Added all required files for documentation + Updated tests for embeddings

docs/_build/html/.buildinfo

@@ -0,0 +1,4 @@
+# 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: 18efb40e970fb2c9b3465eeb13d835bc
+tags: 645f666f9bcd5a90fca523b33c5a78b7

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

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+.. PROTAC-Degradation-Predictor documentation master file, created by
+   sphinx-quickstart on Mon Aug 19 11:16:51 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PROTAC-Degradation-Predictor documentation
+==========================================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   source/modules

docs/_build/html/_sources/source/modules.rst.txt

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+protac_degradation_predictor
+============================
+
+.. toctree::
+   :maxdepth: 4
+
+   protac_degradation_predictor

docs/_build/html/_sources/source/protac_degradation_predictor.optuna.rst.txt

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+protac\_degradation\_predictor.optuna package
+=============================================
+
+Submodules
+----------
+
+protac\_degradation\_predictor.optuna.pytorch\_models module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.pytorch_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna.sklearn\_models module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.sklearn_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna.utils module
+--------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna.xgboost\_models module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna.xgboost_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protac_degradation_predictor.optuna
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_build/html/_sources/source/protac_degradation_predictor.rst.txt

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+protac\_degradation\_predictor package
+======================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   protac_degradation_predictor.optuna
+
+Submodules
+----------
+
+protac\_degradation\_predictor.config module
+--------------------------------------------
+
+.. automodule:: protac_degradation_predictor.config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.data\_utils module
+-------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.data_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna\_utils module
+---------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.optuna\_utils\_xgboost module
+------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.optuna_utils_xgboost
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.protac\_dataset module
+-----------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.protac_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.protac\_degradation\_predictor module
+--------------------------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.protac_degradation_predictor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.pytorch\_models module
+-----------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.pytorch_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protac\_degradation\_predictor.sklearn\_models module
+-----------------------------------------------------
+
+.. automodule:: protac_degradation_predictor.sklearn_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protac_degradation_predictor
+   :members:
+   :undoc-members:
+   :show-inheritance:

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+div.citation > p:last-of-type {
+    margin-bottom: 0em;
+}
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: grid;
+    grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+    font-weight: bold;
+    word-break: break-word;
+    padding-left: 0.5em;
+    padding-right: 5px;
+}
+
+dl.field-list > dd {
+    padding-left: 0.5em;
+    margin-top: 0em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
+dl {
+    margin-bottom: 15px;
+}
+
+dd > :first-child {
+    margin-top: 0px;
+}
+
+dd ul, dd table {
+    margin-bottom: 10px;
+}
+
+dd {
+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
+
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+dl > dd:last-child,
+dl > dd:last-child > :last-child {
+    margin-bottom: 0;
+}
+
+dt:target, span.highlighted {
+    background-color: #fbe54e;
+}
+
+rect.highlighted {
+    fill: #fbe54e;
+}
+
+dl.glossary dt {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+
+.versionmodified {
+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
+.footnote:target  {
+    background-color: #ffa;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+    font-family: sans-serif;
+}
+
+.accelerator {
+    text-decoration: underline;
+}
+
+.classifier {
+    font-style: oblique;
+}
+
+.classifier:before {
+    font-style: normal;
+    margin: 0 0.5em;
+    content: ":";
+    display: inline-block;
+}
+
+abbr, acronym {
+    border-bottom: dotted 1px;
+    cursor: help;
+}
+
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+    overflow-y: hidden;  /* fixes display issues on Chrome browsers */
+}
+
+pre, div[class*="highlight-"] {
+    clear: both;
+}
+
+span.pre {
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -webkit-hyphens: none;
+    hyphens: none;
+    white-space: nowrap;
+}
+
+div[class*="highlight-"] {
+    margin: 1em 0;
+}
+
+td.linenos pre {
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    display: block;
+}
+
+table.highlighttable tbody {
+    display: block;
+}
+
+table.highlighttable tr {
+    display: flex;
+}
+
+table.highlighttable td {
+    margin: 0;
+    padding: 0;
+}
+
+table.highlighttable td.linenos {
+    padding-right: 0.5em;
+}
+
+table.highlighttable td.code {
+    flex: 1;
+    overflow: hidden;
+}
+
+.highlight .hll {
+    display: block;
+}
+
+div.highlight pre,
+table.highlighttable pre {
+    margin: 0;
+}
+
+div.code-block-caption + div {
+    margin-top: 0;
+}
+
+div.code-block-caption {
+    margin-top: 1em;
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+table.highlighttable td.linenos,
+span.linenos,
+div.highlight span.gp {  /* gp: Generic.Prompt */
+  user-select: none;
+  -webkit-user-select: text; /* Safari fallback only */
+  -webkit-user-select: none; /* Chrome/Safari */
+  -moz-user-select: none; /* Firefox */
+  -ms-user-select: none; /* IE10+ */
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    margin: 1em 0;
+}
+
+code.xref, a code {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+    background-color: transparent;
+}
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -10px;
+    padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+span.eqno a.headerlink {
+    position: absolute;
+    z-index: 1;
+}
+
+div.math:hover a.headerlink {
+    visibility: visible;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}

