212/[212]_03_Computing_structural_properties.ipynb

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  {
   "cell_type": "markdown",
   "metadata": {
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   },
   "source": [
    "# Table of Contents\n",
    " <p><div class=\"lev1\"><a href=\"#Load-functions-(ssbio-package-on-212-machine)\"><span class=\"toc-item-num\">1 - </span>Load functions (ssbio package on 212 machine)</a></div><div class=\"lev1\"><a href=\"#Load-the-GEM-PRO\"><span class=\"toc-item-num\">2 - </span>Load the GEM-PRO</a></div><div class=\"lev1\"><a href=\"#Keep-only-the-representative-structures\"><span class=\"toc-item-num\">3 - </span>Keep only the representative structures</a></div><div class=\"lev2\"><a href=\"#For-testing\"><span class=\"toc-item-num\">3.1 - </span>For testing</a></div><div class=\"lev1\"><a href=\"#Calculate-the-number-of-potential-sulfide-bridges-(Biopython)\"><span class=\"toc-item-num\">4 - </span>Calculate the number of potential sulfide bridges (Biopython)</a></div><div class=\"lev1\"><a href=\"#Calculate-SASA,-%-surface/buried,-%-secondary-structure-(DSSP)\"><span class=\"toc-item-num\">5 - </span>Calculate SASA, % surface/buried, % secondary structure (DSSP)</a></div><div class=\"lev1\"><a href=\"#Calculate-surface-&amp;-residue-depth-using-MSMS\"><span class=\"toc-item-num\">6 - </span>Calculate surface &amp; residue depth using MSMS</a></div><div class=\"lev1\"><a href=\"#Calculating-%-polar,-nonpolar,-etc.-residues\"><span class=\"toc-item-num\">7 - </span>Calculating % polar, nonpolar, etc. residues</a></div><div class=\"lev1\"><a href=\"#Merge-all-information\"><span class=\"toc-item-num\">8 - </span>Merge all information</a></div>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd\n",
    "\n",
    "# tqdm is a nice progress bar\n",
    "from tqdm import tqdm\n",
    "\n",
    "pd.set_option('display.max_columns', 500)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "GEM_NAME = 'iJO1366'\n",
    "ROOT_DIR = os.getcwd()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "MODEL_DIR = os.path.join(ROOT_DIR, GEM_NAME)\n",
    "\n",
    "# data_frames - directory where all data frames will be stored (all stages)\n",
    "DATA_FRAMES = os.path.join(MODEL_DIR, 'data_frames')\n",
    "\n",
    "# structure_files - directory where structure related files will be downloaded/are located\n",
    "STRUCT_FILES = os.path.join(MODEL_DIR, 'structure_files')\n",
    "STRUCT_EXP_FILES = os.path.join(STRUCT_FILES, 'experimental')\n",
    "STRUCT_HOMOLOGY_FILES = os.path.join(STRUCT_FILES, 'homology_models')\n",
    "\n",
    "STRUCT_BEST_SET = os.path.join(STRUCT_FILES, 'best_set')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load functions (ssbio package on 212 machine)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# ssbio contains functions to calculate properties\n",
    "import sys\n",
    "sys.path.append(os.path.join(ROOT_DIR, 'ssbio'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load the GEM-PRO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>m_reaction</th>\n",
       "      <th>m_subsystem</th>\n",
       "      <th>m_formula</th>\n",
       "      <th>m_metabolites</th>\n",
       "      <th>m_gene_reaction_rule</th>\n",
       "      <th>m_gene</th>\n",
       "      <th>u_uniprot_acc</th>\n",
       "      <th>u_reviewed</th>\n",
       "      <th>u_gene_name</th>\n",
       "      <th>u_ec_number</th>\n",
       "      <th>u_description</th>\n",
       "      <th>u_seq</th>\n",
       "      <th>u_seq_len</th>\n",
       "      <th>u_pfam</th>\n",
       "      <th>u_kegg_id</th>\n",
       "      <th>u_refseq</th>\n",
       "      <th>u_go</th>\n",
       "      <th>u_pdb_count</th>\n",
       "      <th>u_pdb</th>\n",
       "      <th>p_experiment</th>\n",
       "      <th>p_resolution</th>\n",
       "      <th>p_chemicals</th>\n",
       "      <th>p_chains</th>\n",
       "      <th>p_chain_uniprot_map</th>\n",
       "      <th>p_ec_numbers</th>\n",
       "      <th>p_deposition_date</th>\n",
       "      <th>p_doi</th>\n",
       "      <th>p_pmid</th>\n",
       "      <th>p_space_group</th>\n",
       "      <th>i_entry_name</th>\n",
       "      <th>i_length</th>\n",
       "      <th>i_native</th>\n",
       "      <th>i_tm_helix</th>\n",
       "      <th>i_tm_score</th>\n",
       "      <th>i_url</th>\n",
       "      <th>i_label</th>\n",
       "      <th>i_model_type</th>\n",
       "      <th>ssb_p_aln_score</th>\n",
       "      <th>ssb_p_aln_coverage</th>\n",
       "      <th>ssb_p_percent_seq_ident</th>\n",
       "      <th>ssb_p_no_deletions_in_pdb</th>\n",
       "      <th>ssb_p_aln_coverage_sim</th>\n",
       "      <th>normalized</th>\n",
       "      <th>ssb_si_score</th>\n",
       "      <th>ssb_p_chains_from_org</th>\n",
       "      <th>ssb_p_alpha_beta_comp</th>\n",
       "      <th>ssb_alpha_beta_diff_abs</th>\n",
       "      <th>ssb_alpha_beta_diff</th>\n",
       "      <th>ssb_alpha_beta_res_sim</th>\n",
       "      <th>ssb_alpha_beta_res_sim_score</th>\n",
       "      <th>p_resolution_scaled</th>\n",
       "      <th>ssb_rez_score</th>\n",
       "      <th>ssb_raw_score</th>\n",
       "      <th>ssb_above_cutoffs</th>\n",
       "      <th>ssb_rank</th>\n",
       "      <th>ssb_i_alpha_comp</th>\n",
       "      <th>ssb_i_beta_comp</th>\n",
       "      <th>ssb_i_alpha_beta_comp</th>\n",
       "      <th>ssb_best_file</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>12PPDRtex</td>\n",
       "      <td>Transport, Outer Membrane Porin</td>\n",
       "      <td>12ppd_DASH_R_e &lt;=&gt; 12ppd_DASH_R_p</td>\n",
       "      <td>['12ppd_DASH_R_e', '12ppd_DASH_R_p']</td>\n",
       "      <td>(b0241 or b0929 or b1377 or b2215)</td>\n",
       "      <td>b0241</td>\n",
       "      <td>P02932</td>\n",
       "      <td>True</td>\n",
       "      <td>phoE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['Outer membrane pore protein E']</td>\n",
       "      <td>MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...</td>\n",
       "      <td>351</td>\n",
       "      <td>['PF00267']</td>\n",
       "      <td>['ecj:Y75_p0232', 'eco:b0241']</td>\n",
       "      <td>['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...</td>\n",
       "      <td>['GO:0009279; C:cell outer membrane; IEA:UniPr...</td>\n",
       "      <td>1</td>\n",
       "      <td>1PHO</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['A']</td>\n",
       "      <td>{'A': ['P02932']}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15-JAN-93</td>\n",
       "      <td>10.1038/358727A0</td>\n",
       "      <td>1380671</td>\n",
       "      <td>P 3 2 1</td>\n",
       "      <td>PHOE_ECOLI</td>\n",
