Created docs folder and its content with sphinx.

README.md

@@ -54,42 +54,9 @@ JET is run in its iterative mode, iJET, 10 times and the final conservation leve
 values obtained over the 10 iterations. 
 JET2 configuration file is: default.conf.
 JET2 output file is: myProt_jet.res.
-### Analyzing the ESGEMME output
-By default, ESGEMME will output the following files: 
-* myProt_normPred_evolEpi.txt
-* myProt_normPred_evolInd.txt
-* myProt_normPred_evolCombi.txt
-
-The most important output file is **myProt_normPred_evolCombi.txt**. 
-The values of interest are the normalized predictions (normPred). Each file contains a 20 x n matrix, 
-where n is the number of positions in the query sequence.
-If the user provides her/his own list of mutations, then only the global epistatic model will be run 
-and the output file will contain 2 columns, the first one with the mutations, the second one with the 
-normalized predicted effects.
 
 ## Installation
-ESGEMME is implemented in Python 3 and R. It has been tested only on Linux. Since ESGEMME has many dependencies, we recommend using our web site or our docker image. If you are a determined user, here comes the steps required to install it from the source.
-
-### Installation from the source:
-
-#### Getting the source code and preparing the environment: 
-Download the ESGEMME source code from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.
-Define and export the environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/
-
-```bash
-export ESGEMME_PATH=/path-to-ESGEMME-directory/
-```
-
-#### Installing the dependencies:
-ESGEMME has the following external dependencies:
-* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
-    - naccess: http://www.bioinf.manchester.ac.uk/naccess/
-    - muscle: https://www.drive5.com/muscle/
-**
-* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html 
-* dssp for secondary structure prediction.
-
-These tools should be installed to be able to use ESGEMME.
+ESGEMME is implemented in Python 3 and R. It has been tested only on Linux. Since ESGEMME has many dependencies, we recommend using our web site or our docker image. If you are a determined user, you can find the steps required to install it from the source in the following link (or in the docs folder of this repository):
 
 
 # Cite 

docs/Makefile

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+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
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+
+.PHONY: help Makefile
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+# Catch-all target: route all unknown targets to Sphinx using the new
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+# Prefix for archive names
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+# format: pdf or dvi (used only by archive targets)
+FMT = pdf
+
+LATEX = latexmk -dvi
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\ No newline at end of file

docs/_build/_sources/analysis.rst.txt

+Analyzing the ESGEMME output
+----------------------------
+
+By default, ESGEMME will output the following files: \*
+myProt_normPred_evolEpi.txt \* myProt_normPred_evolInd.txt \*
+myProt_normPred_evolCombi.txt
+
+The most important output file is **myProt_normPred_evolCombi.txt**. The
+values of interest are the normalized predictions (normPred). Each file
+contains a 20 x n matrix, where n is the number of positions (columns) in the
+query sequence. If the user provides her/his own list of mutations, then
+only the global epistatic model will be run and the output file will
+contain 2 columns, the first one with the mutations, the second one with
+the normalized predicted effects.

docs/_build/_sources/docker.rst.txt

+Using ESGEMME via Docker
+========================
+
+Requirements
+------------
+
+You need to have docker installed on your machine. You can consult the
+following page for this: https://docs.docker.com/get-docker/
+
+I am assuming some basic familiarity with Linux/Unix/MacOS terminal
+commands.
+
+Let’s start our favorite terminal app.
+
+You must to create a folder called docker-tutorial and go to that empty
+folder:
+
+.. code:: bash
+
+   mkdir docker-tutorial
+   cd docker-tutorial
+
+Getting the input data
+----------------------
+
+Let’s download the sample data provided in the ESGEMME repository for
+this exercise. First, we will download the multiple sequence alignment
+file in fasta format:
+
+.. code:: bash
+
+   wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
+
+If you don’t have wget, you can try the same command with curl:
+
+.. code:: bash
+
+   curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
+
+Please verify that the aliBLAT.fasta file is in the folder.
+
+Now, we will download the PDB (Protein Databank) file for BLAT:
+
+.. code:: bash
+
+   wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
+
+Single point mutation calculations 
+----------------------------------
+
+In order to make sure that the docker is installed:
+
+.. code:: bash
+
+   sudo docker -h
+
+If it shows you a list of options, you are on a good track. On MacOS,
+you may not need ‘sudo’ word before the docker command at all.
+
+.. code:: bash
+
+   sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
+   tekpinar/esgemme-docker:v1.3.0
+
+You are in the container (your virtual operating system) now. You
+created a folder called myexample in your container with the previous
+command. Let’s change to that folder.
+
+.. code:: bash
+
+   cd ../myexample/
+
+When you check the data in that folder with ‘ls’ command, you are
+supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
+docker-tutorial folder on the host system and myexample folder on the
+docker container are pointing to the same place.
+
+Obtaining the entire single point mutation landscape
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+In this step, we will use only evolutionary information from an MSA file:
+
+.. code:: bash
+
+   python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
+
+After a few minutes of calculation, you must see at least two files named
+BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
+the entire single point mutational landscape of BLAT protein in these
+files.
+
+If you want to utilize structural information (highly recommended) as well as 
+evolutionary information:
+
+.. code:: bash
+
+   python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
+   --pdbfile blat-af2.pdb \
+   --normweightmode sstjetormax 
+
+Obtaining the effect of a subset of single point mutations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+If you are interested in only a bunch of single point mutations, 
+you have to prepare a mut file. The format is a simple text file and 
+each line contains a single point mutation such as D26A....
+Fortunately, we have an example mut in data folder of ESGEMME repository.
+
+.. code:: bash
+
+   wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
+
+Similar to the previous step, there are two possible ways to do the calculations: with or without
+structural information. First, without structural information: 
+
+.. code:: bash
+   
+   python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
+   -m Stiffler_2015_BLAT_ECOLX.mut 
+
+You can include structural information in the following way:
+.. code:: bash
+   
+   python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
+   --pdbfile blat-af2.pdb \
+   --normweightmode sstjetormax \
+   -m Stiffler_2015_BLAT_ECOLX.mut
+
+You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output 
+format is completely different from the entire mutational landscape scanning file.
+Each line of this file is a mutation and its predicted effect separated by a space.
+In addition, you won't have a png file like in the previous case. 
+
+Multiple point mutation calculations 
+------------------------------------
+Sometimes, we need to see effects of double or triple mutations. ESGEMME can 
+perform calculations if you provide a mut file. In this case, the mut file must
+have the following format:
+
+.. code:: bash
+
+   E26D:Y44R
+   E56N:A77F:H94V
+
+The first line of the text file is impact of a double mutations and the second 
+line is the impact of the triple mutations. As you can see, the mutations are 
+separated by a colon(:) character. 
+The output file will be in a similar format. Each line will contain the multiple 
+mutation and its predicted effect, separated by a space.  
+
+
+Running several jobs using docker
+---------------------------------

docs/_build/_sources/index.rst.txt

+.. esgemme documentation master file, created by
+   sphinx-quickstart on Fri May  5 13:52:13 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to esgemme's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   docker.rst
+   analysis.rst
+   installation.rst
+   
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/_build/_sources/installation.rst.txt