docs/_build/html/_static/css/badge_only.css

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docs/_build/html/_static/doctools.js

@@ -0,0 +1,156 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Base JavaScript utilities for all Sphinx HTML documentation.
+ *
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+"use strict";
+
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+  "TEXTAREA",
+  "INPUT",
+  "SELECT",
+  "BUTTON",
+]);
+
+const _ready = (callback) => {
+  if (document.readyState !== "loading") {
+    callback();
+  } else {
+    document.addEventListener("DOMContentLoaded", callback);
+  }
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const Documentation = {
+  init: () => {
+    Documentation.initDomainIndexTable();
+    Documentation.initOnKeyListeners();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS: {},
+  PLURAL_EXPR: (n) => (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: (string) => {
+    const translated = Documentation.TRANSLATIONS[string];
+    switch (typeof translated) {
+      case "undefined":
+        return string; // no translation
+      case "string":
+        return translated; // translation exists
+      default:
+        return translated[0]; // (singular, plural) translation tuple exists
+    }
+  },
+
+  ngettext: (singular, plural, n) => {
+    const translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated !== "undefined")
+      return translated[Documentation.PLURAL_EXPR(n)];
+    return n === 1 ? singular : plural;
+  },
+
+  addTranslations: (catalog) => {
+    Object.assign(Documentation.TRANSLATIONS, catalog.messages);
+    Documentation.PLURAL_EXPR = new Function(
+      "n",
+      `return (${catalog.plural_expr})`
+    );
+    Documentation.LOCALE = catalog.locale;
+  },
+
+  /**
+   * helper function to focus on search bar
+   */
+  focusSearchBar: () => {
+    document.querySelectorAll("input[name=q]")[0]?.focus();
+  },
+
+  /**
+   * Initialise the domain index toggle buttons
+   */
+  initDomainIndexTable: () => {
+    const toggler = (el) => {
+      const idNumber = el.id.substr(7);
+      const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
+      if (el.src.substr(-9) === "minus.png") {
+        el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
+        toggledRows.forEach((el) => (el.style.display = "none"));
+      } else {
+        el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
+        toggledRows.forEach((el) => (el.style.display = ""));
+      }
+    };
+
+    const togglerElements = document.querySelectorAll("img.toggler");
+    togglerElements.forEach((el) =>
+      el.addEventListener("click", (event) => toggler(event.currentTarget))
+    );
+    togglerElements.forEach((el) => (el.style.display = ""));
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
+  },
+
+  initOnKeyListeners: () => {
+    // only install a listener if it is really needed
+    if (
+      !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
+      !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
+    )
+      return;
+
+    document.addEventListener("keydown", (event) => {
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.altKey || event.ctrlKey || event.metaKey) return;
+
+      if (!event.shiftKey) {
+        switch (event.key) {
+          case "ArrowLeft":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const prevLink = document.querySelector('link[rel="prev"]');
+            if (prevLink && prevLink.href) {
+              window.location.href = prevLink.href;
+              event.preventDefault();
+            }
+            break;
+          case "ArrowRight":
+            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
+
+            const nextLink = document.querySelector('link[rel="next"]');
+            if (nextLink && nextLink.href) {
+              window.location.href = nextLink.href;
+              event.preventDefault();
+            }
+            break;
+        }
+      }
+
+      // some keyboard layouts may need Shift to get /
+      switch (event.key) {
+        case "/":
+          if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
+          Documentation.focusSearchBar();
+          event.preventDefault();
+      }
+    });
+  },
+};
+
+// quick alias for translations
+const _ = Documentation.gettext;
+
+_ready(Documentation.init);