       "      <td>351</td>\n",
       "      <td>1phoA</td>\n",
       "      <td>7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...</td>\n",
       "      <td>E12496</td>\n",
       "      <td>template-based</td>\n",
       "      <td>1710</td>\n",
       "      <td>330</td>\n",
       "      <td>0.940171</td>\n",
       "      <td>True</td>\n",
       "      <td>330</td>\n",
       "      <td>0.889829</td>\n",
       "      <td>1.125009</td>\n",
       "      <td>True</td>\n",
       "      <td>0.575758</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.350195</td>\n",
       "      <td>0.698345</td>\n",
       "      <td>0.922169</td>\n",
       "      <td>1</td>\n",
       "      <td>2.823354</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.019943</td>\n",
       "      <td>0.535613</td>\n",
       "      <td>0.555556</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>12PPDStex</td>\n",
       "      <td>Transport, Outer Membrane Porin</td>\n",
       "      <td>12ppd_DASH_S_e &lt;=&gt; 12ppd_DASH_S_p</td>\n",
       "      <td>['12ppd_DASH_S_e', '12ppd_DASH_S_p']</td>\n",
       "      <td>(b0241 or b0929 or b1377 or b2215)</td>\n",
       "      <td>b0241</td>\n",
       "      <td>P02932</td>\n",
       "      <td>True</td>\n",
       "      <td>phoE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['Outer membrane pore protein E']</td>\n",
       "      <td>MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...</td>\n",
       "      <td>351</td>\n",
       "      <td>['PF00267']</td>\n",
       "      <td>['ecj:Y75_p0232', 'eco:b0241']</td>\n",
       "      <td>['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...</td>\n",
       "      <td>['GO:0009279; C:cell outer membrane; IEA:UniPr...</td>\n",
       "      <td>1</td>\n",
       "      <td>1PHO</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['A']</td>\n",
       "      <td>{'A': ['P02932']}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15-JAN-93</td>\n",
       "      <td>10.1038/358727A0</td>\n",
       "      <td>1380671</td>\n",
       "      <td>P 3 2 1</td>\n",
       "      <td>PHOE_ECOLI</td>\n",
       "      <td>351</td>\n",
       "      <td>1phoA</td>\n",
       "      <td>7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...</td>\n",
       "      <td>E12496</td>\n",
       "      <td>template-based</td>\n",
       "      <td>1710</td>\n",
       "      <td>330</td>\n",
       "      <td>0.940171</td>\n",
       "      <td>True</td>\n",
       "      <td>330</td>\n",
       "      <td>0.889829</td>\n",
       "      <td>1.125009</td>\n",
       "      <td>True</td>\n",
       "      <td>0.575758</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.350195</td>\n",
       "      <td>0.698345</td>\n",
       "      <td>0.922169</td>\n",
       "      <td>1</td>\n",
       "      <td>2.823354</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.019943</td>\n",
       "      <td>0.535613</td>\n",
       "      <td>0.555556</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>23CAMPtex</td>\n",
       "      <td>Transport, Outer Membrane Porin</td>\n",
       "      <td>23camp_e &lt;=&gt; 23camp_p</td>\n",
       "      <td>['23camp_e', '23camp_p']</td>\n",
       "      <td>(b0241 or b0929 or b1377 or b2215)</td>\n",
       "      <td>b0241</td>\n",
       "      <td>P02932</td>\n",
       "      <td>True</td>\n",
       "      <td>phoE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['Outer membrane pore protein E']</td>\n",
       "      <td>MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...</td>\n",
       "      <td>351</td>\n",
       "      <td>['PF00267']</td>\n",
       "      <td>['ecj:Y75_p0232', 'eco:b0241']</td>\n",
       "      <td>['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...</td>\n",
       "      <td>['GO:0009279; C:cell outer membrane; IEA:UniPr...</td>\n",
       "      <td>1</td>\n",
       "      <td>1PHO</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['A']</td>\n",
       "      <td>{'A': ['P02932']}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15-JAN-93</td>\n",
       "      <td>10.1038/358727A0</td>\n",
       "      <td>1380671</td>\n",
       "      <td>P 3 2 1</td>\n",
       "      <td>PHOE_ECOLI</td>\n",
       "      <td>351</td>\n",
       "      <td>1phoA</td>\n",
       "      <td>7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...</td>\n",
       "      <td>E12496</td>\n",
       "      <td>template-based</td>\n",
       "      <td>1710</td>\n",
       "      <td>330</td>\n",
       "      <td>0.940171</td>\n",
       "      <td>True</td>\n",
       "      <td>330</td>\n",
       "      <td>0.889829</td>\n",
       "      <td>1.125009</td>\n",
       "      <td>True</td>\n",
       "      <td>0.575758</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.350195</td>\n",
       "      <td>0.698345</td>\n",
       "      <td>0.922169</td>\n",
       "      <td>1</td>\n",
       "      <td>2.823354</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.019943</td>\n",
       "      <td>0.535613</td>\n",
       "      <td>0.555556</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>23CCMPtex</td>\n",
       "      <td>Transport, Outer Membrane Porin</td>\n",
       "      <td>23ccmp_e &lt;=&gt; 23ccmp_p</td>\n",
       "      <td>['23ccmp_e', '23ccmp_p']</td>\n",
       "      <td>(b0241 or b0929 or b1377 or b2215)</td>\n",
       "      <td>b0241</td>\n",
       "      <td>P02932</td>\n",
       "      <td>True</td>\n",
       "      <td>phoE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['Outer membrane pore protein E']</td>\n",
       "      <td>MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...</td>\n",
       "      <td>351</td>\n",
       "      <td>['PF00267']</td>\n",
       "      <td>['ecj:Y75_p0232', 'eco:b0241']</td>\n",
       "      <td>['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...</td>\n",
       "      <td>['GO:0009279; C:cell outer membrane; IEA:UniPr...</td>\n",
       "      <td>1</td>\n",
       "      <td>1PHO</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['A']</td>\n",
       "      <td>{'A': ['P02932']}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15-JAN-93</td>\n",
       "      <td>10.1038/358727A0</td>\n",
       "      <td>1380671</td>\n",
       "      <td>P 3 2 1</td>\n",
       "      <td>PHOE_ECOLI</td>\n",
       "      <td>351</td>\n",
       "      <td>1phoA</td>\n",
       "      <td>7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...</td>\n",
       "      <td>E12496</td>\n",
       "      <td>template-based</td>\n",
       "      <td>1710</td>\n",
       "      <td>330</td>\n",
       "      <td>0.940171</td>\n",