+Installation
+------------
+
+ESGEMME is implemented in Python 3 and R. It has been tested only on
+Linux. Since ESGEMME has many dependencies, we recommend using our web
+site or our docker image. If you are a determined user, here comes the
+steps required to install it from the source.
+
+Installing the dependencies:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ESGEMME has the following external dependencies: \* Joint Evolutionary
+Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies: - naccess:
+http://www.bioinf.manchester.ac.uk/naccess/ - muscle:
+https://www.drive5.com/muscle/ \*\* \* seqinr R package:
+https://cran.r-project.org/web/packages/seqinr/index.html \* dssp for
+secondary structure prediction.
+
+These tools should be installed to be able to use ESGEMME.
+
+Getting the source code and preparing the environment:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Download the ESGEMME source code from
+http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME. Define and export the
+environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/
+
+.. code:: bash
+
+   export ESGEMME_PATH=/path-to-ESGEMME-directory/
+
+Configuring default.conf file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Inside ESGEMME folder, there is an important file called default.conf. 
+This file contains essential parameters of ESGEMME, such as paths of
+external parts, default internal parameters. etc. You have to correct the Software section of this
+file according to your system.
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+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+    "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+    "profile", "profileEnd"];
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+  return decodeURIComponent(x).replace(/\+/g, ' ');
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+  if (typeof s === 'undefined')
+    s = document.location.search;
+  var parts = s.substr(s.indexOf('?') + 1).split('&');
+  var result = {};
+  for (var i = 0; i < parts.length; i++) {
+    var tmp = parts[i].split('=', 2);
+    var key = jQuery.urldecode(tmp[0]);
+    var value = jQuery.urldecode(tmp[1]);
+    if (key in result)
+      result[key].push(value);
+    else
+      result[key] = [value];
+  }
+  return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+  function highlight(node, addItems) {
+    if (node.nodeType === 3) {
+      var val = node.nodeValue;
+      var pos = val.toLowerCase().indexOf(text);
+      if (pos >= 0 &&
+          !jQuery(node.parentNode).hasClass(className) &&
+          !jQuery(node.parentNode).hasClass("nohighlight")) {
+        var span;
+        var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+        if (isInSVG) {
+          span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+        } else {
+          span = document.createElement("span");
+          span.className = className;
+        }
+        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling));
+        node.nodeValue = val.substr(0, pos);
+        if (isInSVG) {
+          var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+          var bbox = node.parentElement.getBBox();
+          rect.x.baseVal.value = bbox.x;
+          rect.y.baseVal.value = bbox.y;
+          rect.width.baseVal.value = bbox.width;
+          rect.height.baseVal.value = bbox.height;
+          rect.setAttribute('class', className);
+          addItems.push({
+              "parent": node.parentNode,
+              "target": rect});
+        }
+      }
+    }
+    else if (!jQuery(node).is("button, select, textarea")) {
+      jQuery.each(node.childNodes, function() {
+        highlight(this, addItems);
+      });
+    }
+  }
+  var addItems = [];
+  var result = this.each(function() {
+    highlight(this, addItems);
+  });
+  for (var i = 0; i < addItems.length; ++i) {
+    jQuery(addItems[i].parent).before(addItems[i].target);
+  }
+  return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+  jQuery.uaMatch = function(ua) {
+    ua = ua.toLowerCase();
+
+    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+      /(msie) ([\w.]+)/.exec(ua) ||
+      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+      [];
+
+    return {
+      browser: match[ 1 ] || "",
+      version: match[ 2 ] || "0"
+    };
+  };
+  jQuery.browser = {};
+  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+  init : function() {
+    this.fixFirefoxAnchorBug();
+    this.highlightSearchWords();
+    this.initIndexTable();
+    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+      this.initOnKeyListeners();
+    }
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS : {},
+  PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
+  LOCALE : 'unknown',
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext : function(string) {
+    var translated = Documentation.TRANSLATIONS[string];
+    if (typeof translated === 'undefined')
+      return string;
+    return (typeof translated === 'string') ? translated : translated[0];
+  },
+
+  ngettext : function(singular, plural, n) {
+    var translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated === 'undefined')
+      return (n == 1) ? singular : plural;
+    return translated[Documentation.PLURALEXPR(n)];
+  },
+
+  addTranslations : function(catalog) {
+    for (var key in catalog.messages)
+      this.TRANSLATIONS[key] = catalog.messages[key];
+    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+    this.LOCALE = catalog.locale;
+  },
+
+  /**
+   * add context elements like header anchor links
+   */
+  addContextElements : function() {
+    $('div[id] > :header:first').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this headline')).
+      appendTo(this);
+    });
+    $('dt[id]').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this definition')).
+      appendTo(this);
+    });
+  },
+
+  /**
+   * workaround a firefox stupidity
+   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
+   */
+  fixFirefoxAnchorBug : function() {
+    if (document.location.hash && $.browser.mozilla)
+      window.setTimeout(function() {
+        document.location.href += '';
+      }, 10);
+  },
+
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords : function() {
+    var params = $.getQueryParameters();
+    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+    if (terms.length) {
+      var body = $('div.body');
+      if (!body.length) {
+        body = $('body');
+      }
+      window.setTimeout(function() {
+        $.each(terms, function() {
+          body.highlightText(this.toLowerCase(), 'highlighted');
+        });
+      }, 10);
+      $('<p class="highlight-link"><a href="javascript:Documentation.' +
+        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+          .appendTo($('#searchbox'));
+    }
+  },
+
+  /**
+   * init the domain index toggle buttons
+   */
+  initIndexTable : function() {
+    var togglers = $('img.toggler').click(function() {
+      var src = $(this).attr('src');
+      var idnum = $(this).attr('id').substr(7);
+      $('tr.cg-' + idnum).toggle();
+      if (src.substr(-9) === 'minus.png')
+        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+      else
+        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+    }).css('display', '');
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+        togglers.click();
+    }
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords : function() {
+    $('#searchbox .highlight-link').fadeOut(300);
+    $('span.highlighted').removeClass('highlighted');
+  },
+
+  /**
+   * make the url absolute
+   */
+  makeURL : function(relativeURL) {
+    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+  },
+
+  /**
+   * get the current relative url
+   */
+  getCurrentURL : function() {
+    var path = document.location.pathname;
+    var parts = path.split(/\//);
+    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+      if (this === '..')
+        parts.pop();
+    });
+    var url = parts.join('/');
+    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  },
+
+  initOnKeyListeners: function() {
+    $(document).keydown(function(event) {
+      var activeElementType = document.activeElement.tagName;
+      // don't navigate when in search box or textarea
+      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
+          && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
+        switch (event.keyCode) {
+          case 37: // left
+            var prevHref = $('link[rel="prev"]').prop('href');
+            if (prevHref) {
+              window.location.href = prevHref;
+              return false;
+            }
+          case 39: // right
+            var nextHref = $('link[rel="next"]').prop('href');
+            if (nextHref) {
+              window.location.href = nextHref;
+              return false;
+            }
+        }
+      }
+    });
+  }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+  Documentation.init();
+});