docs/_build/html/_static/documentation_options.js

@@ -0,0 +1,13 @@
+const DOCUMENTATION_OPTIONS = {
+    VERSION: 'v1.0.1',
+    LANGUAGE: 'en',
+    COLLAPSE_INDEX: false,
+    BUILDER: 'html',
+    FILE_SUFFIX: '.html',
+    LINK_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+    SHOW_SEARCH_SUMMARY: true,
+    ENABLE_SEARCH_SHORTCUTS: true,
+};

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docs/_build/html/_static/js/badge_only.js

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

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docs/_build/html/_static/js/html5shiv.min.js

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docs/_build/html/_static/js/theme.js

@@ -0,0 +1 @@
+!function(n){var e={};function t(i){if(e[i])return e[i].exports;var o=e[i]={i:i,l:!1,exports:{}};return n[i].call(o.exports,o,o.exports,t),o.l=!0,o.exports}t.m=n,t.c=e,t.d=function(n,e,i){t.o(n,e)||Object.defineProperty(n,e,{enumerable:!0,get:i})},t.r=function(n){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(n,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(n,"__esModule",{value:!0})},t.t=function(n,e){if(1&e&&(n=t(n)),8&e)return n;if(4&e&&"object"==typeof n&&n&&n.__esModule)return n;var i=Object.create(null);if(t.r(i),Object.defineProperty(i,"default",{enumerable:!0,value:n}),2&e&&"string"!=typeof n)for(var o in n)t.d(i,o,function(e){return n[e]}.bind(null,o));return i},t.n=function(n){var e=n&&n.__esModule?function(){return n.default}:function(){return n};return t.d(e,"a",e),e},t.o=function(n,e){return Object.prototype.hasOwnProperty.call(n,e)},t.p="",t(t.s=0)}([function(n,e,t){t(1),n.exports=t(3)},function(n,e,t){(function(){var e="undefined"!=typeof window?window.jQuery:t(2);n.exports.ThemeNav={navBar:null,win:null,winScroll:!1,winResize:!1,linkScroll:!1,winPosition:0,winHeight:null,docHeight:null,isRunning:!1,enable:function(n){var t=this;void 0===n&&(n=!0),t.isRunning||(t.isRunning=!0,e((function(e){t.init(e),t.reset(),t.win.on("hashchange",t.reset),n&&t.win.on("scroll",(function(){t.linkScroll||t.winScroll||(t.winScroll=!0,requestAnimationFrame((function(){t.onScroll()})))})),t.win.on("resize",(function(){t.winResize||(t.winResize=!0,requestAnimationFrame((function(){t.onResize()})))})),t.onResize()})))},enableSticky:function(){this.enable(!0)},init:function(n){n(document);var e=this;this.navBar=n("div.wy-side-scroll:first"),this.win=n(window),n(document).on("click","[data-toggle='wy-nav-top']",(function(){n("[data-toggle='wy-nav-shift']").toggleClass("shift"),n("[data-toggle='rst-versions']").toggleClass("shift")})).on("click",".wy-menu-vertical .current ul li a",(function(){var 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[id="'+n.substring(1)+'"]').closest("div.section");0===(t=e.find('[href="#'+i.attr("id")+'"]')).length&&(t=e.find('[href="#"]'))}if(t.length>0){$(".wy-menu-vertical .current").removeClass("current").attr("aria-expanded","false"),t.addClass("current").attr("aria-expanded","true"),t.closest("li.toctree-l1").parent().addClass("current").attr("aria-expanded","true");for(let n=1;n<=10;n++)t.closest("li.toctree-l"+n).addClass("current").attr("aria-expanded","true");t[0].scrollIntoView()}}catch(n){console.log("Error expanding nav for anchor",n)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,t=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(t),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",(function(){this.linkScroll=!1}))},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current").attr("aria-expanded","false"),e.siblings().find("li.current").removeClass("current").attr("aria-expanded","false");var t=e.find("> ul li");t.length&&(t.removeClass("current").attr("aria-expanded","false"),e.toggleClass("current").attr("aria-expanded",(function(n,e){return"true"==e?"false":"true"})))}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:n.exports.ThemeNav,StickyNav:n.exports.ThemeNav}),function(){for(var n=0,e=["ms","moz","webkit","o"],t=0;t<e.length&&!window.requestAnimationFrame;++t)window.requestAnimationFrame=window[e[t]+"RequestAnimationFrame"],window.cancelAnimationFrame=window[e[t]+"CancelAnimationFrame"]||window[e[t]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(e,t){var i=(new Date).getTime(),o=Math.max(0,16-(i-n)),r=window.setTimeout((function(){e(i+o)}),o);return 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docs/_build/html/_static/language_data.js