       "      <td>True</td>\n",
       "      <td>330</td>\n",
       "      <td>0.889829</td>\n",
       "      <td>1.125009</td>\n",
       "      <td>True</td>\n",
       "      <td>0.575758</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.350195</td>\n",
       "      <td>0.698345</td>\n",
       "      <td>0.922169</td>\n",
       "      <td>1</td>\n",
       "      <td>2.823354</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.019943</td>\n",
       "      <td>0.535613</td>\n",
       "      <td>0.555556</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>23CGMPtex</td>\n",
       "      <td>Transport, Outer Membrane Porin</td>\n",
       "      <td>23cgmp_e &lt;=&gt; 23cgmp_p</td>\n",
       "      <td>['23cgmp_e', '23cgmp_p']</td>\n",
       "      <td>(b0241 or b0929 or b1377 or b2215)</td>\n",
       "      <td>b0241</td>\n",
       "      <td>P02932</td>\n",
       "      <td>True</td>\n",
       "      <td>phoE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['Outer membrane pore protein E']</td>\n",
       "      <td>MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...</td>\n",
       "      <td>351</td>\n",
       "      <td>['PF00267']</td>\n",
       "      <td>['ecj:Y75_p0232', 'eco:b0241']</td>\n",
       "      <td>['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...</td>\n",
       "      <td>['GO:0009279; C:cell outer membrane; IEA:UniPr...</td>\n",
       "      <td>1</td>\n",
       "      <td>1PHO</td>\n",
       "      <td>X-RAY DIFFRACTION</td>\n",
       "      <td>3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>['A']</td>\n",
       "      <td>{'A': ['P02932']}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>15-JAN-93</td>\n",
       "      <td>10.1038/358727A0</td>\n",
       "      <td>1380671</td>\n",
       "      <td>P 3 2 1</td>\n",
       "      <td>PHOE_ECOLI</td>\n",
       "      <td>351</td>\n",
       "      <td>1phoA</td>\n",
       "      <td>7</td>\n",
       "      <td>NaN</td>\n",
       "      <td>http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...</td>\n",
       "      <td>E12496</td>\n",
       "      <td>template-based</td>\n",
       "      <td>1710</td>\n",
       "      <td>330</td>\n",
       "      <td>0.940171</td>\n",
       "      <td>True</td>\n",
       "      <td>330</td>\n",
       "      <td>0.889829</td>\n",
       "      <td>1.125009</td>\n",
       "      <td>True</td>\n",
       "      <td>0.575758</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.020202</td>\n",
       "      <td>0.350195</td>\n",
       "      <td>0.698345</td>\n",
       "      <td>0.922169</td>\n",
       "      <td>1</td>\n",
       "      <td>2.823354</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.019943</td>\n",
       "      <td>0.535613</td>\n",
       "      <td>0.555556</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  m_reaction                      m_subsystem  \\\n",
       "0  12PPDRtex  Transport, Outer Membrane Porin   \n",
       "1  12PPDStex  Transport, Outer Membrane Porin   \n",
       "2  23CAMPtex  Transport, Outer Membrane Porin   \n",
       "3  23CCMPtex  Transport, Outer Membrane Porin   \n",
       "4  23CGMPtex  Transport, Outer Membrane Porin   \n",
       "\n",
       "                           m_formula                         m_metabolites  \\\n",
       "0  12ppd_DASH_R_e <=> 12ppd_DASH_R_p  ['12ppd_DASH_R_e', '12ppd_DASH_R_p']   \n",
       "1  12ppd_DASH_S_e <=> 12ppd_DASH_S_p  ['12ppd_DASH_S_e', '12ppd_DASH_S_p']   \n",
       "2              23camp_e <=> 23camp_p              ['23camp_e', '23camp_p']   \n",
       "3              23ccmp_e <=> 23ccmp_p              ['23ccmp_e', '23ccmp_p']   \n",
       "4              23cgmp_e <=> 23cgmp_p              ['23cgmp_e', '23cgmp_p']   \n",
       "\n",
       "                 m_gene_reaction_rule m_gene u_uniprot_acc u_reviewed  \\\n",
       "0  (b0241 or b0929 or b1377 or b2215)  b0241        P02932       True   \n",
       "1  (b0241 or b0929 or b1377 or b2215)  b0241        P02932       True   \n",
       "2  (b0241 or b0929 or b1377 or b2215)  b0241        P02932       True   \n",
       "3  (b0241 or b0929 or b1377 or b2215)  b0241        P02932       True   \n",
       "4  (b0241 or b0929 or b1377 or b2215)  b0241        P02932       True   \n",
       "\n",
       "  u_gene_name u_ec_number                      u_description  \\\n",
       "0        phoE         NaN  ['Outer membrane pore protein E']   \n",
       "1        phoE         NaN  ['Outer membrane pore protein E']   \n",
       "2        phoE         NaN  ['Outer membrane pore protein E']   \n",
       "3        phoE         NaN  ['Outer membrane pore protein E']   \n",
       "4        phoE         NaN  ['Outer membrane pore protein E']   \n",
       "\n",
       "                                               u_seq  u_seq_len       u_pfam  \\\n",
       "0  MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...        351  ['PF00267']   \n",
       "1  MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...        351  ['PF00267']   \n",
       "2  MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...        351  ['PF00267']   \n",
       "3  MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...        351  ['PF00267']   \n",
       "4  MKKSTLALVVMGIVASASVQAAEIYNKDGNKLDVYGKVKAMHYMSD...        351  ['PF00267']   \n",
       "\n",
       "                        u_kegg_id  \\\n",
       "0  ['ecj:Y75_p0232', 'eco:b0241']   \n",
       "1  ['ecj:Y75_p0232', 'eco:b0241']   \n",
       "2  ['ecj:Y75_p0232', 'eco:b0241']   \n",
       "3  ['ecj:Y75_p0232', 'eco:b0241']   \n",
       "4  ['ecj:Y75_p0232', 'eco:b0241']   \n",
       "\n",
       "                                            u_refseq  \\\n",
       "0  ['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...   \n",
       "1  ['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...   \n",
       "2  ['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...   \n",
       "3  ['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...   \n",
       "4  ['NP_414776.1', 'NC_000913.3', 'YP_488536.1', ...   \n",
       "\n",
       "                                                u_go  u_pdb_count u_pdb  \\\n",
       "0  ['GO:0009279; C:cell outer membrane; IEA:UniPr...            1  1PHO   \n",
       "1  ['GO:0009279; C:cell outer membrane; IEA:UniPr...            1  1PHO   \n",
       "2  ['GO:0009279; C:cell outer membrane; IEA:UniPr...            1  1PHO   \n",
       "3  ['GO:0009279; C:cell outer membrane; IEA:UniPr...            1  1PHO   \n",
       "4  ['GO:0009279; C:cell outer membrane; IEA:UniPr...            1  1PHO   \n",
       "\n",
       "        p_experiment  p_resolution p_chemicals p_chains p_chain_uniprot_map  \\\n",
