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<h1>Source code for networkx.readwrite.sparsegraph6</h1><div class="highlight"><pre>
<span class="sd">"""</span>
<span class="sd">**************</span>
<span class="sd">SparseGraph 6</span>
<span class="sd">**************</span>
<span class="sd">Read graphs in graph6 and sparse6 format.</span>
<span class="sd">Format</span>
<span class="sd">------</span>
<span class="sd">"graph6 and sparse6 are formats for storing undirected graphs in a</span>
<span class="sd">compact manner, using only printable ASCII characters. Files in these</span>
<span class="sd">formats have text type and contain one line per graph."</span>
<span class="sd">http://cs.anu.edu.au/~bdm/data/formats.html</span>
<span class="sd">See http://cs.anu.edu.au/~bdm/data/formats.txt for details.</span>
<span class="sd">"""</span>
<span class="c"># Original author: D. Eppstein, UC Irvine, August 12, 2003.</span>
<span class="c"># The original code at http://www.ics.uci.edu/~eppstein/PADS/ is public domain.</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s">"""Aric Hagberg (hagberg@lanl.gov)"""</span>
<span class="c"># Copyright (C) 2004-2010 by </span>
<span class="c"># Aric Hagberg <hagberg@lanl.gov></span>
<span class="c"># Dan Schult <dschult@colgate.edu></span>
<span class="c"># Pieter Swart <swart@lanl.gov></span>
<span class="c"># All rights reserved.</span>
<span class="c"># BSD license.</span>
<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'read_graph6'</span><span class="p">,</span> <span class="s">'parse_graph6'</span><span class="p">,</span> <span class="s">'read_graph6_list'</span><span class="p">,</span>
<span class="s">'read_sparse6'</span><span class="p">,</span> <span class="s">'parse_sparse6'</span><span class="p">,</span> <span class="s">'read_sparse6_list'</span><span class="p">]</span>
<span class="kn">import</span> <span class="nn">networkx</span> <span class="kn">as</span> <span class="nn">nx</span>
<span class="kn">from</span> <span class="nn">networkx.exception</span> <span class="kn">import</span> <span class="n">NetworkXError</span>
<span class="kn">from</span> <span class="nn">networkx.utils</span> <span class="kn">import</span> <span class="n">open_file</span>
<span class="c"># graph6</span>
<div class="viewcode-block" id="read_graph6"><a class="viewcode-back" href="../../../reference/generated/networkx.readwrite.sparsegraph6.read_graph6.html#networkx.readwrite.sparsegraph6.read_graph6">[docs]</a><span class="k">def</span> <span class="nf">read_graph6</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="sd">"""Read simple undirected graphs in graph6 format from path.</span>
<span class="sd"> Returns a single Graph.</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">read_graph6_list</span><span class="p">(</span><span class="n">path</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</div>
<div class="viewcode-block" id="parse_graph6"><a class="viewcode-back" href="../../../reference/generated/networkx.readwrite.sparsegraph6.parse_graph6.html#networkx.readwrite.sparsegraph6.parse_graph6">[docs]</a><span class="k">def</span> <span class="nf">parse_graph6</span><span class="p">(</span><span class="nb">str</span><span class="p">):</span>
<span class="sd">"""Read a simple undirected graph in graph6 format from string.</span>
<span class="sd"> Returns a single Graph.</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">bits</span><span class="p">():</span>
<span class="sd">"""Return sequence of individual bits from 6-bit-per-value</span>
<span class="sd"> list of data values."""</span>
<span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">5</span><span class="p">,</span><span class="mi">4</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">]:</span>
<span class="k">yield</span> <span class="p">(</span><span class="n">d</span><span class="o">>></span><span class="n">i</span><span class="p">)</span><span class="o">&</span><span class="mi">1</span>
<span class="k">if</span> <span class="nb">str</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'>>graph6<<'</span><span class="p">):</span>
<span class="nb">str</span> <span class="o">=</span> <span class="nb">str</span><span class="p">[</span><span class="mi">10</span><span class="p">:]</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">graph6data</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
<span class="n">n</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="n">graph6n</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="n">nd</span> <span class="o">=</span> <span class="p">(</span><span class="n">n</span><span class="o">*</span><span class="p">(</span><span class="n">n</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">//</span><span class="mi">2</span> <span class="o">+</span> <span class="mi">5</span><span class="p">)</span> <span class="o">//</span> <span class="mi">6</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="o">!=</span> <span class="n">nd</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">NetworkXError</span><span class="p">(</span>\
<span class="s">'Expected </span><span class="si">%d</span><span class="s"> bits but got </span><span class="si">%d</span><span class="s"> in graph6'</span> <span class="o">%</span> <span class="p">(</span><span class="n">n</span><span class="o">*</span><span class="p">(</span><span class="n">n</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">//</span><span class="mi">2</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)</span><span class="o">*</span><span class="mi">6</span><span class="p">))</span>