@@ -0,0 +1,199 @@
+/*
+ * language_data.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ *
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
+
+
+/* Non-minified version is copied as a separate JS file, if available */
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+

docs/_build/html/_static/pygments.css

@@ -0,0 +1,75 @@
+pre { line-height: 125%; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #f8f8f8; }
+.highlight .c { color: #3D7B7B; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #008000; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .ch { color: #3D7B7B; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #3D7B7B; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #9C6500 } /* Comment.Preproc */
+.highlight .cpf { color: #3D7B7B; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #3D7B7B; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
+.highlight .gr { color: #E40000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #008400 } /* Generic.Inserted */
+.highlight .go { color: #717171 } /* Generic.Output */
+.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #008000 } /* Keyword.Pseudo */
+.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #B00040 } /* Keyword.Type */
+.highlight .m { color: #666666 } /* Literal.Number */
+.highlight .s { color: #BA2121 } /* Literal.String */
+.highlight .na { color: #687822 } /* Name.Attribute */
+.highlight .nb { color: #008000 } /* Name.Builtin */
+.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
+.highlight .no { color: #880000 } /* Name.Constant */
+.highlight .nd { color: #AA22FF } /* Name.Decorator */
+.highlight .ni { color: #717171; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #CB3F38; font-weight: bold } /* Name.Exception */
+.highlight .nf { color: #0000FF } /* Name.Function */
+.highlight .nl { color: #767600 } /* Name.Label */
+.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #19177C } /* Name.Variable */
+.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mb { color: #666666 } /* Literal.Number.Bin */
+.highlight .mf { color: #666666 } /* Literal.Number.Float */
+.highlight .mh { color: #666666 } /* Literal.Number.Hex */
+.highlight .mi { color: #666666 } /* Literal.Number.Integer */
+.highlight .mo { color: #666666 } /* Literal.Number.Oct */
+.highlight .sa { color: #BA2121 } /* Literal.String.Affix */
+.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
+.highlight .sc { color: #BA2121 } /* Literal.String.Char */
+.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
+.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
+.highlight .se { color: #AA5D1F; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
+.highlight .si { color: #A45A77; font-weight: bold } /* Literal.String.Interpol */
+.highlight .sx { color: #008000 } /* Literal.String.Other */
+.highlight .sr { color: #A45A77 } /* Literal.String.Regex */
+.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
+.highlight .ss { color: #19177C } /* Literal.String.Symbol */
+.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #0000FF } /* Name.Function.Magic */
+.highlight .vc { color: #19177C } /* Name.Variable.Class */
+.highlight .vg { color: #19177C } /* Name.Variable.Global */
+.highlight .vi { color: #19177C } /* Name.Variable.Instance */
+.highlight .vm { color: #19177C } /* Name.Variable.Magic */
+.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */

docs/_build/html/_static/searchtools.js

@@ -0,0 +1,620 @@
+/*
+ * searchtools.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for the full-text search.
+ *
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+"use strict";
+
+/**
+ * Simple result scoring code.
+ */
+if (typeof Scorer === "undefined") {
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [docname, title, anchor, descr, score, filename]
+    // and returns the new score.
+    /*
+    score: result => {
+      const [docname, title, anchor, descr, score, filename] = result
+      return score
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {
+      0: 15, // used to be importantResults
+      1: 5, // used to be objectResults
+      2: -5, // used to be unimportantResults
+    },
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    partialTitle: 7,
+    // query found in terms
+    term: 5,
+    partialTerm: 2,
+  };
+}
+
+const _removeChildren = (element) => {
+  while (element && element.lastChild) element.removeChild(element.lastChild);
+};
+
+/**
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping
+ */
+const _escapeRegExp = (string) =>
+  string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+
+const _displayItem = (item, searchTerms, highlightTerms) => {
+  const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+  const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+  const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
+  const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
+
+  const [docName, title, anchor, descr, score, _filename] = item;
+
+  let listItem = document.createElement("li");
+  let requestUrl;
+  let linkUrl;
+  if (docBuilder === "dirhtml") {
+    // dirhtml builder
+    let dirname = docName + "/";
+    if (dirname.match(/\/index\/$/))
+      dirname = dirname.substring(0, dirname.length - 6);
+    else if (dirname === "index/") dirname = "";
+    requestUrl = contentRoot + dirname;
+    linkUrl = requestUrl;
+  } else {
+    // normal html builders
+    requestUrl = contentRoot + docName + docFileSuffix;
+    linkUrl = docName + docLinkSuffix;
+  }
+  let linkEl = listItem.appendChild(document.createElement("a"));
+  linkEl.href = linkUrl + anchor;
+  linkEl.dataset.score = score;
+  linkEl.innerHTML = title;
+  if (descr) {
+    listItem.appendChild(document.createElement("span")).innerHTML =
+      " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
+  else if (showSearchSummary)
+    fetch(requestUrl)
+      .then((responseData) => responseData.text())
+      .then((data) => {
+        if (data)
+          listItem.appendChild(
+            Search.makeSearchSummary(data, searchTerms, anchor)
+          );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+      });
+  Search.output.appendChild(listItem);
+};
+const _finishSearch = (resultCount) => {
+  Search.stopPulse();
+  Search.title.innerText = _("Search Results");
+  if (!resultCount)
+    Search.status.innerText = Documentation.gettext(
+      "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
+    );
+  else
+    Search.status.innerText = _(
+      "Search finished, found ${resultCount} page(s) matching the search query."
+    ).replace('${resultCount}', resultCount);
+};
+const _displayNextItem = (
+  results,
+  resultCount,
+  searchTerms,
+  highlightTerms,
+) => {
+  // results left, load the summary and display it
+  // this is intended to be dynamic (don't sub resultsCount)
+  if (results.length) {
+    _displayItem(results.pop(), searchTerms, highlightTerms);
+    setTimeout(
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
+      5
+    );
+  }
+  // search finished, update title and status message
+  else _finishSearch(resultCount);
+};
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+  const leftScore = a[4];
+  const rightScore = b[4];
+  if (leftScore === rightScore) {
+    // same score: sort alphabetically
+    const leftTitle = a[1].toLowerCase();
+    const rightTitle = b[1].toLowerCase();
+    if (leftTitle === rightTitle) return 0;
+    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+  }
+  return leftScore > rightScore ? 1 : -1;
+};
+
+/**
+ * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
+ * custom function per language.
+ *
+ * The regular expression works by splitting the string on consecutive characters
+ * that are not Unicode letters, numbers, underscores, or emoji characters.
+ * This is the same as ``\W+`` in Python, preserving the surrogate pair area.
+ */
+if (typeof splitQuery === "undefined") {
+  var splitQuery = (query) => query
+      .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu)
+      .filter(term => term)  // remove remaining empty strings
+}
+
+/**
+ * Search Module
+ */
+const Search = {
+  _index: null,
+  _queued_query: null,
+  _pulse_status: -1,
+
+  htmlToText: (htmlString, anchor) => {
+    const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
+    for (const removalQuery of [".headerlink", "script", "style"]) {
+      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+    }
+    if (anchor) {
+      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+      if (anchorContent) return anchorContent.textContent;
+
+      console.warn(
+        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+      );
+    }
+
+    // if anchor not specified or not found, fall back to main content
+    const docContent = htmlElement.querySelector('[role="main"]');
+    if (docContent) return docContent.textContent;
+
+    console.warn(
+      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
+    );
+    return "";
+  },
+
+  init: () => {
+    const query = new URLSearchParams(window.location.search).get("q");
+    document
+      .querySelectorAll('input[name="q"]')
+      .forEach((el) => (el.value = query));
+    if (query) Search.performSearch(query);
+  },
+
+  loadIndex: (url) =>
+    (document.body.appendChild(document.createElement("script")).src = url),
+
+  setIndex: (index) => {
