Horizontal_display_SVGmols.ipynb

{
 "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 = '<div style=\"float: left; padding: 10px;\">{0}</div>'\n",
    "        return \"\\n\".join(template.format(arg)\n",
    "                         for arg in self.args)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
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     },
     "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": [
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       "<path class=\"bond-14\" d=\"M 150.143,53.2049 L 157.456,47.8803\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-15\" d=\"M 142.83,58.5294 L 122.239,43.5858\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-16\" d=\"M 122.239,43.5858 L 130.075,19.3871\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-17\" d=\"M 130.075,19.3871 L 155.52,19.3668\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-18\" d=\"M 155.52,19.3668 L 158.423,28.281\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-18\" d=\"M 158.423,28.281 L 161.325,37.1953\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"middle\" x=\"167.111\" y=\"170.034\"><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"start\" x=\"162.87\" y=\"182.754\"><tspan>H</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"middle\" x=\"167.075\" y=\"128.877\"><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"end\" x=\"103.07\" y=\"136.789\"><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"middle\" x=\"120.891\" y=\"174.934\"><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"end\" x=\"80.9418\" y=\"175.16\"><tspan>H</tspan><tspan style=\"baseline-shift:sub;font-size:9px;\">2</tspan><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#FF0000\" text-anchor=\"end\" x=\"125.498\" y=\"98.613\"><tspan>O</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#FF0000\" text-anchor=\"start\" x=\"158.728\" y=\"45.4633\"><tspan>O</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"188.409\" y=\"148.96\"><tspan>0</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"176.57\" y=\"178.061\"><tspan>1</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"139.164\" y=\"156.574\"><tspan>2</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"139.152\" y=\"141.424\"><tspan>3</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"170.996\" y=\"116.299\"><tspan>4</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"120.86\" y=\"136.296\"><tspan>5</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"87.8083\" y=\"129.96\"><tspan>6</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"109.861\" y=\"155.383\"><tspan>7</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"120.902\" y=\"187.177\"><tspan>8</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"76.84\" y=\"187.212\"><tspan>9</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"120.819\" y=\"85.4159\"><tspan>10</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"153.872\" y=\"91.7462\"><tspan>11</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"154.169\" y=\"65.7249\"><tspan>12</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"110.145\" y=\"48.9569\"><tspan>13</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"126.332\" y=\"15.6761\"><tspan>14</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"159.255\" y=\"15.6497\"><tspan>15</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000\" text-anchor=\"middle\" x=\"181.548\" y=\"50.8674\"><tspan>16</tspan></text>\n",
       "</svg>"
      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "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": [
    {
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       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"end\" x=\"110.797\" y=\"135.662\"><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"middle\" x=\"128.478\" y=\"173.506\"><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF\" text-anchor=\"end\" x=\"88.8436\" y=\"173.731\"><tspan>H</tspan><tspan style=\"baseline-shift:sub;font-size:9px;\">2</tspan><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#FF0000\" text-anchor=\"end\" x=\"133.048\" y=\"97.7877\"><tspan>O</tspan></text>\n",
       "<text dominant-baseline=\"central\" style=\"font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#FF0000\" text-anchor=\"start\" x=\"166.016\" y=\"45.0572\"><tspan>O</tspan></text>\n",
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      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "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": {
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      "text/plain": [
       "<IPython.core.display.SVG object>"
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     },
     "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": [
    {
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       "<text dominant-baseline=\"central\" text-anchor=\"start\" x='162.87' y='182.754' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF' ><tspan>H</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='167.075' y='128.877' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF' ><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"end\" x='103.07' y='136.789' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF' ><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='120.891' y='174.934' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF' ><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"end\" x='80.9418' y='175.16' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#0000FF' ><tspan>H</tspan><tspan style='baseline-shift:sub;font-size:9px;'>2</tspan><tspan>N</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"end\" x='125.498' y='98.613' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#FF0000' ><tspan>O</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"start\" x='158.728' y='45.4633' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#FF0000' ><tspan>O</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='188.409' y='148.96' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>0</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='176.57' y='178.061' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>1</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='139.164' y='156.574' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>2</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='139.152' y='141.424' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>3</tspan></text>\n",
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       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='120.86' y='136.296' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>5</tspan></text>\n",
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       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='109.861' y='155.383' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>7</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='120.902' y='187.177' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>8</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='76.84' y='187.212' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>9</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='120.819' y='85.4159' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>10</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='153.872' y='91.7462' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>11</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='154.169' y='65.7249' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>12</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='110.145' y='48.9569' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>13</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='126.332' y='15.6761' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>14</tspan></text>\n",
       "<text dominant-baseline=\"central\" text-anchor=\"middle\" x='159.255' y='15.6497' style='font-size:9px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000' ><tspan>15</tspan></text>\n",
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   "source": [
    "HorizontalDisplay(text1, text2, text3, text4)"
   ]
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   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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