       "0  X-RAY DIFFRACTION             3         NaN    ['A']   {'A': ['P02932']}   \n",
       "1  X-RAY DIFFRACTION             3         NaN    ['A']   {'A': ['P02932']}   \n",
       "2  X-RAY DIFFRACTION             3         NaN    ['A']   {'A': ['P02932']}   \n",
       "3  X-RAY DIFFRACTION             3         NaN    ['A']   {'A': ['P02932']}   \n",
       "4  X-RAY DIFFRACTION             3         NaN    ['A']   {'A': ['P02932']}   \n",
       "\n",
       "  p_ec_numbers p_deposition_date             p_doi   p_pmid p_space_group  \\\n",
       "0          NaN         15-JAN-93  10.1038/358727A0  1380671       P 3 2 1   \n",
       "1          NaN         15-JAN-93  10.1038/358727A0  1380671       P 3 2 1   \n",
       "2          NaN         15-JAN-93  10.1038/358727A0  1380671       P 3 2 1   \n",
       "3          NaN         15-JAN-93  10.1038/358727A0  1380671       P 3 2 1   \n",
       "4          NaN         15-JAN-93  10.1038/358727A0  1380671       P 3 2 1   \n",
       "\n",
       "  i_entry_name  i_length i_native  i_tm_helix  i_tm_score  \\\n",
       "0   PHOE_ECOLI       351    1phoA           7         NaN   \n",
       "1   PHOE_ECOLI       351    1phoA           7         NaN   \n",
       "2   PHOE_ECOLI       351    1phoA           7         NaN   \n",
       "3   PHOE_ECOLI       351    1phoA           7         NaN   \n",
       "4   PHOE_ECOLI       351    1phoA           7         NaN   \n",
       "\n",
       "                                               i_url i_label    i_model_type  \\\n",
       "0  http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...  E12496  template-based   \n",
       "1  http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...  E12496  template-based   \n",
       "2  http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...  E12496  template-based   \n",
       "3  http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...  E12496  template-based   \n",
       "4  http://zhanglab.ccmb.med.umich.edu/QUARK/ecoli...  E12496  template-based   \n",
       "\n",
       "   ssb_p_aln_score  ssb_p_aln_coverage  ssb_p_percent_seq_ident  \\\n",
       "0             1710                 330                 0.940171   \n",
       "1             1710                 330                 0.940171   \n",
       "2             1710                 330                 0.940171   \n",
       "3             1710                 330                 0.940171   \n",
       "4             1710                 330                 0.940171   \n",
       "\n",
       "  ssb_p_no_deletions_in_pdb  ssb_p_aln_coverage_sim  normalized  ssb_si_score  \\\n",
       "0                      True                     330    0.889829      1.125009   \n",
       "1                      True                     330    0.889829      1.125009   \n",
       "2                      True                     330    0.889829      1.125009   \n",
       "3                      True                     330    0.889829      1.125009   \n",
       "4                      True                     330    0.889829      1.125009   \n",
       "\n",
       "  ssb_p_chains_from_org  ssb_p_alpha_beta_comp  ssb_alpha_beta_diff_abs  \\\n",
       "0                  True               0.575758                 0.020202   \n",
       "1                  True               0.575758                 0.020202   \n",
       "2                  True               0.575758                 0.020202   \n",
       "3                  True               0.575758                 0.020202   \n",
       "4                  True               0.575758                 0.020202   \n",
       "\n",
       "   ssb_alpha_beta_diff  ssb_alpha_beta_res_sim  ssb_alpha_beta_res_sim_score  \\\n",
       "0             0.020202                0.350195                      0.698345   \n",
       "1             0.020202                0.350195                      0.698345   \n",
       "2             0.020202                0.350195                      0.698345   \n",
       "3             0.020202                0.350195                      0.698345   \n",
       "4             0.020202                0.350195                      0.698345   \n",
       "\n",
       "   p_resolution_scaled  ssb_rez_score  ssb_raw_score ssb_above_cutoffs  \\\n",
       "0             0.922169              1       2.823354             False   \n",
       "1             0.922169              1       2.823354             False   \n",
       "2             0.922169              1       2.823354             False   \n",
       "3             0.922169              1       2.823354             False   \n",
       "4             0.922169              1       2.823354             False   \n",
       "\n",
       "   ssb_rank  ssb_i_alpha_comp  ssb_i_beta_comp  ssb_i_alpha_beta_comp  \\\n",
       "0       NaN          0.019943         0.535613               0.555556   \n",
       "1       NaN          0.019943         0.535613               0.555556   \n",
       "2       NaN          0.019943         0.535613               0.555556   \n",
       "3       NaN          0.019943         0.535613               0.555556   \n",
       "4       NaN          0.019943         0.535613               0.555556   \n",
       "\n",
       "           ssb_best_file  \n",
       "0  PHOE_ECOLI_model1.pdb  \n",
       "1  PHOE_ECOLI_model1.pdb  \n",
       "2  PHOE_ECOLI_model1.pdb  \n",
       "3  PHOE_ECOLI_model1.pdb  \n",
       "4  PHOE_ECOLI_model1.pdb  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DF_GEM_PRO_EC = pd.read_pickle(os.path.join(DATA_FRAMES, 'DF_03_GEMPRO_pub.pckl'))\n",
    "DF_GEM_PRO_EC.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Keep only the representative structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>m_gene</th>\n",
       "      <th>ssb_best_file</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>b0241</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>b0929</td>\n",
       "      <td>2zfg.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>b1377</td>\n",
       "      <td>OMPN_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>b2215</td>\n",
       "      <td>2j1n.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>b4032</td>\n",
       "      <td>3pux.pdb</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  m_gene          ssb_best_file\n",
       "0  b0241  PHOE_ECOLI_model1.pdb\n",
       "1  b0929               2zfg.pdb\n",
       "2  b1377  OMPN_ECOLI_model1.pdb\n",
       "3  b2215               2j1n.pdb\n",
       "4  b4032               3pux.pdb"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "best_files = DF_GEM_PRO_EC[['m_gene','ssb_best_file']].drop_duplicates().reset_index(drop=True)\n",