+    Search._index = index;
+    if (Search._queued_query !== null) {
+      const query = Search._queued_query;
+      Search._queued_query = null;
+      Search.query(query);
+    }
+  },
+
+  hasIndex: () => Search._index !== null,
+
+  deferQuery: (query) => (Search._queued_query = query),
+
+  stopPulse: () => (Search._pulse_status = -1),
+
+  startPulse: () => {
+    if (Search._pulse_status >= 0) return;
+
+    const pulse = () => {
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      Search.dots.innerText = ".".repeat(Search._pulse_status);
+      if (Search._pulse_status >= 0) window.setTimeout(pulse, 500);
+    };
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch: (query) => {
+    // create the required interface elements
+    const searchText = document.createElement("h2");
+    searchText.textContent = _("Searching");
+    const searchSummary = document.createElement("p");
+    searchSummary.classList.add("search-summary");
+    searchSummary.innerText = "";
+    const searchList = document.createElement("ul");
+    searchList.classList.add("search");
+
+    const out = document.getElementById("search-results");
+    Search.title = out.appendChild(searchText);
+    Search.dots = Search.title.appendChild(document.createElement("span"));
+    Search.status = out.appendChild(searchSummary);
+    Search.output = out.appendChild(searchList);
+
+    const searchProgress = document.getElementById("search-progress");
+    // Some themes don't use the search progress node
+    if (searchProgress) {
+      searchProgress.innerText = _("Preparing search...");
+    }
+    Search.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (Search.hasIndex()) Search.query(query);
+    else Search.deferQuery(query);
+  },
+
+  _parseQuery: (query) => {
+    // stem the search terms and add them to the correct list
+    const stemmer = new Stemmer();
+    const searchTerms = new Set();
+    const excludedTerms = new Set();
+    const highlightTerms = new Set();
+    const objectTerms = new Set(splitQuery(query.toLowerCase().trim()));
+    splitQuery(query.trim()).forEach((queryTerm) => {
+      const queryTermLower = queryTerm.toLowerCase();
+
+      // maybe skip this "word"
+      // stopwords array is from language_data.js
+      if (
+        stopwords.indexOf(queryTermLower) !== -1 ||
+        queryTerm.match(/^\d+$/)
+      )
+        return;
+
+      // stem the word
+      let word = stemmer.stemWord(queryTermLower);
+      // select the correct list
+      if (word[0] === "-") excludedTerms.add(word.substr(1));
+      else {
+        searchTerms.add(word);
+        highlightTerms.add(queryTermLower);
+      }
+    });
+
+    if (SPHINX_HIGHLIGHT_ENABLED) {  // set in sphinx_highlight.js
+      localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
+    }
+
+    // console.debug("SEARCH: searching for:");
+    // console.info("required: ", [...searchTerms]);
+    // console.info("excluded: ", [...excludedTerms]);
+
+    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
+    // Collect multiple result groups to be sorted separately and then ordered.
+    // Each is an array of [docname, title, anchor, descr, score, filename].
+    const normalResults = [];
+    const nonMainIndexResults = [];
+
+    _removeChildren(document.getElementById("search-progress"));
+
+    const queryLower = query.toLowerCase().trim();
+    for (const [title, foundTitles] of Object.entries(allTitles)) {
+      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
+        for (const [file, id] of foundTitles) {
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
+          normalResults.push([
+            docNames[file],
+            titles[file] !== title ? `${titles[file]} > ${title}` : title,
+            id !== null ? "#" + id : "",
+            null,
+            score + boost,
+            filenames[file],
+          ]);
+        }
+      }
+    }
+
+    // search for explicit entries in index directives
+    for (const [entry, foundEntries] of Object.entries(indexEntries)) {
+      if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
+        for (const [file, id, isMain] of foundEntries) {
+          const score = Math.round(100 * queryLower.length / entry.length);
+          const result = [
+            docNames[file],
+            titles[file],
+            id ? "#" + id : "",
+            null,
+            score,
+            filenames[file],
+          ];
+          if (isMain) {
+            normalResults.push(result);
+          } else {
+            nonMainIndexResults.push(result);
+          }
+        }
+      }
+    }
+
+    // lookup as object
+    objectTerms.forEach((term) =>
+      normalResults.push(...Search.performObjectSearch(term, objectTerms))
+    );
+
+    // lookup as search terms in fulltext
+    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+    }
+
+    // Sort each group of results by score and then alphabetically by name.
+    normalResults.sort(_orderResultsByScoreThenName);
+    nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+    // Combine the result groups in (reverse) order.
+    // Non-main index entries are typically arbitrary cross-references,
+    // so display them after other results.
+    let results = [...nonMainIndexResults, ...normalResults];
+
+    // remove duplicate search results
+    // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
+    let seen = new Set();
+    results = results.reverse().reduce((acc, result) => {
+      let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(',');
+      if (!seen.has(resultStr)) {
+        acc.push(result);
+        seen.add(resultStr);
+      }
+      return acc;
+    }, []);
+
+    return results.reverse();
+  },
+
+  query: (query) => {
+    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    // console.info("search results:", Search.lastresults);
+
+    // print the results
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch: (object, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const objects = Search._index.objects;