docs/_build/_static/documentation_options.js

+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+    VERSION: '1.3.0',
+    LANGUAGE: 'None',
+    COLLAPSE_INDEX: false,
+    BUILDER: 'html',
+    FILE_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false
+};
\ No newline at end of file

docs/_build/_static/js/badge_only.js

+!function(e){var t={};function r(n){if(t[n])return t[n].exports;var o=t[n]={i:n,l:!1,exports:{}};return e[n].call(o.exports,o,o.exports,r),o.l=!0,o.exports}r.m=e,r.c=t,r.d=function(e,t,n){r.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:n})},r.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})},r.t=function(e,t){if(1&t&&(e=r(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)r.d(n,o,function(t){return e[t]}.bind(null,o));return n},r.n=function(e){var t=e&&e.__esModule?function(){return e.default}:function(){return e};return r.d(t,"a",t),t},r.o=function(e,t){return Object.prototype.hasOwnProperty.call(e,t)},r.p="",r(r.s=4)}({4:function(e,t,r){}});
\ No newline at end of file

docs/_build/_static/js/html5shiv-printshiv.min.js

+/**
+* @preserve HTML5 Shiv 3.7.3-pre | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
+*/
+!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x<style>"+b+"</style>",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=y.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=y.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),y.elements=c+" "+a,j(b)}function f(a){var b=x[a[v]];return b||(b={},w++,a[v]=w,x[w]=b),b}function g(a,c,d){if(c||(c=b),q)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():u.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||t.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),q)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return y.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(y,b.frag)}function j(a){a||(a=b);var d=f(a);return!y.shivCSS||p||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),q||i(a,d),a}function k(a){for(var b,c=a.getElementsByTagName("*"),e=c.length,f=RegExp("^(?:"+d().join("|")+")$","i"),g=[];e--;)b=c[e],f.test(b.nodeName)&&g.push(b.applyElement(l(b)));return g}function l(a){for(var b,c=a.attributes,d=c.length,e=a.ownerDocument.createElement(A+":"+a.nodeName);d--;)b=c[d],b.specified&&e.setAttribute(b.nodeName,b.nodeValue);return e.style.cssText=a.style.cssText,e}function m(a){for(var b,c=a.split("{"),e=c.length,f=RegExp("(^|[\\s,>+~])("+d().join("|")+")(?=[[\\s,>+~#.:]|$)","gi"),g="$1"+A+"\\:$2";e--;)b=c[e]=c[e].split("}"),b[b.length-1]=b[b.length-1].replace(f,g),c[e]=b.join("}");return c.join("{")}function n(a){for(var b=a.length;b--;)a[b].removeNode()}function o(a){function b(){clearTimeout(g._removeSheetTimer),d&&d.removeNode(!0),d=null}var d,e,g=f(a),h=a.namespaces,i=a.parentWindow;return!B||a.printShived?a:("undefined"==typeof h[A]&&h.add(A),i.attachEvent("onbeforeprint",function(){b();for(var f,g,h,i=a.styleSheets,j=[],l=i.length,n=Array(l);l--;)n[l]=i[l];for(;h=n.pop();)if(!h.disabled&&z.test(h.media)){try{f=h.imports,g=f.length}catch(o){g=0}for(l=0;g>l;l++)n.push(f[l]);try{j.push(h.cssText)}catch(o){}}j=m(j.reverse().join("")),e=k(a),d=c(a,j)}),i.attachEvent("onafterprint",function(){n(e),clearTimeout(g._removeSheetTimer),g._removeSheetTimer=setTimeout(b,500)}),a.printShived=!0,a)}var p,q,r="3.7.3",s=a.html5||{},t=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,u=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,v="_html5shiv",w=0,x={};!function(){try{var a=b.createElement("a");a.innerHTML="<xyz></xyz>",p="hidden"in a,q=1==a.childNodes.length||function(){b.createElement("a");var a=b.createDocumentFragment();return"undefined"==typeof a.cloneNode||"undefined"==typeof a.createDocumentFragment||"undefined"==typeof a.createElement}()}catch(c){p=!0,q=!0}}();var y={elements:s.elements||"abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output picture progress section summary template time video",version:r,shivCSS:s.shivCSS!==!1,supportsUnknownElements:q,shivMethods:s.shivMethods!==!1,type:"default",shivDocument:j,createElement:g,createDocumentFragment:h,addElements:e};a.html5=y,j(b);var z=/^$|\b(?:all|print)\b/,A="html5shiv",B=!q&&function(){var c=b.documentElement;return!("undefined"==typeof b.namespaces||"undefined"==typeof b.parentWindow||"undefined"==typeof c.applyElement||"undefined"==typeof c.removeNode||"undefined"==typeof a.attachEvent)}();y.type+=" print",y.shivPrint=o,o(b),"object"==typeof module&&module.exports&&(module.exports=y)}("undefined"!=typeof window?window:this,document);
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docs/_build/_static/js/html5shiv.min.js

+/**
+* @preserve HTML5 Shiv 3.7.3 | @afarkas @jdalton @jon_neal @rem | MIT/GPL2 Licensed
+*/
+!function(a,b){function c(a,b){var c=a.createElement("p"),d=a.getElementsByTagName("head")[0]||a.documentElement;return c.innerHTML="x<style>"+b+"</style>",d.insertBefore(c.lastChild,d.firstChild)}function d(){var a=t.elements;return"string"==typeof a?a.split(" "):a}function e(a,b){var c=t.elements;"string"!=typeof c&&(c=c.join(" ")),"string"!=typeof a&&(a=a.join(" ")),t.elements=c+" "+a,j(b)}function f(a){var b=s[a[q]];return b||(b={},r++,a[q]=r,s[r]=b),b}function g(a,c,d){if(c||(c=b),l)return c.createElement(a);d||(d=f(c));var e;return e=d.cache[a]?d.cache[a].cloneNode():p.test(a)?(d.cache[a]=d.createElem(a)).cloneNode():d.createElem(a),!e.canHaveChildren||o.test(a)||e.tagUrn?e:d.frag.appendChild(e)}function h(a,c){if(a||(a=b),l)return a.createDocumentFragment();c=c||f(a);for(var e=c.frag.cloneNode(),g=0,h=d(),i=h.length;i>g;g++)e.createElement(h[g]);return e}function i(a,b){b.cache||(b.cache={},b.createElem=a.createElement,b.createFrag=a.createDocumentFragment,b.frag=b.createFrag()),a.createElement=function(c){return t.shivMethods?g(c,a,b):b.createElem(c)},a.createDocumentFragment=Function("h,f","return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&("+d().join().replace(/[\w\-:]+/g,function(a){return b.createElem(a),b.frag.createElement(a),'c("'+a+'")'})+");return n}")(t,b.frag)}function j(a){a||(a=b);var d=f(a);return!t.shivCSS||k||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),l||i(a,d),a}var k,l,m="3.7.3-pre",n=a.html5||{},o=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,p=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,q="_html5shiv",r=0,s={};!function(){try{var a=b.createElement("a");a.innerHTML="<xyz></xyz>",k="hidden"in a,l=1==a.childNodes.length||function(){b.createElement("a");var a=b.createDocumentFragment();return"undefined"==typeof a.cloneNode||"undefined"==typeof a.createDocumentFragment||"undefined"==typeof a.createElement}()}catch(c){k=!0,l=!0}}();var t={elements:n.elements||"abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output picture progress section summary template time video",version:m,shivCSS:n.shivCSS!==!1,supportsUnknownElements:l,shivMethods:n.shivMethods!==!1,type:"default",shivDocument:j,createElement:g,createDocumentFragment:h,addElements:e};a.html5=t,j(b),"object"==typeof module&&module.exports&&(module.exports=t)}("undefined"!=typeof window?window:this,document);
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docs/_build/_static/js/theme.js