    "best_files.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## For testing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "STRUCT_BEST_SET = 'ssbio/properties/test_structures'\n",
    "list_of_pdbs = os.listdir(STRUCT_BEST_SET)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Calculate the number of potential sulfide bridges (Biopython)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from ssbio.properties.ssbond import count_ss_bond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "?count_ss_bond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 11/11 [00:01<00:00,  5.30it/s]\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ssb_cys_bridge</th>\n",
       "      <th>ssb_file</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>OMPC_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>NAGK_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>OMPA_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>OMPG_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   ssb_cys_bridge               ssb_file\n",
       "0               0  PHOE_ECOLI_model1.pdb\n",
       "1               0  OMPC_ECOLI_model1.pdb\n",
       "2               3  NAGK_ECOLI_model1.pdb\n",
       "3               1  OMPA_ECOLI_model1.pdb\n",
       "4               0  OMPG_ECOLI_model1.pdb"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ss_bond_list = []\n",
    "for f in tqdm(list_of_pdbs, leave=True):\n",
    "    ss_bond = count_ss_bond(os.path.join(STRUCT_BEST_SET, f))\n",
    "    ss_bond_list.append({'ssb_file':f, 'ssb_cys_bridge':ss_bond})\n",
    "\n",
    "DF_PROP_SSBOND = pd.DataFrame(ss_bond_list)\n",
    "DF_PROP_SSBOND.to_csv(os.path.join(DATA_FRAMES, 'DF_PROP_SSBOND.csv'))\n",
    "DF_PROP_SSBOND.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Calculate SASA, % surface/buried, % secondary structure (DSSP)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ssbio.properties.dsspprops import all_dssp_props"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "?all_dssp_props"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 11/11 [00:02<00:00,  4.30it/s]\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ssb_file</th>\n",
       "      <th>ssb_mean_rel_exposed</th>\n",
       "      <th>ssb_per_310_helix</th>\n",
       "      <th>ssb_per_5_helix</th>\n",
       "      <th>ssb_per_B</th>\n",
       "      <th>ssb_per_B_NP</th>\n",
       "      <th>ssb_per_B_P</th>\n",
       "      <th>ssb_per_B_neg</th>\n",
       "      <th>ssb_per_B_pos</th>\n",
       "      <th>ssb_per_S</th>\n",
       "      <th>ssb_per_S_NP</th>\n",
       "      <th>ssb_per_S_P</th>\n",
       "      <th>ssb_per_S_neg</th>\n",
       "      <th>ssb_per_S_pos</th>\n",
       "      <th>ssb_per_alpha</th>\n",
       "      <th>ssb_per_bent</th>\n",
       "      <th>ssb_per_beta_bridge</th>\n",
       "      <th>ssb_per_ext_beta</th>\n",
       "      <th>ssb_per_hbond_turn</th>\n",
       "      <th>ssb_per_irr</th>\n",
       "      <th>ssb_sasa</th>\n",
       "      <th>ssb_size</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "      <td>0.289705</td>\n",
       "      <td>0.022792</td>\n",
       "      <td>0</td>\n",
       "      <td>0.182336</td>\n",
       "      <td>0.094017</td>\n",
       "      <td>0.068376</td>\n",
       "      <td>0.017094</td>\n",
       "      <td>0.002849</td>\n",
       "      <td>0.817664</td>\n",
       "      <td>0.353276</td>\n",
       "      <td>0.247863</td>\n",
       "      <td>0.111111</td>\n",
       "      <td>0.105413</td>\n",
       "      <td>0.011396</td>\n",
       "      <td>0.125356</td>\n",
       "      <td>0.011396</td>\n",
       "      <td>0.524217</td>\n",
       "      <td>0.094017</td>\n",
       "      <td>0.210826</td>\n",
       "      <td>16901</td>\n",
       "      <td>351</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>OMPC_ECOLI_model1.pdb</td>\n",
       "      <td>0.297066</td>\n",
       "      <td>0.024523</td>\n",
       "      <td>0</td>\n",
       "      <td>0.163488</td>\n",
       "      <td>0.087193</td>\n",
       "      <td>0.062670</td>\n",
       "      <td>0.010899</td>\n",
       "      <td>0.002725</td>\n",
       "      <td>0.836512</td>\n",
       "      <td>0.376022</td>\n",
       "      <td>0.272480</td>\n",
       "      <td>0.106267</td>\n",
       "      <td>0.081744</td>\n",
       "      <td>0.043597</td>\n",
       "      <td>0.106267</td>\n",
       "      <td>0.019074</td>\n",
       "      <td>0.528610</td>\n",
       "      <td>0.095368</td>\n",
       "      <td>0.182561</td>\n",
       "      <td>17732</td>\n",
       "      <td>367</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NAGK_ECOLI_model1.pdb</td>\n",
       "      <td>0.276746</td>\n",
       "      <td>0.052805</td>\n",
       "      <td>0</td>\n",
       "      <td>0.254125</td>\n",
       "      <td>0.211221</td>\n",
       "      <td>0.033003</td>\n",
       "      <td>0.006601</td>\n",
       "      <td>0.003300</td>\n",
       "      <td>0.745875</td>\n",
       "      <td>0.356436</td>\n",
       "      <td>0.161716</td>\n",
       "      <td>0.115512</td>\n",
       "      <td>0.112211</td>\n",
       "      <td>0.359736</td>\n",
       "      <td>0.112211</td>\n",
       "      <td>0.019802</td>\n",
       "      <td>0.188119</td>\n",
       "      <td>0.099010</td>\n",
       "      <td>0.168317</td>\n",
       "      <td>13819</td>\n",
       "      <td>303</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>OMPA_ECOLI_model1.pdb</td>\n",
       "      <td>0.535638</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0</td>\n",
       "      <td>0.014451</td>\n",
       "      <td>0.008671</td>\n",
       "      <td>0.002890</td>\n",
       "      <td>0.002890</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.985549</td>\n",
       "      <td>0.511561</td>\n",
       "      <td>0.268786</td>\n",
       "      <td>0.098266</td>\n",
       "      <td>0.106936</td>\n",
       "      <td>0.167630</td>\n",
       "      <td>0.138728</td>\n",
       "      <td>0.002890</td>\n",
       "      <td>0.150289</td>\n",
       "      <td>0.078035</td>\n",
       "      <td>0.462428</td>\n",
       "      <td>29514</td>\n",
       "      <td>346</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>OMPG_ECOLI_model1.pdb</td>\n",
       "      <td>0.474059</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0</td>\n",
       "      <td>0.023256</td>\n",
       "      <td>0.019934</td>\n",
       "      <td>0.003322</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.976744</td>\n",
       "      <td>0.435216</td>\n",
       "      <td>0.272425</td>\n",
       "      <td>0.166113</td>\n",