<span class="n">G</span><span class="o">=</span><span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_nodes_from</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">n</span><span class="p">))</span>
<span class="k">for</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">),</span><span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">([(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j</span><span class="p">)],</span> <span class="n">bits</span><span class="p">()):</span>
<span class="k">if</span> <span class="n">b</span><span class="p">:</span> <span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span>
<span class="k">return</span> <span class="n">G</span>
</div>
<span class="nd">@open_file</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">mode</span><span class="o">=</span><span class="s">'rt'</span><span class="p">)</span>
<div class="viewcode-block" id="read_graph6_list"><a class="viewcode-back" href="../../../reference/generated/networkx.readwrite.sparsegraph6.read_graph6_list.html#networkx.readwrite.sparsegraph6.read_graph6_list">[docs]</a><span class="k">def</span> <span class="nf">read_graph6_list</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="sd">"""Read simple undirected graphs in graph6 format from path.</span>
<span class="sd"> Returns a list of Graphs, one for each line in file.</span>
<span class="sd"> """</span>
<span class="n">glist</span><span class="o">=</span><span class="p">[]</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">path</span><span class="p">:</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">):</span> <span class="k">continue</span>
<span class="n">glist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">parse_graph6</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
<span class="k">return</span> <span class="n">glist</span>
<span class="c"># sparse6</span>
</div>
<div class="viewcode-block" id="read_sparse6"><a class="viewcode-back" href="../../../reference/generated/networkx.readwrite.sparsegraph6.read_sparse6.html#networkx.readwrite.sparsegraph6.read_sparse6">[docs]</a><span class="k">def</span> <span class="nf">read_sparse6</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="sd">"""Read simple undirected graphs in sparse6 format from path.</span>
<span class="sd"> Returns a single MultiGraph."""</span>
<span class="k">return</span> <span class="n">read_sparse6_list</span><span class="p">(</span><span class="n">path</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
</div>
<span class="nd">@open_file</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">mode</span><span class="o">=</span><span class="s">'rt'</span><span class="p">)</span>
<div class="viewcode-block" id="read_sparse6_list"><a class="viewcode-back" href="../../../reference/generated/networkx.readwrite.sparsegraph6.read_sparse6_list.html#networkx.readwrite.sparsegraph6.read_sparse6_list">[docs]</a><span class="k">def</span> <span class="nf">read_sparse6_list</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="sd">"""Read undirected graphs in sparse6 format from path.</span>
<span class="sd"> Returns a list of MultiGraphs, one for each line in file."""</span>
<span class="n">glist</span><span class="o">=</span><span class="p">[]</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">path</span><span class="p">:</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">):</span> <span class="k">continue</span>
<span class="n">glist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">parse_sparse6</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
<span class="k">return</span> <span class="n">glist</span>
</div>
<div class="viewcode-block" id="parse_sparse6"><a class="viewcode-back" href="../../../reference/generated/networkx.readwrite.sparsegraph6.parse_sparse6.html#networkx.readwrite.sparsegraph6.parse_sparse6">[docs]</a><span class="k">def</span> <span class="nf">parse_sparse6</span><span class="p">(</span><span class="n">string</span><span class="p">):</span>
<span class="sd">"""Read undirected graph in sparse6 format from string.</span>
<span class="sd"> Returns a MultiGraph.</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">string</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'>>sparse6<<'</span><span class="p">):</span>
<span class="n">string</span> <span class="o">=</span> <span class="nb">str</span><span class="p">[</span><span class="mi">10</span><span class="p">:]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">string</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">':'</span><span class="p">):</span>
<span class="k">raise</span> <span class="n">NetworkXError</span><span class="p">(</span><span class="s">'Expected colon in sparse6'</span><span class="p">)</span>
<span class="n">n</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="n">graph6n</span><span class="p">(</span><span class="n">graph6data</span><span class="p">(</span><span class="n">string</span><span class="p">[</span><span class="mi">1</span><span class="p">:]))</span>
<span class="n">k</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">while</span> <span class="mi">1</span><span class="o"><<</span><span class="n">k</span> <span class="o"><</span> <span class="n">n</span><span class="p">:</span>
<span class="n">k</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">def</span> <span class="nf">parseData</span><span class="p">():</span>
<span class="sd">"""Return stream of pairs b[i], x[i] for sparse6 format."""</span>