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docs/_build/analysis.html

+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Analyzing the ESGEMME output &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing the ESGEMME output</a></li>
+</ul>
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+           <div itemprop="articleBody">
+             
+  <div class="section" id="analyzing-the-esgemme-output">
+<h1>Analyzing the ESGEMME output<a class="headerlink" href="#analyzing-the-esgemme-output" title="Permalink to this headline"></a></h1>
+<p>By default, ESGEMME will output the following files: *
+myProt_normPred_evolEpi.txt * myProt_normPred_evolInd.txt *
+myProt_normPred_evolCombi.txt</p>
+<p>The most important output file is <strong>myProt_normPred_evolCombi.txt</strong>. The
+values of interest are the normalized predictions (normPred). Each file
+contains a 20 x n matrix, where n is the number of positions (columns) in the
+query sequence. If the user provides her/his own list of mutations, then
+only the global epistatic model will be run and the output file will
+contain 2 columns, the first one with the mutations, the second one with
+the normalized predicted effects.</p>
+</div>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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\ No newline at end of file

docs/_build/footnotehyper-sphinx.sty

+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{footnotehyper-sphinx}%
+ [2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)]
+%%
+%% Package: footnotehyper-sphinx
+%% Version: based on footnotehyper.sty 2017/03/07 v1.0
+%% as available at https://www.ctan.org/pkg/footnotehyper
+%% License: the one applying to Sphinx
+%%
+%% Refer to the PDF documentation  at https://www.ctan.org/pkg/footnotehyper for
+%% the code comments.
+%%
+%% Differences:
+%% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up),
+%% 2. use of \spx@opt@BeforeFootnote from sphinx.sty,
+%% 3. use of \sphinxunactivateextrasandspace from sphinx.sty,
+%% 4. macro definition \sphinxfootnotemark,
+%% 5. macro definition \sphinxlongtablepatch
+%% 6. replaced an \undefined by \@undefined
+\DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}%
+\ProcessOptions\relax
+\newbox\FNH@notes
+\newdimen\FNH@width
+\let\FNH@colwidth\columnwidth
+\newif\ifFNH@savingnotes
+\AtBeginDocument {%
+    \let\FNH@latex@footnote    \footnote
+    \let\FNH@latex@footnotetext\footnotetext
+    \let\FNH@H@@footnotetext   \@footnotetext
+    \newenvironment{savenotes}
+        {\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}%
+    \let\spewnotes      \FNH@spewnotes
+    \let\footnote       \FNH@footnote
+    \let\footnotetext   \FNH@footnotetext
+    \let\endfootnote    \FNH@endfntext
+    \let\endfootnotetext\FNH@endfntext
+    \@ifpackageloaded{hyperref}
+     {\ifHy@hyperfootnotes
+         \let\FNH@H@@footnotetext\H@@footnotetext
+      \else
+         \let\FNH@hyper@fntext\FNH@nohyp@fntext
+      \fi}%
+     {\let\FNH@hyper@fntext\FNH@nohyp@fntext}%
+}%
+\def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}%
+\def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}%
+\def\FNH@fntext #1{%
+  \ifx\ifmeasuring@\@undefined
+    \expandafter\@secondoftwo\else\expandafter\@firstofone\fi
+% these two lines modified for Sphinx (tabulary compatibility):
+    {\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}%
+    {\ifx\equation$\expandafter\@gobbletwo\fi #1}%$
+}%
+\long\def\FNH@hyper@fntext@i#1{%
+  \global\setbox\FNH@notes\vbox
+  {\unvbox\FNH@notes
+   \FNH@startnote
+   \@makefntext
+    {\rule\z@\footnotesep\ignorespaces
+     \ifHy@nesting\expandafter\ltx@firstoftwo
+             \else\expandafter\ltx@secondoftwo
+     \fi
+     {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}%
+     {\Hy@raisedlink
+       {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}%
+       {\relax}}%
+      \let\@currentHref\Hy@footnote@currentHref
+      \let\@currentlabelname\@empty
+      #1}%
+     \@finalstrut\strutbox
+    }%
+   \FNH@endnote
+  }%
+}%
+\long\def\FNH@nohyp@fntext@i#1{%
+  \global\setbox\FNH@notes\vbox
+  {\unvbox\FNH@notes
+   \FNH@startnote
+   \@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}%
+   \FNH@endnote
+  }%
+}%
+\def\FNH@startnote{%
+  \hsize\FNH@colwidth
+  \interlinepenalty\interfootnotelinepenalty
+  \reset@font\footnotesize
+  \floatingpenalty\@MM
+  \@parboxrestore
+  \protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
+  \color@begingroup
+}%
+\def\FNH@endnote{\color@endgroup}%
+\def\FNH@savenotes{%
+  \begingroup
+  \ifFNH@savingnotes\else
+    \FNH@savingnotestrue
+    \let\@footnotetext    \FNH@hyper@fntext
+    \let\@mpfootnotetext  \FNH@hyper@fntext
+    \let\H@@mpfootnotetext\FNH@nohyp@fntext
+    \FNH@width\columnwidth
+    \let\FNH@colwidth\FNH@width
+    \global\setbox\FNH@notes\box\voidb@x
+    \let\FNH@thempfn\thempfn
+    \let\FNH@mpfn\@mpfn
+    \ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
+    \expandafter\def\expandafter\@minipagerestore\expandafter{%
+      \@minipagerestore
+      \let\thempfn\FNH@thempfn
+      \let\@mpfn\FNH@mpfn
+    }%
+  \fi
+}%
+\def\FNH@spewnotes {%
+  \endgroup
+  \ifFNH@savingnotes\else
+   \ifvoid\FNH@notes\else
+    \begingroup
+     \let\@makefntext\@empty
+     \let\@finalstrut\@gobble
+     \let\rule\@gobbletwo
+     \FNH@H@@footnotetext{\unvbox\FNH@notes}%
+    \endgroup
+   \fi
+  \fi
+}%
+\def\FNH@footnote@envname    {footnote}%
+\def\FNH@footnotetext@envname{footnotetext}%
+\def\FNH@footnote{%
+% this line added for Sphinx:
+    \spx@opt@BeforeFootnote
+    \ifx\@currenvir\FNH@footnote@envname
+        \expandafter\FNH@footnoteenv
+    \else
+        \expandafter\FNH@latex@footnote
+    \fi
+}%
+\def\FNH@footnoteenv{%
+% this line added for Sphinx (footnotes in parsed literal blocks):
+    \catcode13=5 \sphinxunactivateextrasandspace
+    \@ifnextchar[%
+      \FNH@footnoteenv@i %]
+      {\stepcounter\@mpfn
+       \protected@xdef\@thefnmark{\thempfn}%
+       \@footnotemark
+       \def\FNH@endfntext@fntext{\@footnotetext}%
+       \FNH@startfntext}%
+}%
+\def\FNH@footnoteenv@i[#1]{%
+    \begingroup
+     \csname c@\@mpfn\endcsname #1\relax
+     \unrestored@protected@xdef\@thefnmark{\thempfn}%
+    \endgroup
+    \@footnotemark
+    \def\FNH@endfntext@fntext{\@footnotetext}%
+    \FNH@startfntext
+}%
+\def\FNH@footnotetext{%
+    \ifx\@currenvir\FNH@footnotetext@envname
+        \expandafter\FNH@footnotetextenv
+    \else
+        \expandafter\FNH@latex@footnotetext
+    \fi
+}%
+\def\FNH@footnotetextenv{%
+    \@ifnextchar[%
+      \FNH@footnotetextenv@i %]
+      {\protected@xdef\@thefnmark{\thempfn}%
+       \def\FNH@endfntext@fntext{\@footnotetext}%
+       \FNH@startfntext}%
+}%
+\def\FNH@footnotetextenv@i[#1]{%
+    \begingroup
+     \csname c@\@mpfn\endcsname #1\relax
+     \unrestored@protected@xdef\@thefnmark{\thempfn}%
+    \endgroup
+    \ifFNH@savingnotes
+      \def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
+    \else
+      \def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
+    \fi
+    \FNH@startfntext
+}%
+\def\FNH@startfntext{%
+  \setbox\z@\vbox\bgroup
+    \FNH@startnote
+    \FNH@prefntext
+    \rule\z@\footnotesep\ignorespaces
+}%
+\def\FNH@endfntext {%
+    \@finalstrut\strutbox
+    \FNH@postfntext
+    \FNH@endnote
+    \egroup
+  \begingroup
+    \let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
+    \FNH@endfntext@fntext {\unvbox\z@}%
+  \endgroup
+}%
+\AtBeginDocument{%
+   \let\FNH@@makefntext\@makefntext
+   \ifx\@makefntextFB\@undefined
+   \expandafter\@gobble\else\expandafter\@firstofone\fi
+   {\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
+                         \let\FNH@@makefntext\@makefntextORI\fi}%
+   \expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
+               \FNH@@@1.2!3?4,\FNH@@@\relax
+}%
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+    \ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
+    \FNH@bad@makefntext@alert
+    {\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
+}%
+\def\FNH@check@b #1\relax{%
+    \expandafter\expandafter\expandafter\FNH@check@c
+    \expandafter\meaning\expandafter\FNH@prefntext
+    \meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
+}%
+\def\FNH@check@c #11.2!3?4,#2#3\relax{%
+    \ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
+}%
+% slight reformulation for Sphinx
+\def\FNH@bad@makefntext@alert{%
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+    {Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
+  some package modifying macro \string\@makefntext.^^J
+  You can try to report this incompatibility at^^J
+  https://github.com/sphinx-doc/sphinx with this info:}%
+    \typeout{\meaning\@makefntext}%
+    \let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
+}%
+% this macro from original footnote.sty is not used anymore by Sphinx
+% but for simplicity sake let's just keep it as is
+\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
+\def\FNH@msne@i #1{%
+  \expandafter\let\csname FNH$#1\expandafter\endcsname %$
+                  \csname #1\endcsname
+  \expandafter\let\csname endFNH$#1\expandafter\endcsname %$
+                  \csname end#1\endcsname
+  \FNH@msne@ii[#1]{FNH$#1}%$
+}%
+\def\FNH@msne@ii[#1]#2{%
+  \expandafter\edef\csname#1\endcsname{%
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+    \expandafter\noexpand\csname#2\endcsname
+  }%
+  \expandafter\edef\csname end#1\endcsname{%
+    \expandafter\noexpand\csname end#2\endcsname
+    \noexpand\expandafter
+    \noexpand\spewnotes
+    \noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
+  }%
+}%
+% end of footnotehyper 2017/02/16 v0.99
+% some extras for Sphinx :
+% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
+\def\sphinxfootnotemark [#1]%
+   {\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
+                             \protect\footnotemark[#1]\fi}%
+\AtBeginDocument{%
+   % let hyperref less complain
+   \pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
+   % to obtain hyperlinked footnotes in longtable environment we must replace
+   % hyperref's patch of longtable's patch of \@footnotetext by our own
+   \let\LT@p@ftntext\FNH@hyper@fntext
+   % this *requires* longtable to be used always wrapped in savenotes environment
+}%
+\endinput
+%%
+%% End of file `footnotehyper-sphinx.sty'.