       "      <td>0.102990</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.189369</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.421927</td>\n",
       "      <td>0.013289</td>\n",
       "      <td>0.375415</td>\n",
       "      <td>24231</td>\n",
       "      <td>301</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                ssb_file  ssb_mean_rel_exposed  ssb_per_310_helix  \\\n",
       "0  PHOE_ECOLI_model1.pdb              0.289705           0.022792   \n",
       "1  OMPC_ECOLI_model1.pdb              0.297066           0.024523   \n",
       "2  NAGK_ECOLI_model1.pdb              0.276746           0.052805   \n",
       "3  OMPA_ECOLI_model1.pdb              0.535638           0.000000   \n",
       "4  OMPG_ECOLI_model1.pdb              0.474059           0.000000   \n",
       "\n",
       "   ssb_per_5_helix  ssb_per_B  ssb_per_B_NP  ssb_per_B_P  ssb_per_B_neg  \\\n",
       "0                0   0.182336      0.094017     0.068376       0.017094   \n",
       "1                0   0.163488      0.087193     0.062670       0.010899   \n",
       "2                0   0.254125      0.211221     0.033003       0.006601   \n",
       "3                0   0.014451      0.008671     0.002890       0.002890   \n",
       "4                0   0.023256      0.019934     0.003322       0.000000   \n",
       "\n",
       "   ssb_per_B_pos  ssb_per_S  ssb_per_S_NP  ssb_per_S_P  ssb_per_S_neg  \\\n",
       "0       0.002849   0.817664      0.353276     0.247863       0.111111   \n",
       "1       0.002725   0.836512      0.376022     0.272480       0.106267   \n",
       "2       0.003300   0.745875      0.356436     0.161716       0.115512   \n",
       "3       0.000000   0.985549      0.511561     0.268786       0.098266   \n",
       "4       0.000000   0.976744      0.435216     0.272425       0.166113   \n",
       "\n",
       "   ssb_per_S_pos  ssb_per_alpha  ssb_per_bent  ssb_per_beta_bridge  \\\n",
       "0       0.105413       0.011396      0.125356             0.011396   \n",
       "1       0.081744       0.043597      0.106267             0.019074   \n",
       "2       0.112211       0.359736      0.112211             0.019802   \n",
       "3       0.106936       0.167630      0.138728             0.002890   \n",
       "4       0.102990       0.000000      0.189369             0.000000   \n",
       "\n",
       "   ssb_per_ext_beta  ssb_per_hbond_turn  ssb_per_irr  ssb_sasa  ssb_size  \n",
       "0          0.524217            0.094017     0.210826     16901       351  \n",
       "1          0.528610            0.095368     0.182561     17732       367  \n",
       "2          0.188119            0.099010     0.168317     13819       303  \n",
       "3          0.150289            0.078035     0.462428     29514       346  \n",
       "4          0.421927            0.013289     0.375415     24231       301  "
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dssp_props_list = []\n",
    "for f in tqdm(list_of_pdbs, leave=True):\n",
    "    dssp_props = all_dssp_props(os.path.join(STRUCT_BEST_SET, f))\n",
    "    dssp_props['ssb_file'] = f\n",
    "    dssp_props_list.append(dssp_props)\n",
    "\n",
    "DF_PROP_DSSP = pd.DataFrame(dssp_props_list)\n",
    "DF_PROP_DSSP.to_csv(os.path.join(DATA_FRAMES, 'DF_PROP_DSSP.csv'))\n",
    "DF_PROP_DSSP.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Calculate surface & residue depth using MSMS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ssbio.properties.msmsprops import msms_output, residue_depth"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "?msms_output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "?residue_depth"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 11/11 [01:33<00:00, 12.35s/it]\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ssb_file</th>\n",
       "      <th>ssb_msms</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "      <td>[[X, 1, 1.82956377516, 1.99945048291], [X, 2, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>OMPC_ECOLI_model1.pdb</td>\n",
       "      <td>[[X, 1, 1.82965439368, 1.9996068297], [X, 2, 2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NAGK_ECOLI_model1.pdb</td>\n",
       "      <td>[[X, 1, 1.96540883302, 2.00019860426], [X, 2, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>OMPA_ECOLI_model1.pdb</td>\n",
       "      <td>[[X, 1, 1.82960163044, 1.99979346159], [X, 2, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>OMPG_ECOLI_model1.pdb</td>\n",
       "      <td>[[X, 1, 1.82956501513, 1.99973236858], [X, 2, ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                ssb_file                                           ssb_msms\n",
       "0  PHOE_ECOLI_model1.pdb  [[X, 1, 1.82956377516, 1.99945048291], [X, 2, ...\n",
       "1  OMPC_ECOLI_model1.pdb  [[X, 1, 1.82965439368, 1.9996068297], [X, 2, 2...\n",
       "2  NAGK_ECOLI_model1.pdb  [[X, 1, 1.96540883302, 2.00019860426], [X, 2, ...\n",
       "3  OMPA_ECOLI_model1.pdb  [[X, 1, 1.82960163044, 1.99979346159], [X, 2, ...\n",
       "4  OMPG_ECOLI_model1.pdb  [[X, 1, 1.82956501513, 1.99973236858], [X, 2, ..."
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "msmsinfo = []\n",
    "redinfo = []\n",
    "\n",
    "msms_errors = []\n",
    "\n",
    "for i in tqdm(list_of_pdbs, leave=True):\n",
    "    try:\n",
    "        msms_stuff = msms_output(os.path.join(STRUCT_BEST_SET, i))\n",
    "    except:\n",
    "        msms_errors.append(i)\n",
    "        continue\n",
    "        \n",
    "    msmsinfo.append([i, msms_stuff])\n",
    "    \n",
    "    red_dict = residue_depth(msms_stuff)\n",
    "    red_dict['ssb_file'] = i\n",
    "    redinfo.append(red_dict)\n",
    "    \n",
    "DF_PROP_MSMS = pd.DataFrame(msmsinfo)\n",
    "DF_PROP_MSMS.columns=['ssb_file','ssb_msms']\n",
    "DF_PROP_MSMS.to_csv('DF_PROP_MSMS.csv')\n",
    "DF_PROP_MSMS.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ssb_avg_res_depth</th>\n",
       "      <th>ssb_ca_depth</th>\n",
       "      <th>ssb_file</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2.466982</td>\n",
       "      <td>2.641946</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2.414181</td>\n",
       "      <td>2.627883</td>\n",
       "      <td>OMPC_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2.731797</td>\n",
       "      <td>2.815295</td>\n",
       "      <td>NAGK_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1.980120</td>\n",
       "      <td>2.195048</td>\n",
       "      <td>OMPA_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.982505</td>\n",
       "      <td>2.280696</td>\n",
       "      <td>OMPG_ECOLI_model1.pdb</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   ssb_avg_res_depth  ssb_ca_depth               ssb_file\n",