+    const objNames = Search._index.objnames;
+    const titles = Search._index.titles;
+
+    const results = [];
+
+    const objectSearchCallback = (prefix, match) => {
+      const name = match[4]
+      const fullname = (prefix ? prefix + "." : "") + name;
+      const fullnameLower = fullname.toLowerCase();
+      if (fullnameLower.indexOf(object) < 0) return;
+
+      let score = 0;
+      const parts = fullnameLower.split(".");
+
+      // check for different match types: exact matches of full name or
+      // "last name" (i.e. last dotted part)
+      if (fullnameLower === object || parts.slice(-1)[0] === object)
+        score += Scorer.objNameMatch;
+      else if (parts.slice(-1)[0].indexOf(object) > -1)
+        score += Scorer.objPartialMatch; // matches in last name
+
+      const objName = objNames[match[1]][2];
+      const title = titles[match[0]];
+
+      // If more than one term searched for, we require other words to be
+      // found in the name/title/description
+      const otherTerms = new Set(objectTerms);
+      otherTerms.delete(object);
+      if (otherTerms.size > 0) {
+        const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase();
+        if (
+          [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0)
+        )
+          return;
+      }
+
+      let anchor = match[3];
+      if (anchor === "") anchor = fullname;
+      else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname;
+
+      const descr = objName + _(", in ") + title;
+
+      // add custom score for some objects according to scorer
+      if (Scorer.objPrio.hasOwnProperty(match[2]))
+        score += Scorer.objPrio[match[2]];
+      else score += Scorer.objPrioDefault;
+
+      results.push([
+        docNames[match[0]],
+        fullname,
+        "#" + anchor,
+        descr,
+        score,
+        filenames[match[0]],
+      ]);
+    };
+    Object.keys(objects).forEach((prefix) =>
+      objects[prefix].forEach((array) =>
+        objectSearchCallback(prefix, array)
+      )
+    );
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch: (searchTerms, excludedTerms) => {
+    // prepare search
+    const terms = Search._index.terms;
+    const titleTerms = Search._index.titleterms;
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+
+    const scoreMap = new Map();
+    const fileMap = new Map();
+
+    // perform the search on the required terms
+    searchTerms.forEach((word) => {
+      const files = [];
+      const arr = [
+        { files: terms[word], score: Scorer.term },
+        { files: titleTerms[word], score: Scorer.title },
+      ];
+      // add support for partial matches
+      if (word.length > 2) {
+        const escapedWord = _escapeRegExp(word);
+        if (!terms.hasOwnProperty(word)) {
+          Object.keys(terms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: terms[term], score: Scorer.partialTerm });
+          });
+        }
+        if (!titleTerms.hasOwnProperty(word)) {
+          Object.keys(titleTerms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+          });
+        }
+      }
+
+      // no match but word was a required one
+      if (arr.every((record) => record.files === undefined)) return;
+
+      // found search word in contents
+      arr.forEach((record) => {
+        if (record.files === undefined) return;
+
+        let recordFiles = record.files;
+        if (recordFiles.length === undefined) recordFiles = [recordFiles];
+        files.push(...recordFiles);
+
+        // set score for the word in each file
+        recordFiles.forEach((file) => {
+          if (!scoreMap.has(file)) scoreMap.set(file, {});
+          scoreMap.get(file)[word] = record.score;
+        });
+      });
+
+      // create the mapping
+      files.forEach((file) => {
+        if (!fileMap.has(file)) fileMap.set(file, [word]);
+        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
+      });
+    });
+
+    // now check if the files don't contain excluded terms
+    const results = [];
+    for (const [file, wordList] of fileMap) {
+      // check if all requirements are matched
+
+      // as search terms with length < 3 are discarded
+      const filteredTermCount = [...searchTerms].filter(
+        (term) => term.length > 2
+      ).length;
+      if (
+        wordList.length !== searchTerms.size &&
+        wordList.length !== filteredTermCount
+      )
+        continue;
+
+      // ensure that none of the excluded terms is in the search result
+      if (
+        [...excludedTerms].some(
+          (term) =>
+            terms[term] === file ||
+            titleTerms[term] === file ||
+            (terms[term] || []).includes(file) ||
+            (titleTerms[term] || []).includes(file)
+        )
+      )
+        break;
+
+      // select one (max) score for the file.
+      const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w]));
+      // add result to the result list
+      results.push([
+        docNames[file],
+        titles[file],
+        "",
+        null,
+        score,
+        filenames[file],
+      ]);
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words.
+   */
+  makeSearchSummary: (htmlText, keywords, anchor) => {
+    const text = Search.htmlToText(htmlText, anchor);
+    if (text === "") return null;
+
+    const textLower = text.toLowerCase();
+    const actualStartPosition = [...keywords]
+      .map((k) => textLower.indexOf(k.toLowerCase()))
+      .filter((i) => i > -1)
+      .slice(-1)[0];
+    const startWithContext = Math.max(actualStartPosition - 120, 0);
+
+    const top = startWithContext === 0 ? "" : "...";
+    const tail = startWithContext + 240 < text.length ? "..." : "";
+
+    let summary = document.createElement("p");
+    summary.classList.add("context");
+    summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
+
+    return summary;
+  },
+};
+
+_ready(Search.init);

