Example: Structural alignment with biopython

biopython_qcpsuperimposer.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# `biopython`\n",
    "## Structural alignment using Quaternion Characteristic Polynomial (QCP)\n",
    "\n",
    "https://biopython.org/docs/dev/api/Bio.PDB.QCPSuperimposer.html"
   ]
  },
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   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "\n",
    "from Bio.PDB import QCPSuperimposer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Example coordinates\n",
    "reference_coords = np.array([[0, 0, 0], [1, 1, 1]])\n",
    "coords = np.array([[1, 0, 0], [3, 1, 1]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Get untransformed coordinate sets:\n",
      "Reference coordinates\n",
      "[[0 0 0]\n",
      " [1 1 1]]\n",
      "\n",
      "Mobile coordinates\n",
      "[[1 0 0]\n",
      " [3 1 1]]\n",
      "\n",
      "Get tranformed coordinate set\n",
      "[[-0.5  0.   0. ]\n",
      " [ 1.5  1.   1. ]]\n",
      "\n",
      "Rotation matrix\n",
      "[[1. 0. 0.]\n",
      " [0. 1. 0.]\n",
      " [0. 0. 1.]]\n",
      "\n",
      "Translation\n",
      "[-1.5  0.   0. ]\n",
      "\n",
      "RMS\n",
      "0.3587194598822338\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Initialize class\n",
    "superimposer = QCPSuperimposer.QCPSuperimposer()\n",
    "\n",
    "# Set the coordinates to be superimposed\n",
    "superimposer.set(reference_coords, coords)\n",
    "\n",
    "# Superimpose the coordinate sets\n",
    "superimposer.run()\n",
    "\n",
    "print(f'Get untransformed coordinate sets:')\n",
    "print(f'Reference coordinates\\n{reference_coords}\\n')\n",
    "print(f'Mobile coordinates\\n{coords}\\n')\n",
    "print(f'Get tranformed coordinate set\\n{superimposer.get_transformed()}\\n')\n",
    "print(f'Rotation matrix\\n{superimposer.get_rotran()[0]}\\n')\n",
    "print(f'Translation\\n{superimposer.get_rotran()[1]}\\n')\n",
    "print(f'RMS\\n{superimposer.get_rms()}\\n')"
   ]
  }
 ],
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