       "0           2.466982      2.641946  PHOE_ECOLI_model1.pdb\n",
       "1           2.414181      2.627883  OMPC_ECOLI_model1.pdb\n",
       "2           2.731797      2.815295  NAGK_ECOLI_model1.pdb\n",
       "3           1.980120      2.195048  OMPA_ECOLI_model1.pdb\n",
       "4           1.982505      2.280696  OMPG_ECOLI_model1.pdb"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DF_PROP_DEPTH = pd.DataFrame(redinfo)\n",
    "DF_PROP_DEPTH.to_csv(os.path.join(DATA_FRAMES, 'DF_PROP_DEPTH.csv'))\n",
    "DF_PROP_DEPTH.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['1u8f.cif']\n"
     ]
    }
   ],
   "source": [
    "print(msms_errors)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Calculating % polar, nonpolar, etc. residues"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ssbio.properties.resprops import residue_props"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "?residue_props"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 11/11 [00:01<00:00,  5.25it/s]\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ssb_file</th>\n",
       "      <th>ssb_per_NP</th>\n",
       "      <th>ssb_per_P</th>\n",
       "      <th>ssb_per_neg</th>\n",
       "      <th>ssb_per_pos</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "      <td>0.447293</td>\n",
       "      <td>0.316239</td>\n",
       "      <td>0.128205</td>\n",
       "      <td>0.108262</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>OMPC_ECOLI_model1.pdb</td>\n",
       "      <td>0.463215</td>\n",
       "      <td>0.335150</td>\n",
       "      <td>0.117166</td>\n",
       "      <td>0.084469</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NAGK_ECOLI_model1.pdb</td>\n",
       "      <td>0.567657</td>\n",
       "      <td>0.194719</td>\n",
       "      <td>0.122112</td>\n",
       "      <td>0.115512</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>OMPA_ECOLI_model1.pdb</td>\n",
       "      <td>0.520231</td>\n",
       "      <td>0.271676</td>\n",
       "      <td>0.101156</td>\n",
       "      <td>0.106936</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>OMPG_ECOLI_model1.pdb</td>\n",
       "      <td>0.455150</td>\n",
       "      <td>0.275748</td>\n",
       "      <td>0.166113</td>\n",
       "      <td>0.102990</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                ssb_file  ssb_per_NP  ssb_per_P  ssb_per_neg  ssb_per_pos\n",
       "0  PHOE_ECOLI_model1.pdb    0.447293   0.316239     0.128205     0.108262\n",
       "1  OMPC_ECOLI_model1.pdb    0.463215   0.335150     0.117166     0.084469\n",
       "2  NAGK_ECOLI_model1.pdb    0.567657   0.194719     0.122112     0.115512\n",
       "3  OMPA_ECOLI_model1.pdb    0.520231   0.271676     0.101156     0.106936\n",
       "4  OMPG_ECOLI_model1.pdb    0.455150   0.275748     0.166113     0.102990"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nlist = []\n",
    "\n",
    "for i in tqdm(list_of_pdbs, leave=True):\n",
    "    res_dict = residue_props(os.path.join(STRUCT_BEST_SET, i))\n",
    "    res_dict['ssb_file'] = i\n",
    "    nlist.append(res_dict)\n",
    "    \n",
    "DF_PROP_RES = pd.DataFrame(nlist)\n",
    "DF_PROP_RES.to_csv(os.path.join(DATA_FRAMES, 'DF_PROP_RES.csv'))\n",
    "DF_PROP_RES.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Merge all information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ssb_cys_bridge</th>\n",
       "      <th>ssb_file</th>\n",
       "      <th>ssb_avg_res_depth</th>\n",
       "      <th>ssb_ca_depth</th>\n",
       "      <th>ssb_per_NP</th>\n",
       "      <th>ssb_per_P</th>\n",
       "      <th>ssb_per_neg</th>\n",
       "      <th>ssb_per_pos</th>\n",
       "      <th>ssb_mean_rel_exposed</th>\n",
       "      <th>ssb_per_310_helix</th>\n",
       "      <th>ssb_per_5_helix</th>\n",
       "      <th>ssb_per_B</th>\n",
       "      <th>ssb_per_B_NP</th>\n",
       "      <th>ssb_per_B_P</th>\n",
       "      <th>ssb_per_B_neg</th>\n",
       "      <th>ssb_per_B_pos</th>\n",
       "      <th>ssb_per_S</th>\n",
       "      <th>ssb_per_S_NP</th>\n",
       "      <th>ssb_per_S_P</th>\n",
       "      <th>ssb_per_S_neg</th>\n",
       "      <th>ssb_per_S_pos</th>\n",
       "      <th>ssb_per_alpha</th>\n",
       "      <th>ssb_per_bent</th>\n",
       "      <th>ssb_per_beta_bridge</th>\n",
       "      <th>ssb_per_ext_beta</th>\n",
       "      <th>ssb_per_hbond_turn</th>\n",
       "      <th>ssb_per_irr</th>\n",
       "      <th>ssb_sasa</th>\n",
       "      <th>ssb_size</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>PHOE_ECOLI_model1.pdb</td>\n",
       "      <td>2.466982</td>\n",
       "      <td>2.641946</td>\n",
       "      <td>0.447293</td>\n",
       "      <td>0.316239</td>\n",
       "      <td>0.128205</td>\n",
       "      <td>0.108262</td>\n",
       "      <td>0.289705</td>\n",
       "      <td>0.022792</td>\n",
       "      <td>0</td>\n",
       "      <td>0.182336</td>\n",
       "      <td>0.094017</td>\n",
       "      <td>0.068376</td>\n",
       "      <td>0.017094</td>\n",
       "      <td>0.002849</td>\n",
       "      <td>0.817664</td>\n",
       "      <td>0.353276</td>\n",
       "      <td>0.247863</td>\n",
       "      <td>0.111111</td>\n",
       "      <td>0.105413</td>\n",
       "      <td>0.011396</td>\n",
       "      <td>0.125356</td>\n",
       "      <td>0.011396</td>\n",
       "      <td>0.524217</td>\n",
       "      <td>0.094017</td>\n",
       "      <td>0.210826</td>\n",
       "      <td>16901</td>\n",
       "      <td>351</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>OMPC_ECOLI_model1.pdb</td>\n",
       "      <td>2.414181</td>\n",
       "      <td>2.627883</td>\n",
       "      <td>0.463215</td>\n",
       "      <td>0.335150</td>\n",
       "      <td>0.117166</td>\n",
       "      <td>0.084469</td>\n",
       "      <td>0.297066</td>\n",
       "      <td>0.024523</td>\n",
       "      <td>0</td>\n",
       "      <td>0.163488</td>\n",
       "      <td>0.087193</td>\n",
       "      <td>0.062670</td>\n",
       "      <td>0.010899</td>\n",
       "      <td>0.002725</td>\n",
       "      <td>0.836512</td>\n",
       "      <td>0.376022</td>\n",
       "      <td>0.272480</td>\n",
       "      <td>0.106267</td>\n",
       "      <td>0.081744</td>\n",
       "      <td>0.043597</td>\n",
       "      <td>0.106267</td>\n",
       "      <td>0.019074</td>\n",
       "      <td>0.528610</td>\n",
       "      <td>0.095368</td>\n",
       "      <td>0.182561</td>\n",
       "      <td>17732</td>\n",
       "      <td>367</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>NAGK_ECOLI_model1.pdb</td>\n",