docs/_build/genindex.html

+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Index &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  <script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
+        <script src="_static/doctools.js"></script>
+        <script src="_static/language_data.js"></script>
+    <script src="_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="#" />
+    <link rel="search" title="Search" href="search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="index.html" class="icon icon-home">
+            esgemme
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="index.html">esgemme</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Index</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ 
+</div>
+
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+   
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
\ No newline at end of file

docs/_build/html/.buildinfo

+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 2b63f8059aa2ad903c52bf6ea56d7c9d
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/docker.rst.txt

+Using ESGEMME via Docker
+========================
+
+Requirements
+------------
+
+You need to have docker installed on your machine. You can consult the
+following page for this: https://docs.docker.com/get-docker/
+
+I am assuming some basic familiarity with Linux/Unix/MacOS terminal
+commands.
+
+Let’s start our favorite terminal app.
+
+You must to create a folder called docker-tutorial and go to that empty
+folder:
+
+.. code:: bash
+
+   mkdir docker-tutorial
+   cd docker-tutorial
+
+Getting the input data
+----------------------
+
+Let’s download the sample data provided in the ESGEMME repository for
+this exercise. First, we will download the multiple sequence alignment
+file in fasta format:
+
+.. code:: bash
+
+   wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
+
+If you don’t have wget, you can try the same command with curl:
+
+.. code:: bash
+
+   curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
+
+Please verify that the aliBLAT.fasta file is in the folder.
+
+Now, we will download the PDB (Protein Databank) file for BLAT:
+
+.. code:: bash
+
+   wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
+
+Running a calculation for a single sequence/protein
+---------------------------------------------------
+
+In order to make sure that the docker is installed:
+
+.. code:: bash
+
+    docker -h
+
+If it shows you a list of options, you are on a good track. On MacOS,
+you may not need ‘sudo’ word before the docker command at all.
+
+.. code:: bash
+
+   sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0
+
+You are in the container (your virtual operating system) now. You
+created a folder called myexample in your container with the previous
+command. Let’s change to that folder.
+
+.. code:: bash
+
+   cd ../myexample/
+
+When you check the data in that folder with ‘ls’ command, you are
+supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
+docker-tutorial folder on the host system and myexample folder on the
+docker container are pointing to the same place.
+
+One last step and we are done:
+
+.. code:: bash
+
+   python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb
+
+After a few minutes of calculation, you must see two files named
+BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
+the entire single point mutational landscape of BLAT protein in these
+files.
+
+Running several jobs using docker
+---------------------------------

docs/_build/html/_sources/index.rst.txt

+.. esgemme documentation master file, created by
+   sphinx-quickstart on Fri May  5 13:52:13 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to esgemme's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   docker.rst
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/_build/html/_static/custom.css

