view_dna.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "id": "initial_id",
   "metadata": {
    "collapsed": true,
    "ExecuteTime": {
     "end_time": "2024-12-02T20:06:29.999443Z",
     "start_time": "2024-12-02T20:06:28.606817Z"
    }
   },
   "source": [
    "import py3Dmol\n",
    "from IPython.display import display\n",
    "from helix_drawer import calculate_helix_coordinates, parse_ancestry_dna, load_config, DNAConfig\n",
    "\n",
    "# Initialize viewer with larger dimensions to accommodate legend\n",
    "viewer = py3Dmol.view(width=1000, height=800)\n",
    "display(viewer)\n",
    "\n",
    "# Load data\n",
    "config = load_config()\n",
    "file_path = config['dna_file_path']\n",
    "base_pairs = config.get('base_pairs', 200)\n",
    "dna_data = parse_ancestry_dna(file_path)\n",
    "\n",
    "# Add DNA structure for both strands\n",
    "coords = calculate_helix_coordinates(base_pairs)\n",
    "for i in range(base_pairs):\n",
    "    # First strand\n",
    "    viewer.addSphere({\n",
    "        'center': {'x': coords[i,0], 'y': coords[i,1], 'z': coords[i,2]},\n",
    "        'radius': 0.5,\n",
    "        'color': DNAConfig.BASE_COLORS_3D[dna_data[i][3][0]]\n",
    "    })\n",
    "    # Second strand\n",
    "    viewer.addSphere({\n",
    "        'center': {'x': coords[i,3], 'y': coords[i,4], 'z': coords[i,5]},\n",
    "        'radius': 0.5,\n",
    "        'color': DNAConfig.BASE_COLORS_3D[dna_data[i][3][1]]\n",
    "    })\n",
    "    # Add connecting cylinder between base pairs\n",
    "    viewer.addCylinder({\n",
    "        'start': {'x': coords[i,0], 'y': coords[i,1], 'z': coords[i,2]},\n",
    "        'end': {'x': coords[i,3], 'y': coords[i,4], 'z': coords[i,5]},\n",
    "        'radius': 0.2,\n",
    "        'color': 'gray'\n",
    "    })\n",
    "\n",
    "# Add legend\n",
    "viewer.addLabel(\"Adenine (A)\", {'position': {'x': -10, 'y': 0, 'z': 0}, 'backgroundColor': '#FF0000', 'fontColor': 'white'})\n",
    "viewer.addLabel(\"Thymine (T)\", {'position': {'x': -10, 'y': -2, 'z': 0}, 'backgroundColor': '#0000FF', 'fontColor': 'white'})\n",
    "viewer.addLabel(\"Cytosine (C)\", {'position': {'x': -10, 'y': -4, 'z': 0}, 'backgroundColor': '#00FF00', 'fontColor': 'black'})\n",
    "viewer.addLabel(\"Guanine (G)\", {'position': {'x': -10, 'y': -6, 'z': 0}, 'backgroundColor': '#FFFF00', 'fontColor': 'black'})\n",
    "\n",
    "viewer.zoomTo()\n",
    "viewer.update()\n"
   ],
   "outputs": [
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       "<py3Dmol.view at 0x30ba98970>"
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     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2024-12-02 21:06:28,619 - INFO - Loading configuration from config/settings.yaml\n",
      "2024-12-02 21:06:28,621 - INFO - Parsing DNA data from test/large_test_ancestry_data.txt\n"
     ]
    },
    {
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   "source": "",
   "id": "5d04273bb28ab14f"
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