OpenCADD's structure object has no chain IDs - why?

opencadd_structure_no_chainids.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "8f0581b0-dbe3-4666-8c6a-f71b86003651",
   "metadata": {},
   "source": [
    "## MDAnalysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "6382efba-5b4b-401a-ad44-8505d6e27874",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2.0.0'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import MDAnalysis\n",
    "MDAnalysis.__version__"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "850e481c-ae32-4fa5-b129-d30c43cf1ecd",
   "metadata": {},
   "outputs": [],
   "source": [
    "from MDAnalysis import Universe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "53ad98d6-592a-4e03-a167-b6c3e392d03f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2021-10-27 08:22:08--  https://files.rcsb.org/download/4WSQ.pdb\n",
      "Resolving files.rcsb.org (files.rcsb.org)... 128.6.158.49\n",
      "Connecting to files.rcsb.org (files.rcsb.org)|128.6.158.49|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: unspecified [application/octet-stream]\n",
      "Saving to: '4WSQ.pdb.2'\n",
      "\n",
      "4WSQ.pdb.2              [    <=>             ] 867.43K  1.27MB/s    in 0.7s    \n",
      "\n",
      "2021-10-27 08:22:09 (1.27 MB/s) - '4WSQ.pdb.2' saved [888246]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://files.rcsb.org/download/4WSQ.pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "6116c6f3-5b27-4dde-872d-f727ad0eef6f",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<Universe with 5271 atoms>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u = Universe(\"4WSQ.pdb\")\n",
    "u"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "586530cf-b2f0-4f90-9816-351340a75aee",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AtomGroup with 2664 atoms>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u.select_atoms(\"chainID A\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "1707bc39-7bcc-4139-95d0-dd0f26b96446",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['A', 'A', 'A', ..., 'B', 'B', 'B'], dtype=object)"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u.atoms.segids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f85d1fb5-3239-417c-90a9-92a1eb1d8dad",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['A', 'A', 'A', ..., 'B', 'B', 'B'], dtype=object)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u.atoms.chainIDs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9f2e6b57-2f42-4fe9-9075-dc822ec59d1a",
   "metadata": {},
   "source": [
    "## OpenCADD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "18a1cebc-9c01-4671-8846-1235d7724e5f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# packages in environment at /home/dominique/.local/miniconda/envs/toc:\n",
      "#\n",
      "# Name                    Version                   Build  Channel\n",
      "opencadd                  0.2.2              pyhd8ed1ab_0    conda-forge\n",
      "teachopencadd             1.3.0+689.ge36208e.dirty          pypi_0    pypi\n"
     ]
    }
   ],
   "source": [
    "!conda list opencadd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "e9c9adaa-ba0d-486a-916f-add8ec918d70",
   "metadata": {},
   "outputs": [],
   "source": [
    "from opencadd.structure.core import Structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "fbcefdb0-5d54-49ab-83c1-672f17754943",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Universe with 5271 atoms>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structure = Structure.from_pdbid(\"4wsq\")\n",
    "structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "65324cac-08bd-469f-b7e4-b970d37e24e2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['A', 'A', 'A', ..., 'B', 'B', 'B'], dtype=object)"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "structure.atoms.segids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "738094ae-932b-468d-9c2a-03bebfb822c3",
   "metadata": {},
   "outputs": [
    {
     "ename": "NoDataError",
     "evalue": "This Universe does not contain chainID information",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNoDataError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_6240/2940815569.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0matoms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchainIDs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/groups.py\u001b[0m in \u001b[0;36m__getattr__\u001b[0;34m(self, attr)\u001b[0m\n\u001b[1;32m   2500\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0mattr\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'positions'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2501\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mNoDataError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'This Universe has no coordinates'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2502\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mAtomGroup\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2503\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2504\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mproperty\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/groups.py\u001b[0m in \u001b[0;36m__getattr__\u001b[0;34m(self, attr)\u001b[0m\n\u001b[1;32m    593\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    594\u001b[0m                 \u001b[0merr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'This Universe does not contain {singular} information'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 595\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mNoDataError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msingular\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcls\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msingular\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    596\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    597\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mGroupBase\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNoDataError\u001b[0m: This Universe does not contain chainID information"
     ]
    }
   ],
   "source": [
    "structure.atoms.chainIDs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "477be8b2-e758-43c6-9ba8-f07b81bc8833",
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'Topology' object has no attribute 'chainIDs'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_6240/1826298726.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mselect_atoms\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"chainID A\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/universe.py\u001b[0m in \u001b[0;36mselect_atoms\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    638\u001b[0m         \u001b[0;34m:\u001b[0m\u001b[0mmeth\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;31m`\u001b[0m\u001b[0mMDAnalysis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgroups\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mAtomGroup\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mselect_atoms\u001b[0m\u001b[0;31m`\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    639\u001b[0m         \"\"\"\n\u001b[0;32m--> 640\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0matoms\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mselect_atoms\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    641\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    642\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mproperty\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/groups.py\u001b[0m in \u001b[0;36mselect_atoms\u001b[0;34m(self, sel, periodic, rtol, atol, updating, sorted, rdkit_kwargs, *othersel, **selgroups)\u001b[0m\n\u001b[1;32m   3155\u001b[0m             \u001b[0;31m# Apply the first selection and sum to it\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3156\u001b[0m             atomgrp = sum([sel.apply(self) for sel in selections[1:]],\n\u001b[0;32m-> 3157\u001b[0;31m                           selections[0].apply(self))\n\u001b[0m\u001b[1;32m   3158\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0matomgrp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/selection.py\u001b[0m in \u001b[0;36mapply\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    239\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    240\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 241\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_apply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0masunique\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msorted\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparser\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msorted\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    242\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    243\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/selection.py\u001b[0m in \u001b[0;36m_apply\u001b[0;34m(self, group)\u001b[0m\n\u001b[1;32m    219\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgroup\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    220\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 221\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    222\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0m_apply\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    223\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.local/miniconda/envs/toc/lib/python3.9/site-packages/MDAnalysis/core/selection.py\u001b[0m in \u001b[0;36m_apply\u001b[0;34m(self, group)\u001b[0m\n\u001b[1;32m    585\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_apply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    586\u001b[0m         \u001b[0;31m# rather than work on group.names, cheat and look at the lookup table\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 587\u001b[0;31m         \u001b[0mnmattr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgroup\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0muniverse\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_topology\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    588\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    589\u001b[0m         \u001b[0mmatches\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m  \u001b[0;31m# list of passing indices\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'Topology' object has no attribute 'chainIDs'"
     ]
    }
   ],
   "source": [
    "structure.select_atoms(\"chainID A\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "330f6111-7b58-41ff-a669-c1181fc23fcb",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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