+/* This file intentionally left blank. */

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+ *
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+/**
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+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta charset="utf-8" />
+    <title>Using ESGEMME via Docker &#8212; esgemme 1.3.0 documentation</title>
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+          
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+            
+  <div class="section" id="using-esgemme-via-docker">
+<h1>Using ESGEMME via Docker<a class="headerlink" href="#using-esgemme-via-docker" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="requirements">
+<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
+<p>You need to have docker installed on your machine. You can consult the
+following page for this: <a class="reference external" href="https://docs.docker.com/get-docker/">https://docs.docker.com/get-docker/</a></p>
+<p>I am assuming some basic familiarity with Linux/Unix/MacOS terminal
+commands.</p>
+<p>Let’s start our favorite terminal app.</p>
+<p>You must to create a folder called docker-tutorial and go to that empty
+folder:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir docker-tutorial
+<span class="nb">cd</span> docker-tutorial
+</pre></div>
+</div>
+</div>
+<div class="section" id="getting-the-input-data">
+<h2>Getting the input data<a class="headerlink" href="#getting-the-input-data" title="Permalink to this headline">¶</a></h2>
+<p>Let’s download the sample data provided in the ESGEMME repository for
+this exercise. First, we will download the multiple sequence alignment
+file in fasta format:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
+</pre></div>
+</div>
+<p>If you don’t have wget, you can try the same command with curl:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
+</pre></div>
+</div>
+<p>Please verify that the aliBLAT.fasta file is in the folder.</p>
+<p>Now, we will download the PDB (Protein Databank) file for BLAT:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
+</pre></div>
+</div>
+</div>
+<div class="section" id="running-a-calculation-for-a-single-sequence-protein">
+<h2>Running a calculation for a single sequence/protein<a class="headerlink" href="#running-a-calculation-for-a-single-sequence-protein" title="Permalink to this headline">¶</a></h2>
+<p>In order to make sure that the docker is installed:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker -h
+</pre></div>
+</div>
+<p>If it shows you a list of options, you are on a good track. On MacOS,
+you may not need ‘sudo’ word before the docker command at all.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0
+</pre></div>
+</div>
+<p>You are in the container (your virtual operating system) now. You
+created a folder called myexample in your container with the previous
+command. Let’s change to that folder.</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ../myexample/
+</pre></div>
+</div>
+<p>When you check the data in that folder with ‘ls’ command, you are
+supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
+docker-tutorial folder on the host system and myexample folder on the
+docker container are pointing to the same place.</p>
+<p>One last step and we are done:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python <span class="nv">$ESGEMME_PATH</span>/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb
+</pre></div>
+</div>
+<p>After a few minutes of calculation, you must see two files named
+BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
+the entire single point mutational landscape of BLAT protein in these
+files.</p>
+</div>
+<div class="section" id="running-several-jobs-using-docker">
+<h2>Running several jobs using docker<a class="headerlink" href="#running-several-jobs-using-docker" title="Permalink to this headline">¶</a></h2>
+</div>
+</div>
+
+
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+<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#getting-the-input-data">Getting the input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#running-a-calculation-for-a-single-sequence-protein">Running a calculation for a single sequence/protein</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#running-several-jobs-using-docker">Running several jobs using docker</a></li>
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+
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+
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docs/_build/index.html

+<!DOCTYPE html>
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+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+             
+  <div class="section" id="welcome-to-esgemme-s-documentation">
+<h1>Welcome to esgemme’s documentation!<a class="headerlink" href="#welcome-to-esgemme-s-documentation" title="Permalink to this headline"></a></h1>
+<div class="toctree-wrapper compound">
+<p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#requirements">Requirements</a></li>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#getting-the-input-data">Getting the input data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#single-point-mutation-calculations">Single point mutation calculations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#multiple-point-mutation-calculations">Multiple point mutation calculations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="installation.html#installing-the-dependencies">Installing the dependencies:</a></li>
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+<li class="toctree-l2"><a class="reference internal" href="installation.html#configuring-default-conf-file">Configuring default.conf file</a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline"></a></h1>
+<ul class="simple">
+<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
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+    <p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
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+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Installation &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#getting-the-source-code-and-preparing-the-environment">Getting the source code and preparing the environment:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#configuring-default-conf-file">Configuring default.conf file</a></li>
+</ul>
+</li>
+</ul>
+
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+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <div class="section" id="installation">
+<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1>
+<p>ESGEMME is implemented in Python 3 and R. It has been tested only on
+Linux. Since ESGEMME has many dependencies, we recommend using our web
+site or our docker image. If you are a determined user, here comes the
+steps required to install it from the source.</p>
+<div class="section" id="installing-the-dependencies">
+<h2>Installing the dependencies:<a class="headerlink" href="#installing-the-dependencies" title="Permalink to this headline"></a></h2>
+<p>ESGEMME has the following external dependencies: * Joint Evolutionary
+Trees: <a class="reference external" href="http://www.lcqb.upmc.fr/JET2/">http://www.lcqb.upmc.fr/JET2/</a> and its dependencies: - naccess:
+<a class="reference external" href="http://www.bioinf.manchester.ac.uk/naccess/">http://www.bioinf.manchester.ac.uk/naccess/</a> - muscle:
+<a class="reference external" href="https://www.drive5.com/muscle/">https://www.drive5.com/muscle/</a> ** * seqinr R package:
+<a class="reference external" href="https://cran.r-project.org/web/packages/seqinr/index.html">https://cran.r-project.org/web/packages/seqinr/index.html</a> * dssp for
+secondary structure prediction.</p>
+<p>These tools should be installed to be able to use ESGEMME.</p>
+</div>
+<div class="section" id="getting-the-source-code-and-preparing-the-environment">
+<h2>Getting the source code and preparing the environment:<a class="headerlink" href="#getting-the-source-code-and-preparing-the-environment" title="Permalink to this headline"></a></h2>
+<p>Download the ESGEMME source code from
+<a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME">http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME</a>. Define and export the
+environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">ESGEMME_PATH</span><span class="o">=</span>/path-to-ESGEMME-directory/
+</pre></div>
+</div>
+</div>
+<div class="section" id="configuring-default-conf-file">
+<h2>Configuring default.conf file<a class="headerlink" href="#configuring-default-conf-file" title="Permalink to this headline"></a></h2>
+<p>Inside ESGEMME folder, there is an important file called default.conf.
+This file contains essential parameters of ESGEMME, such as paths of
+external parts, default internal parameters. etc. You have to correct the Software section of this
+file according to your system.</p>
+</div>
+</div>
+
+
+           </div>
+          </div>
+          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
+        <a href="analysis.html" class="btn btn-neutral float-left" title="Analyzing the ESGEMME output" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, Mustafa Tekpinar.</p>
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+
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+</html>
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+(merge-rule "\IeC {\cyrzh }" "ж" :string)

