iML1515_GP - Loading and Exploring the GEM-PRO.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# *i*ML1515_GP - Loading and Exploring the GEM-PRO\n",
    "\n",
    "This notebook guides you through loading the GEM-PRO model for ***i*ML1515** and exploring the contents of it.\n",
    "\n",
    "Requirements:\n",
    "- ``ssbio`` - installation instructions [here](http://ssbio.readthedocs.io/en/latest/#installation), documentation [here](http://ssbio.readthedocs.io/en/latest/index.html)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Loading the GEM-PRO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Loading the JSON file\n",
    "# Change the location of the .json file if it is located somewhere else\n",
    "from ssbio.core.io import load_json\n",
    "iML1515_GP = load_json('iML1515_GP.json.gz', decompression=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "## Alternative - loading the pickle file\n",
    "## Uncomment and use this loading method if the JSON file fails to load\n",
    "# from ssbio.core.io import load_pickle\n",
    "# iML1515_GP = load_pickle('iML1515_GP/model/iML1515_GP.pckl')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Basic information & DataFrames"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Genes with and without structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<GenePro b0870 at 0x7f68737174a8>,\n",
       " <GenePro b2551 at 0x7f68734d5208>,\n",
       " <GenePro b3500 at 0x7f68734f9dd8>,\n",
       " <GenePro b0945 at 0x7f68734a1828>,\n",
       " <GenePro b3916 at 0x7f6873462fd0>,\n",
       " <GenePro b1260 at 0x7f687348d9e8>,\n",
       " <GenePro b1261 at 0x7f687341fe80>,\n",
       " <GenePro b3426 at 0x7f68734365c0>,\n",
       " <GenePro b3770 at 0x7f687340e4e0>,\n",
       " <GenePro b4054 at 0x7f687340ef28>]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# List all genes that have at least one experimental PDB structure\n",
    "iML1515_GP.genes_with_experimental_structures[:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<GenePro b0870 at 0x7f68737174a8>,\n",
       " <GenePro b2551 at 0x7f68734d5208>,\n",
       " <GenePro b3368 at 0x7f68734e2550>,\n",
       " <GenePro b2436 at 0x7f68734f9358>,\n",
       " <GenePro b3500 at 0x7f68734f9dd8>,\n",
       " <GenePro b0945 at 0x7f68734a1828>,\n",
       " <GenePro b4467 at 0x7f68734c9080>,\n",
       " <GenePro b2979 at 0x7f68734cfb70>,\n",
       " <GenePro b4468 at 0x7f68734625c0>,\n",
       " <GenePro b3916 at 0x7f6873462fd0>]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# List all genes that have at least one homology model\n",
    "iML1515_GP.genes_with_homology_models[:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Summary DataFrames"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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>uniprot</th>\n",
       "      <th>kegg</th>\n",
       "      <th>num_pdbs</th>\n",
       "      <th>pdbs</th>\n",
       "      <th>seq_len</th>\n",
       "      <th>sequence_file</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>gene</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>b0002</th>\n",
       "      <td>P00561</td>\n",
       "      <td>ecj:JW0001;eco:b0002</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>820</td>\n",
       "      <td>P00561.fasta</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0003</th>\n",
       "      <td>P00547</td>\n",
       "      <td>ecj:JW0002;eco:b0003</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>310</td>\n",
       "      <td>P00547.fasta</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0004</th>\n",
       "      <td>P00934</td>\n",
       "      <td>ecj:JW0003;eco:b0004</td>\n",
       "      <td>1</td>\n",
       "      <td>1VB3</td>\n",
       "      <td>428</td>\n",
       "      <td>P00934.fasta</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0007</th>\n",
       "      <td>P30143</td>\n",
       "      <td>ecj:JW0006;eco:b0007</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>476</td>\n",
       "      <td>P30143.fasta</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0008</th>\n",
       "      <td>P0A870</td>\n",
       "      <td>ecj:JW0007;eco:b0008</td>\n",
       "      <td>12</td>\n",
       "      <td>1I2N;1I2Q;4S2B;1I2R;1ONR;4RZ6;1I2O;4RZ5;4S2C;3...</td>\n",
       "      <td>317</td>\n",
       "      <td>P0A870.fasta</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      uniprot                  kegg  num_pdbs  \\\n",
       "gene                                            \n",
       "b0002  P00561  ecj:JW0001;eco:b0002         0   \n",
       "b0003  P00547  ecj:JW0002;eco:b0003         0   \n",
       "b0004  P00934  ecj:JW0003;eco:b0004         1   \n",
       "b0007  P30143  ecj:JW0006;eco:b0007         0   \n",
       "b0008  P0A870  ecj:JW0007;eco:b0008        12   \n",
       "\n",
       "                                                    pdbs  seq_len  \\\n",
       "gene                                                                \n",
       "b0002                                                NaN      820   \n",
       "b0003                                                NaN      310   \n",
       "b0004                                               1VB3      428   \n",
       "b0007                                                NaN      476   \n",
