MDTraj_exam_6.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
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   "source": [
    "### Cálculo de observables de RMN con mdtraj.nmr()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "import mdtraj as md"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Cargar trayectoria"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "trj = md.load_pdb('http://www.rcsb.org/pdb/files/1vii.pdb', no_boxchk=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Cálculo de los cambios químicos con el programa SPARTA +"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "ename": "OSError",
     "evalue": "External command not found. Looked for sparta+, SPARTA+, SPARTA+.linux in PATH. `chemical_shifts_spartaplus` requires the external program SPARTA+, available at http://spin.niddk.nih.gov/bax/software/SPARTA+/",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mOSError\u001b[0m                                   Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-e3b232346959>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mshifts\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnmr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchemical_shifts_spartaplus\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtrj\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      2\u001b[0m \u001b[0mshifts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/Myopt/Miniconda/miniconda3/envs/UIBCDF_lab/lib/python3.7/site-packages/mdtraj/nmr/shift_wrappers.py\u001b[0m in \u001b[0;36mchemical_shifts_spartaplus\u001b[0;34m(trj, rename_HN)\u001b[0m\n\u001b[1;32m    274\u001b[0m     \u001b[0mbinary\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfind_executable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSPARTA_PLUS\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    275\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mbinary\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 276\u001b[0;31m         \u001b[0;32mraise\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'External command not found. Looked for %s in PATH. `chemical_shifts_spartaplus` requires the external program SPARTA+, available at http://spin.niddk.nih.gov/bax/software/SPARTA+/'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0;34m', '\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSPARTA_PLUS\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    277\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    278\u001b[0m     \u001b[0mnames\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m\"resSeq\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"resName\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"name\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"SS_SHIFT\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"SHIFT\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"RC_SHIFT\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"HM_SHIFT\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"EF_SHIFT\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"SIGMA\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mOSError\u001b[0m: External command not found. Looked for sparta+, SPARTA+, SPARTA+.linux in PATH. `chemical_shifts_spartaplus` requires the external program SPARTA+, available at http://spin.niddk.nih.gov/bax/software/SPARTA+/"
     ]
    }
   ],
   "source": [
    "shifts = md.nmr.chemical_shifts_spartaplus(trj)\n",
    "shifts[0:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Notas**\n",
    "\n",
    "1) el programa SPARTA nos ayuda a calcular desplazamientos químicos.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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