atom coordinates in images.ipynb

atom coordinates in images.ipynb

{
  "cells": [
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "from rdkit import Chem\nfrom rdkit import Geometry\nfrom rdkit.Chem import Draw\nfrom rdkit.Chem import rdDepictor",
      "execution_count": 6,
      "outputs": []
    },
    {
      "metadata": {
        "trusted": true
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      "cell_type": "code",
      "source": "m = Chem.MolFromSmiles('CCCOC')\nrdDepictor.Compute2DCoords(m)\nd2d = Draw.MolDraw2DCairo(350,300)\nd2d.DrawMolecule(m)\nd2d.FinishDrawing()\nd2d.WriteDrawingText('foo.png')\n\nconf = m.GetConformer()\n\n# we can get the draw location of atom coordinates directly with atom indices:\nfor i in range(m.GetNumAtoms()):\n    p = conf.GetAtomPosition(i)\n    drawp = d2d.GetDrawCoords(i)\n    print('Mol coords:','%.3f,%.3f'%(p.x,p.y),\"Draw coords: \",'%.3f,%.3f'%(drawp.x,drawp.y) )",
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "stream",
          "text": "Mol coords: -2.598,-0.300 Draw coords:  15.909,179.472\nMol coords: -1.299,0.450 Draw coords:  95.455,133.546\nMol coords: 0.000,-0.300 Draw coords:  175.000,179.472\nMol coords: 1.299,0.450 Draw coords:  254.545,133.546\nMol coords: 2.598,-0.300 Draw coords:  334.091,179.472\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "# it's also possible to translate arbitrary point locations from molecule coords into draw coords:\nprint(list(d2d.GetDrawCoords(Geometry.Point2D(0.0,0.0))))",
      "execution_count": 12,
      "outputs": [
        {
          "output_type": "stream",
          "text": "[174.99999999999997, 161.10164986855384]\n",
          "name": "stdout"
        }
      ]
    },
    {
      "metadata": {
        "trusted": true
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      "cell_type": "code",
      "source": "",
      "execution_count": null,
      "outputs": []
    }
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