       "b0008  1I2N;1I2Q;4S2B;1I2R;1ONR;4RZ6;1I2O;4RZ5;4S2C;3...      317   \n",
       "\n",
       "      sequence_file  \n",
       "gene                 \n",
       "b0002  P00561.fasta  \n",
       "b0003  P00547.fasta  \n",
       "b0004  P00934.fasta  \n",
       "b0007  P30143.fasta  \n",
       "b0008  P0A870.fasta  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Summarize the sequences mapped to each protein\n",
    "iML1515_GP.df_representative_sequences.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
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   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>is_experimental</th>\n",
       "      <th>reference_seq_top_coverage</th>\n",
       "      <th>structure_file</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>gene</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>b0002</th>\n",
       "      <td>AK1H_ECOLI-X</td>\n",
       "      <td>False</td>\n",
       "      <td>100.0</td>\n",
       "      <td>AK1H_ECOLI_model1_clean-X_clean.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0003</th>\n",
       "      <td>KHSE_ECOLI-X</td>\n",
       "      <td>False</td>\n",
       "      <td>100.0</td>\n",
       "      <td>KHSE_ECOLI_model1_clean-X_clean.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0004</th>\n",
       "      <td>1vb3-A</td>\n",
       "      <td>True</td>\n",
       "      <td>100.0</td>\n",
       "      <td>1vb3-A_clean.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0007</th>\n",
       "      <td>YAAJ_ECOLI-X</td>\n",
       "      <td>False</td>\n",
       "      <td>100.0</td>\n",
       "      <td>YAAJ_ECOLI_model1_clean-X_clean.pdb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b0008</th>\n",
       "      <td>4s2b-A</td>\n",
       "      <td>True</td>\n",
       "      <td>99.1</td>\n",
       "      <td>4s2b-A_clean.pdb</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
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      "text/plain": [
       "                 id is_experimental  reference_seq_top_coverage  \\\n",
       "gene                                                              \n",
       "b0002  AK1H_ECOLI-X           False                       100.0   \n",
       "b0003  KHSE_ECOLI-X           False                       100.0   \n",
       "b0004        1vb3-A            True                       100.0   \n",
       "b0007  YAAJ_ECOLI-X           False                       100.0   \n",
       "b0008        4s2b-A            True                        99.1   \n",
       "\n",
       "                            structure_file  \n",
       "gene                                        \n",
       "b0002  AK1H_ECOLI_model1_clean-X_clean.pdb  \n",
       "b0003  KHSE_ECOLI_model1_clean-X_clean.pdb  \n",
       "b0004                     1vb3-A_clean.pdb  \n",
       "b0007  YAAJ_ECOLI_model1_clean-X_clean.pdb  \n",
       "b0008                     4s2b-A_clean.pdb  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Summarize the structures mapped to each protein\n",
    "iML1515_GP.df_representative_structures.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Inspecting the content of one gene and its protein"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Protein b3916 at 0x7f687348d080>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Looking at the content stored per gene\n",
    "my_protein = iML1515_GP.genes.b3916.protein\n",
    "my_protein"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Protein sequences and structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<KEGGProp eco:b3916 at 0x7f687341f978>,\n",
       " <UniProtProp P0A796 at 0x7f687341fb00>]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_protein.sequences"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<PDBProp 1pfk at 0x7f68734c9160>,\n",
       " <PDBProp 2pfk at 0x7f687348dac8>,\n",
       " <StructProp K6PF1_ECOLI at 0x7f687341f048>,\n",
       " <StructProp E03690 at 0x7f687341f0f0>]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_protein.structures"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Domain information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['PDP:1ZXXAa', 'PDP:1ZXXAb']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_protein.representative_sequence.domains"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['PDP:1ZXXAa', 'PDP:1ZXXAb']"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_protein.representative_structure.domains"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Viewing 3D structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<PDBProp 1pfk at 0x7f68734c9160>,\n",
       " <PDBProp 2pfk at 0x7f687348dac8>,\n",
       " <StructProp K6PF1_ECOLI at 0x7f687341f048>,\n",
       " <StructProp E03690 at 0x7f687341f0f0>]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Listing all mapped structures for this protein\n",
    "iML1515_GP.genes.b3916.protein.structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Displaying the original PDB structure\n",
    "iML1515_GP.genes.b3916.protein.structures.get_by_id('1pfk').view_structure(recolor=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Displaying the single chain set as the protein's representative structure\n",
    "iML1515_GP.genes.b3916.protein.representative_structure.view_structure(recolor=False)"
   ]
  }
 ],
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