alignto bug

bug.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "from MDAnalysisTests.datafiles import PDB, XTC\n",
    "import MDAnalysis as mda\n",
    "from MDAnalysis.analysis import align, rms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "u = mda.Universe(PDB, XTC)\n",
    "ref = mda.Universe(PDB)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Make the selections for alignment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "ref_res1 = ref.residues[1].atoms\n",
    "res1 = u.residues[1].atoms\n",
    "\n",
    "res1 = u.residues[1].atoms\n",
    "res2 = u.residues[2].atoms"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now we establish some the coordiantes before the alignment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[53.60167  40.359165 33.607082]\n",
      "[54.53948  44.632107 27.00737 ]\n",
      "[55.88809  45.152588 35.58592 ]\n"
     ]
    }
   ],
   "source": [
    "u.trajectory[8]\n",
    "print(res1.centroid())\n",
    "print(res2.centroid())\n",
    "print(ref_res1.centroid())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(0.7390031832695271, 0.3307034032341618)"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "align.alignto(res1, ref_res1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The  centroid of res2 has changed as well. According to the docs these coordinates shouldn't have been updated."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[56.212128 47.95514  28.18765 ]\n"
     ]
    }
   ],
   "source": [
    "print(res2.centroid())"
   ]
  }
 ],
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