0.95,0.7,0.95)) #ハイライトの色指定\n",
    "    drawer.DrawMolecule(tm, highlightAtoms=hitatomsSum)\n",
    "    drawer.FinishDrawing()\n",
    "    # generate and write the svg strings\n",
    "    svg = drawer.GetDrawingText().replace('svg:', '')\n",
    "    with open(\"static/images/svgs/\"+smiles+\"_\"+smarts+\".svg\", \"w\") as f:\n",
    "        f.write(svg)"
   ]
  }
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