docs/_build/latex/Makefile

+# Makefile for Sphinx LaTeX output
+
+ALLDOCS = $(basename $(wildcard *.tex))
+ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
+ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
+ALLXDV =
+ALLPS  = $(addsuffix .ps,$(ALLDOCS))
+ALLIMGS = $(wildcard *.png *.gif *.jpg *.jpeg)
+
+# Prefix for archive names
+ARCHIVEPREFIX =
+# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
+export LATEXOPTS ?=
+# Additional latexmk options
+LATEXMKOPTS ?=
+# format: pdf or dvi (used only by archive targets)
+FMT = pdf
+
+LATEX = latexmk -dvi
+PDFLATEX = latexmk -pdf -dvi- -ps-
+
+
+%.png %.gif %.jpg %.jpeg: FORCE_MAKE
+	extractbb '$@'
+
+%.dvi: %.tex FORCE_MAKE
+	$(LATEX) $(LATEXMKOPTS) '$<'
+
+%.ps: %.dvi
+	dvips '$<'
+
+%.pdf: %.tex FORCE_MAKE
+	$(PDFLATEX) $(LATEXMKOPTS) '$<'
+
+all: $(ALLPDF)
+
+all-dvi: $(ALLDVI)
+
+all-ps: $(ALLPS)
+
+all-pdf: $(ALLPDF)
+
+zip: all-$(FMT)
+	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
+	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
+	zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
+	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
+
+tar: all-$(FMT)
+	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
+	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
+	tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
+	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
+
+gz: tar
+	gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
+
+bz2: tar
+	bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
+
+xz: tar
+	xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
+
+clean:
+	rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk
+
+.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
+.PHONY: FORCE_MAKE
\ No newline at end of file

docs/_build/latex/footnotehyper-sphinx.sty

+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{footnotehyper-sphinx}%
+ [2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)]
+%%
+%% Package: footnotehyper-sphinx
+%% Version: based on footnotehyper.sty 2017/03/07 v1.0
+%% as available at https://www.ctan.org/pkg/footnotehyper
+%% License: the one applying to Sphinx
+%%
+%% Refer to the PDF documentation  at https://www.ctan.org/pkg/footnotehyper for
+%% the code comments.
+%%
+%% Differences:
+%% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up),
+%% 2. use of \spx@opt@BeforeFootnote from sphinx.sty,
+%% 3. use of \sphinxunactivateextrasandspace from sphinx.sty,
+%% 4. macro definition \sphinxfootnotemark,
+%% 5. macro definition \sphinxlongtablepatch
+%% 6. replaced an \undefined by \@undefined
+\DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}%
+\ProcessOptions\relax
+\newbox\FNH@notes
+\newdimen\FNH@width
+\let\FNH@colwidth\columnwidth
+\newif\ifFNH@savingnotes
+\AtBeginDocument {%
+    \let\FNH@latex@footnote    \footnote
+    \let\FNH@latex@footnotetext\footnotetext
+    \let\FNH@H@@footnotetext   \@footnotetext
+    \newenvironment{savenotes}
+        {\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}%
+    \let\spewnotes      \FNH@spewnotes
+    \let\footnote       \FNH@footnote
+    \let\footnotetext   \FNH@footnotetext
+    \let\endfootnote    \FNH@endfntext
+    \let\endfootnotetext\FNH@endfntext
+    \@ifpackageloaded{hyperref}
+     {\ifHy@hyperfootnotes
+         \let\FNH@H@@footnotetext\H@@footnotetext
+      \else
+         \let\FNH@hyper@fntext\FNH@nohyp@fntext
+      \fi}%
+     {\let\FNH@hyper@fntext\FNH@nohyp@fntext}%
+}%
+\def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}%
+\def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}%
+\def\FNH@fntext #1{%
+  \ifx\ifmeasuring@\@undefined
+    \expandafter\@secondoftwo\else\expandafter\@firstofone\fi
+% these two lines modified for Sphinx (tabulary compatibility):
+    {\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}%
+    {\ifx\equation$\expandafter\@gobbletwo\fi #1}%$
+}%
+\long\def\FNH@hyper@fntext@i#1{%
+  \global\setbox\FNH@notes\vbox
+  {\unvbox\FNH@notes
+   \FNH@startnote
+   \@makefntext
+    {\rule\z@\footnotesep\ignorespaces
+     \ifHy@nesting\expandafter\ltx@firstoftwo
+             \else\expandafter\ltx@secondoftwo
+     \fi
+     {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}%
+     {\Hy@raisedlink
+       {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}%
+       {\relax}}%
+      \let\@currentHref\Hy@footnote@currentHref
+      \let\@currentlabelname\@empty
+      #1}%
+     \@finalstrut\strutbox
+    }%
+   \FNH@endnote
+  }%
+}%
+\long\def\FNH@nohyp@fntext@i#1{%
+  \global\setbox\FNH@notes\vbox
+  {\unvbox\FNH@notes
+   \FNH@startnote
+   \@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}%
+   \FNH@endnote
+  }%
+}%
+\def\FNH@startnote{%
+  \hsize\FNH@colwidth
+  \interlinepenalty\interfootnotelinepenalty
+  \reset@font\footnotesize
+  \floatingpenalty\@MM
+  \@parboxrestore
+  \protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
+  \color@begingroup
+}%
+\def\FNH@endnote{\color@endgroup}%
+\def\FNH@savenotes{%
+  \begingroup
+  \ifFNH@savingnotes\else
+    \FNH@savingnotestrue
+    \let\@footnotetext    \FNH@hyper@fntext
+    \let\@mpfootnotetext  \FNH@hyper@fntext
+    \let\H@@mpfootnotetext\FNH@nohyp@fntext
+    \FNH@width\columnwidth
+    \let\FNH@colwidth\FNH@width
+    \global\setbox\FNH@notes\box\voidb@x
+    \let\FNH@thempfn\thempfn
+    \let\FNH@mpfn\@mpfn
+    \ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
+    \expandafter\def\expandafter\@minipagerestore\expandafter{%
+      \@minipagerestore
+      \let\thempfn\FNH@thempfn
+      \let\@mpfn\FNH@mpfn
+    }%
+  \fi
+}%
+\def\FNH@spewnotes {%
+  \endgroup
+  \ifFNH@savingnotes\else
+   \ifvoid\FNH@notes\else
+    \begingroup
+     \let\@makefntext\@empty
+     \let\@finalstrut\@gobble
+     \let\rule\@gobbletwo
+     \FNH@H@@footnotetext{\unvbox\FNH@notes}%
+    \endgroup
+   \fi
+  \fi
+}%
+\def\FNH@footnote@envname    {footnote}%
+\def\FNH@footnotetext@envname{footnotetext}%
+\def\FNH@footnote{%
+% this line added for Sphinx:
+    \spx@opt@BeforeFootnote
+    \ifx\@currenvir\FNH@footnote@envname
+        \expandafter\FNH@footnoteenv
+    \else
+        \expandafter\FNH@latex@footnote
+    \fi
+}%
+\def\FNH@footnoteenv{%
+% this line added for Sphinx (footnotes in parsed literal blocks):
+    \catcode13=5 \sphinxunactivateextrasandspace
+    \@ifnextchar[%
+      \FNH@footnoteenv@i %]
+      {\stepcounter\@mpfn
+       \protected@xdef\@thefnmark{\thempfn}%
+       \@footnotemark
+       \def\FNH@endfntext@fntext{\@footnotetext}%
+       \FNH@startfntext}%
+}%
+\def\FNH@footnoteenv@i[#1]{%
+    \begingroup
+     \csname c@\@mpfn\endcsname #1\relax
+     \unrestored@protected@xdef\@thefnmark{\thempfn}%
+    \endgroup
+    \@footnotemark
+    \def\FNH@endfntext@fntext{\@footnotetext}%
+    \FNH@startfntext
+}%
+\def\FNH@footnotetext{%
+    \ifx\@currenvir\FNH@footnotetext@envname
+        \expandafter\FNH@footnotetextenv
+    \else
+        \expandafter\FNH@latex@footnotetext
+    \fi
+}%
+\def\FNH@footnotetextenv{%
+    \@ifnextchar[%
+      \FNH@footnotetextenv@i %]
+      {\protected@xdef\@thefnmark{\thempfn}%
+       \def\FNH@endfntext@fntext{\@footnotetext}%
+       \FNH@startfntext}%
+}%
+\def\FNH@footnotetextenv@i[#1]{%
+    \begingroup
+     \csname c@\@mpfn\endcsname #1\relax
+     \unrestored@protected@xdef\@thefnmark{\thempfn}%
+    \endgroup
+    \ifFNH@savingnotes
+      \def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
+    \else
+      \def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
+    \fi
+    \FNH@startfntext
+}%
+\def\FNH@startfntext{%
+  \setbox\z@\vbox\bgroup
+    \FNH@startnote
+    \FNH@prefntext
+    \rule\z@\footnotesep\ignorespaces
+}%
+\def\FNH@endfntext {%
+    \@finalstrut\strutbox
+    \FNH@postfntext
+    \FNH@endnote
+    \egroup
+  \begingroup
+    \let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
+    \FNH@endfntext@fntext {\unvbox\z@}%
+  \endgroup
+}%
+\AtBeginDocument{%
+   \let\FNH@@makefntext\@makefntext
+   \ifx\@makefntextFB\@undefined
+   \expandafter\@gobble\else\expandafter\@firstofone\fi
+   {\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
+                         \let\FNH@@makefntext\@makefntextORI\fi}%
+   \expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
+               \FNH@@@1.2!3?4,\FNH@@@\relax
+}%
+\long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{%
+    \ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
+    \FNH@bad@makefntext@alert
+    {\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
+}%
+\def\FNH@check@b #1\relax{%
+    \expandafter\expandafter\expandafter\FNH@check@c
+    \expandafter\meaning\expandafter\FNH@prefntext
+    \meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
+}%
+\def\FNH@check@c #11.2!3?4,#2#3\relax{%
+    \ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
+}%
+% slight reformulation for Sphinx
+\def\FNH@bad@makefntext@alert{%
+  \PackageWarningNoLine{footnotehyper-sphinx}%
+    {Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
+  some package modifying macro \string\@makefntext.^^J
+  You can try to report this incompatibility at^^J
+  https://github.com/sphinx-doc/sphinx with this info:}%
+    \typeout{\meaning\@makefntext}%
+    \let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
+}%
+% this macro from original footnote.sty is not used anymore by Sphinx
+% but for simplicity sake let's just keep it as is
+\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
+\def\FNH@msne@i #1{%
+  \expandafter\let\csname FNH$#1\expandafter\endcsname %$
+                  \csname #1\endcsname
+  \expandafter\let\csname endFNH$#1\expandafter\endcsname %$
+                  \csname end#1\endcsname
+  \FNH@msne@ii[#1]{FNH$#1}%$
+}%
+\def\FNH@msne@ii[#1]#2{%
+  \expandafter\edef\csname#1\endcsname{%
+    \noexpand\savenotes
+    \expandafter\noexpand\csname#2\endcsname
+  }%
+  \expandafter\edef\csname end#1\endcsname{%
+    \expandafter\noexpand\csname end#2\endcsname
+    \noexpand\expandafter
+    \noexpand\spewnotes
+    \noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
+  }%
+}%
+% end of footnotehyper 2017/02/16 v0.99
+% some extras for Sphinx :
+% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
+\def\sphinxfootnotemark [#1]%
+   {\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
+                             \protect\footnotemark[#1]\fi}%
+\AtBeginDocument{%
+   % let hyperref less complain
+   \pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
+   % to obtain hyperlinked footnotes in longtable environment we must replace
+   % hyperref's patch of longtable's patch of \@footnotetext by our own
+   \let\LT@p@ftntext\FNH@hyper@fntext
+   % this *requires* longtable to be used always wrapped in savenotes environment
+}%
+\endinput
+%%
+%% End of file `footnotehyper-sphinx.sty'.

