{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# FATCAT - Structure Similarity\n",
    "\n",
    "This notebook shows how to run and parse FATCAT, a structural similarity calculator."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import ssbio.protein.structure.properties.fatcat as fatcat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import os\n",
    "import os.path as op\n",
    "import tempfile\n",
    "\n",
    "ROOT_DIR = tempfile.gettempdir()\n",
    "OUT_DIR = op.join(ROOT_DIR, 'fatcat_testing')\n",
    "if not op.exists(OUT_DIR):\n",
    "    os.mkdir(OUT_DIR)\n",
    "FATCAT_SH = 'fatcat'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Pairwise"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fatcat_outfile = fatcat.run_fatcat(structure_path_1='../../ssbio/test/test_files/structures/12as-A_clean.pdb', \n",
    "                                   structure_path_2='../../ssbio/test/test_files/structures/1a9x-A_clean.pdb',\n",
    "                                   outdir=OUT_DIR,\n",
    "                                   fatcat_sh=FATCAT_SH, print_cmd=True, force_rerun=True)\n",
    "print('Output file:', fatcat_outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "fatcat.parse_fatcat(fatcat_outfile)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### All-by-all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "structs = ['../../ssbio/test/test_files/structures/12as-A_clean.pdb', \n",
    "           '../../ssbio/test/test_files/structures/1af6-A_clean.pdb',\n",
    "           '../../ssbio/test/test_files/structures/1a9x-A_clean.pdb']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "tm_scores = fatcat.run_fatcat_all_by_all(structs, fatcat_sh=FATCAT_SH, outdir=OUT_DIR)\n",
    "tm_scores"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "import seaborn as sns\n",
    "sns.heatmap(tm_scores)"
   ]
  }
 ],
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