       "      <td>2.731797</td>\n",
       "      <td>2.815295</td>\n",
       "      <td>0.567657</td>\n",
       "      <td>0.194719</td>\n",
       "      <td>0.122112</td>\n",
       "      <td>0.115512</td>\n",
       "      <td>0.276746</td>\n",
       "      <td>0.052805</td>\n",
       "      <td>0</td>\n",
       "      <td>0.254125</td>\n",
       "      <td>0.211221</td>\n",
       "      <td>0.033003</td>\n",
       "      <td>0.006601</td>\n",
       "      <td>0.003300</td>\n",
       "      <td>0.745875</td>\n",
       "      <td>0.356436</td>\n",
       "      <td>0.161716</td>\n",
       "      <td>0.115512</td>\n",
       "      <td>0.112211</td>\n",
       "      <td>0.359736</td>\n",
       "      <td>0.112211</td>\n",
       "      <td>0.019802</td>\n",
       "      <td>0.188119</td>\n",
       "      <td>0.099010</td>\n",
       "      <td>0.168317</td>\n",
       "      <td>13819</td>\n",
       "      <td>303</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>OMPA_ECOLI_model1.pdb</td>\n",
       "      <td>1.980120</td>\n",
       "      <td>2.195048</td>\n",
       "      <td>0.520231</td>\n",
       "      <td>0.271676</td>\n",
       "      <td>0.101156</td>\n",
       "      <td>0.106936</td>\n",
       "      <td>0.535638</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0</td>\n",
       "      <td>0.014451</td>\n",
       "      <td>0.008671</td>\n",
       "      <td>0.002890</td>\n",
       "      <td>0.002890</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.985549</td>\n",
       "      <td>0.511561</td>\n",
       "      <td>0.268786</td>\n",
       "      <td>0.098266</td>\n",
       "      <td>0.106936</td>\n",
       "      <td>0.167630</td>\n",
       "      <td>0.138728</td>\n",
       "      <td>0.002890</td>\n",
       "      <td>0.150289</td>\n",
       "      <td>0.078035</td>\n",
       "      <td>0.462428</td>\n",
       "      <td>29514</td>\n",
       "      <td>346</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>OMPG_ECOLI_model1.pdb</td>\n",
       "      <td>1.982505</td>\n",
       "      <td>2.280696</td>\n",
       "      <td>0.455150</td>\n",
       "      <td>0.275748</td>\n",
       "      <td>0.166113</td>\n",
       "      <td>0.102990</td>\n",
       "      <td>0.474059</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0</td>\n",
       "      <td>0.023256</td>\n",
       "      <td>0.019934</td>\n",
       "      <td>0.003322</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.976744</td>\n",
       "      <td>0.435216</td>\n",
       "      <td>0.272425</td>\n",
       "      <td>0.166113</td>\n",
       "      <td>0.102990</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.189369</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.421927</td>\n",
       "      <td>0.013289</td>\n",
       "      <td>0.375415</td>\n",
       "      <td>24231</td>\n",
       "      <td>301</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   ssb_cys_bridge               ssb_file  ssb_avg_res_depth  ssb_ca_depth  \\\n",
       "0               0  PHOE_ECOLI_model1.pdb           2.466982      2.641946   \n",
       "1               0  OMPC_ECOLI_model1.pdb           2.414181      2.627883   \n",
       "2               3  NAGK_ECOLI_model1.pdb           2.731797      2.815295   \n",
       "3               1  OMPA_ECOLI_model1.pdb           1.980120      2.195048   \n",
       "4               0  OMPG_ECOLI_model1.pdb           1.982505      2.280696   \n",
       "\n",
       "   ssb_per_NP  ssb_per_P  ssb_per_neg  ssb_per_pos  ssb_mean_rel_exposed  \\\n",
       "0    0.447293   0.316239     0.128205     0.108262              0.289705   \n",
       "1    0.463215   0.335150     0.117166     0.084469              0.297066   \n",
       "2    0.567657   0.194719     0.122112     0.115512              0.276746   \n",
       "3    0.520231   0.271676     0.101156     0.106936              0.535638   \n",
       "4    0.455150   0.275748     0.166113     0.102990              0.474059   \n",
       "\n",
       "   ssb_per_310_helix  ssb_per_5_helix  ssb_per_B  ssb_per_B_NP  ssb_per_B_P  \\\n",
       "0           0.022792                0   0.182336      0.094017     0.068376   \n",
       "1           0.024523                0   0.163488      0.087193     0.062670   \n",
       "2           0.052805                0   0.254125      0.211221     0.033003   \n",
       "3           0.000000                0   0.014451      0.008671     0.002890   \n",
       "4           0.000000                0   0.023256      0.019934     0.003322   \n",
       "\n",
       "   ssb_per_B_neg  ssb_per_B_pos  ssb_per_S  ssb_per_S_NP  ssb_per_S_P  \\\n",
       "0       0.017094       0.002849   0.817664      0.353276     0.247863   \n",
       "1       0.010899       0.002725   0.836512      0.376022     0.272480   \n",
       "2       0.006601       0.003300   0.745875      0.356436     0.161716   \n",
       "3       0.002890       0.000000   0.985549      0.511561     0.268786   \n",
       "4       0.000000       0.000000   0.976744      0.435216     0.272425   \n",
       "\n",
       "   ssb_per_S_neg  ssb_per_S_pos  ssb_per_alpha  ssb_per_bent  \\\n",
       "0       0.111111       0.105413       0.011396      0.125356   \n",
       "1       0.106267       0.081744       0.043597      0.106267   \n",
       "2       0.115512       0.112211       0.359736      0.112211   \n",
       "3       0.098266       0.106936       0.167630      0.138728   \n",
       "4       0.166113       0.102990       0.000000      0.189369   \n",
       "\n",
       "   ssb_per_beta_bridge  ssb_per_ext_beta  ssb_per_hbond_turn  ssb_per_irr  \\\n",
       "0             0.011396          0.524217            0.094017     0.210826   \n",
       "1             0.019074          0.528610            0.095368     0.182561   \n",
       "2             0.019802          0.188119            0.099010     0.168317   \n",
       "3             0.002890          0.150289            0.078035     0.462428   \n",
       "4             0.000000          0.421927            0.013289     0.375415   \n",
       "\n",
       "   ssb_sasa  ssb_size  \n",
       "0     16901       351  \n",
       "1     17732       367  \n",
       "2     13819       303  \n",
       "3     29514       346  \n",
       "4     24231       301  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "DF_PROP_ALL = DF_PROP_SSBOND.merge(DF_PROP_DEPTH).merge(DF_PROP_RES).merge(DF_PROP_DSSP)\n",
    "DF_PROP_ALL.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "DF_PROP_ALL.to_pickle(os.path.join(DATA_FRAMES, 'DF_PROP_ALL.pckl'))"
   ]
  }
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