<span class="n">chunks</span> <span class="o">=</span> <span class="nb">iter</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="n">d</span> <span class="o">=</span> <span class="bp">None</span> <span class="c"># partial data word</span>
<span class="n">dLen</span> <span class="o">=</span> <span class="mi">0</span> <span class="c"># how many unparsed bits are left in d</span>
<span class="k">while</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">if</span> <span class="n">dLen</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">d</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">chunks</span><span class="p">)</span>
<span class="n">dLen</span> <span class="o">=</span> <span class="mi">6</span>
<span class="n">dLen</span> <span class="o">-=</span> <span class="mi">1</span>
<span class="n">b</span> <span class="o">=</span> <span class="p">(</span><span class="n">d</span><span class="o">>></span><span class="n">dLen</span><span class="p">)</span> <span class="o">&</span> <span class="mi">1</span> <span class="c"># grab top remaining bit</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">d</span> <span class="o">&</span> <span class="p">((</span><span class="mi">1</span><span class="o"><<</span><span class="n">dLen</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="c"># partially built up value of x</span>
<span class="n">xLen</span> <span class="o">=</span> <span class="n">dLen</span> <span class="c"># how many bits included so far in x</span>
<span class="k">while</span> <span class="n">xLen</span> <span class="o"><</span> <span class="n">k</span><span class="p">:</span> <span class="c"># now grab full chunks until we have enough</span>
<span class="n">d</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">chunks</span><span class="p">)</span>
<span class="n">dLen</span> <span class="o">=</span> <span class="mi">6</span>
<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">x</span><span class="o"><<</span><span class="mi">6</span><span class="p">)</span> <span class="o">+</span> <span class="n">d</span>
<span class="n">xLen</span> <span class="o">+=</span> <span class="mi">6</span>
<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">x</span> <span class="o">>></span> <span class="p">(</span><span class="n">xLen</span> <span class="o">-</span> <span class="n">k</span><span class="p">))</span> <span class="c"># shift back the extra bits</span>
<span class="n">dLen</span> <span class="o">=</span> <span class="n">xLen</span> <span class="o">-</span> <span class="n">k</span>
<span class="k">yield</span> <span class="n">b</span><span class="p">,</span><span class="n">x</span>
<span class="n">v</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">G</span><span class="o">=</span><span class="n">nx</span><span class="o">.</span><span class="n">MultiGraph</span><span class="p">()</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_nodes_from</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">n</span><span class="p">))</span>
<span class="k">for</span> <span class="n">b</span><span class="p">,</span><span class="n">x</span> <span class="ow">in</span> <span class="n">parseData</span><span class="p">():</span>
<span class="k">if</span> <span class="n">b</span><span class="p">:</span> <span class="n">v</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">x</span> <span class="o">>=</span> <span class="n">n</span><span class="p">:</span> <span class="k">break</span> <span class="c"># padding with ones can cause overlarge number here</span>
<span class="k">elif</span> <span class="n">x</span> <span class="o">></span> <span class="n">v</span><span class="p">:</span> <span class="n">v</span> <span class="o">=</span> <span class="n">x</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">v</span><span class="p">)</span>
<span class="k">return</span> <span class="n">G</span>
<span class="c"># helper functions</span>
</div>
<span class="k">def</span> <span class="nf">graph6data</span><span class="p">(</span><span class="nb">str</span><span class="p">):</span>
<span class="sd">"""Convert graph6 character sequence to 6-bit integers."""</span>
<span class="n">v</span> <span class="o">=</span> <span class="p">[</span><span class="nb">ord</span><span class="p">(</span><span class="n">c</span><span class="p">)</span><span class="o">-</span><span class="mi">63</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">str</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">min</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="o"><</span> <span class="mi">0</span> <span class="ow">or</span> <span class="nb">max</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="o">></span> <span class="mi">63</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">return</span> <span class="n">v</span>
<span class="k">def</span> <span class="nf">graph6n</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
<span class="sd">"""Read initial one or four-unit value from graph6 sequence. </span>
<span class="sd"> Return value, rest of seq."""</span>
<span class="k">if</span> <span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o"><=</span> <span class="mi">62</span><span class="p">:</span>
<span class="k">return</span> <span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
<span class="k">return</span> <span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o"><<</span><span class="mi">12</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o"><<</span><span class="mi">6</span><span class="p">)</span> <span class="o">+</span> <span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="mi">4</span><span class="p">:]</span>
</pre></div>
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