updated

Author: hamidrgh

docs/_modules/idpet/comparison.html

@@ -940,17 +940,17 @@ <h1>Source code for idpet.comparison</h1><div class="highlight"><pre>
 <span class="sd">        this case, IDPET will directly compare each pair of ensemble $i$ and</span>
 <span class="sd">        $j$ by using all of their conformers and perform the comparison only</span>
 <span class="sd">        once. On the other hand, if providing an integer value to this</span>
-<span class="sd">        argument, each pair of ensembles $i$ and $j$ will be compared</span>
+<span class="sd">        argument, each pair of ensembles *i* and *j* will be compared</span>
 <span class="sd">        `bootstrap_iters` times by randomly selecting (bootstrapping)</span>
 <span class="sd">        conformations from them. Additionally, each ensemble will be</span>
 <span class="sd">        auto-compared with itself by subsampling conformers via</span>
 <span class="sd">        bootstrapping. Then IDPET will perform a statistical test to</span>
-<span class="sd">        establish if the inter-ensemble ($i != j$) scores are significantly</span>
-<span class="sd">        different from the intra-ensemble ($i == j$) scores. The tests work</span>
-<span class="sd">        as follows: for each ensemble pair $i != j$ IDPET will get their</span>
+<span class="sd">        establish if the inter-ensemble (*i* != *j*) scores are significantly</span>
+<span class="sd">        different from the intra-ensemble (*i* == *j*) scores. The tests work</span>
+<span class="sd">        as follows: for each ensemble pair *i* != *j* IDPET will get their</span>
 <span class="sd">        inter-ensemble comparison scores obtained in bootstrapping. Then, it</span>
 <span class="sd">        will get the bootstrapping scores from auto-comparisons of ensemble</span>
-<span class="sd">        $i$ and $j$ and the scores with the higher mean here are selected as</span>
+<span class="sd">        *i* and *j* and the scores with the higher mean here are selected as</span>
 <span class="sd">        reference intra-ensemble scores. Finally, the inter-ensemble and</span>
 <span class="sd">        intra-ensemble scores are compared via a one-sided Mann-Whitney U</span>
 <span class="sd">        test with the alternative hypothesis being: inter-ensemble scores</span>

docs/comparison.html

@@ -139,17 +139,17 @@ <h2>Parameters<a class="headerlink" href="#parameters" title="Permalink to this
 this case, IDPET will directly compare each pair of ensemble $i$ and
 $j$ by using all of their conformers and perform the comparison only
 once. On the other hand, if providing an integer value to this
-argument, each pair of ensembles $i$ and $j$ will be compared
+argument, each pair of ensembles <em>i</em> and <em>j</em> will be compared
 <cite>bootstrap_iters</cite> times by randomly selecting (bootstrapping)
 conformations from them. Additionally, each ensemble will be
 auto-compared with itself by subsampling conformers via
 bootstrapping. Then IDPET will perform a statistical test to
-establish if the inter-ensemble ($i != j$) scores are significantly
-different from the intra-ensemble ($i == j$) scores. The tests work
-as follows: for each ensemble pair $i != j$ IDPET will get their
+establish if the inter-ensemble (<em>i</em> != <em>j</em>) scores are significantly
+different from the intra-ensemble (<em>i</em> == <em>j</em>) scores. The tests work
+as follows: for each ensemble pair <em>i</em> != <em>j</em> IDPET will get their
 inter-ensemble comparison scores obtained in bootstrapping. Then, it
 will get the bootstrapping scores from auto-comparisons of ensemble
-$i$ and $j$ and the scores with the higher mean here are selected as
+<em>i</em> and <em>j</em> and the scores with the higher mean here are selected as
 reference intra-ensemble scores. Finally, the inter-ensemble and
 intra-ensemble scores are compared via a one-sided Mann-Whitney U
 test with the alternative hypothesis being: inter-ensemble scores

docs/idpet.html

@@ -273,17 +273,17 @@ <h3>Parameters<a class="headerlink" href="#parameters" title="Permalink to this
 this case, IDPET will directly compare each pair of ensemble $i$ and
 $j$ by using all of their conformers and perform the comparison only
 once. On the other hand, if providing an integer value to this
-argument, each pair of ensembles $i$ and $j$ will be compared
+argument, each pair of ensembles <em>i</em> and <em>j</em> will be compared
 <cite>bootstrap_iters</cite> times by randomly selecting (bootstrapping)
 conformations from them. Additionally, each ensemble will be
 auto-compared with itself by subsampling conformers via
 bootstrapping. Then IDPET will perform a statistical test to
-establish if the inter-ensemble ($i != j$) scores are significantly
-different from the intra-ensemble ($i == j$) scores. The tests work
-as follows: for each ensemble pair $i != j$ IDPET will get their
+establish if the inter-ensemble (<em>i</em> != <em>j</em>) scores are significantly
+different from the intra-ensemble (<em>i</em> == <em>j</em>) scores. The tests work
+as follows: for each ensemble pair <em>i</em> != <em>j</em> IDPET will get their
 inter-ensemble comparison scores obtained in bootstrapping. Then, it
 will get the bootstrapping scores from auto-comparisons of ensemble
-$i$ and $j$ and the scores with the higher mean here are selected as
+<em>i</em> and <em>j</em> and the scores with the higher mean here are selected as
 reference intra-ensemble scores. Finally, the inter-ensemble and
 intra-ensemble scores are compared via a one-sided Mann-Whitney U
 test with the alternative hypothesis being: inter-ensemble scores

docs/searchindex.js

@@ -860,17 +860,17 @@ def all_vs_all_comparison(
         this case, IDPET will directly compare each pair of ensemble $i$ and
         $j$ by using all of their conformers and perform the comparison only
         once. On the other hand, if providing an integer value to this
-        argument, each pair of ensembles $i$ and $j$ will be compared
+        argument, each pair of ensembles *i* and *j* will be compared
         `bootstrap_iters` times by randomly selecting (bootstrapping)
         conformations from them. Additionally, each ensemble will be
         auto-compared with itself by subsampling conformers via
         bootstrapping. Then IDPET will perform a statistical test to
-        establish if the inter-ensemble ($i != j$) scores are significantly
-        different from the intra-ensemble ($i == j$) scores. The tests work
-        as follows: for each ensemble pair $i != j$ IDPET will get their
+        establish if the inter-ensemble (*i* != *j*) scores are significantly
+        different from the intra-ensemble (*i* == *j*) scores. The tests work
+        as follows: for each ensemble pair *i* != *j* IDPET will get their
         inter-ensemble comparison scores obtained in bootstrapping. Then, it
         will get the bootstrapping scores from auto-comparisons of ensemble
-        $i$ and $j$ and the scores with the higher mean here are selected as
+        *i* and *j* and the scores with the higher mean here are selected as
         reference intra-ensemble scores. Finally, the inter-ensemble and
         intra-ensemble scores are compared via a one-sided Mann-Whitney U
         test with the alternative hypothesis being: inter-ensemble scores