docs/_build/latex/latexmkjarc

+$latex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' -kanji=utf8 %O %S';
+$dvipdf = 'dvipdfmx %O -o %D %S';
+$makeindex = 'internal mendex %S %B %D';
+sub mendex {
+  my ($source, $basename, $destination) = @_;
+  my $dictfile = $basename . ".dic";
+  unlink($destination);
+  system("mendex", "-U", "-f", "-d", $dictfile, "-s", "python.ist", $source);
+  if ($? > 0) {
+    print("mendex exited with error code $? (ignored)\n");
+  }
+  if (!-e $destination) {
+    # create an empty .ind file if nothing
+    open(FH, ">" . $destination);
+    close(FH);
+  }
+  return 0;
+}
+add_cus_dep( "glo", "gls", 0, "makeglo" );
+sub makeglo {
+ return system( "mendex -J -f -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
+}
\ No newline at end of file

docs/_build/latex/latexmkrc

+$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$makeindex = 'makeindex -s python.ist %O -o %D %S';
+add_cus_dep( "glo", "gls", 0, "makeglo" );
+sub makeglo {
+ return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
+}
\ No newline at end of file

docs/_build/latex/make.bat

+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+pushd %~dp0
+
+set PDFLATEX=latexmk -pdf -dvi- -ps-
+
+set "LATEXOPTS= "
+
+if "%1" == "" goto all-pdf
+
+if "%1" == "all-pdf" (
+	:all-pdf
+	for %%i in (*.tex) do (
+		%PDFLATEX% %LATEXMKOPTS% %%i
+	)
+	goto end
+)
+
+if "%1" == "all-pdf-ja" (
+	goto all-pdf
+)
+
+if "%1" == "clean" (
+	del /q /s *.dvi *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz *.fls *.fdb_latexmk
+	goto end
+)
+
+:end
+popd
\ No newline at end of file

docs/_build/latex/python.ist

+line_max 100
+headings_flag 1
+heading_prefix "  \\bigletter "
+
+preamble "\\begin{sphinxtheindex}
+\\let\\bigletter\\sphinxstyleindexlettergroup
+\\let\\spxpagem \\sphinxstyleindexpagemain
+\\let\\spxentry \\sphinxstyleindexentry
+\\let\\spxextra \\sphinxstyleindexextra
+
+"
+
+postamble "\n\n\\end{sphinxtheindex}\n"
+
+symhead_positive "{\\sphinxsymbolsname}"
+numhead_positive "{\\sphinxnumbersname}"