docs/_build/html/_static/sphinx_highlight.js

@@ -0,0 +1,154 @@
+/* Highlighting utilities for Sphinx HTML documentation. */
+"use strict";
+
+const SPHINX_HIGHLIGHT_ENABLED = true
+
+/**
+ * highlight a given string on a node by wrapping it in
+ * span elements with the given class name.
+ */
+const _highlight = (node, addItems, text, className) => {
+  if (node.nodeType === Node.TEXT_NODE) {
+    const val = node.nodeValue;
+    const parent = node.parentNode;
+    const pos = val.toLowerCase().indexOf(text);
+    if (
+      pos >= 0 &&
+      !parent.classList.contains(className) &&
+      !parent.classList.contains("nohighlight")
+    ) {
+      let span;
+
+      const closestNode = parent.closest("body, svg, foreignObject");
+      const isInSVG = closestNode && closestNode.matches("svg");
+      if (isInSVG) {
+        span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+      } else {
+        span = document.createElement("span");
+        span.classList.add(className);
+      }
+
+      span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
+      parent.insertBefore(
+        span,
+        parent.insertBefore(
+          rest,
+          node.nextSibling
+        )
+      );
+      node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
+
+      if (isInSVG) {
+        const rect = document.createElementNS(
+          "http://www.w3.org/2000/svg",
+          "rect"
+        );
+        const bbox = parent.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: parent, target: rect });
+      }
+    }
+  } else if (node.matches && !node.matches("button, select, textarea")) {
+    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
+  }
+};
+const _highlightText = (thisNode, text, className) => {
+  let addItems = [];
+  _highlight(thisNode, addItems, text, className);
+  addItems.forEach((obj) =>
+    obj.parent.insertAdjacentElement("beforebegin", obj.target)
+  );
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+const SphinxHighlight = {
+
+  /**
+   * highlight the search words provided in localstorage in the text
+   */
+  highlightSearchWords: () => {
+    if (!SPHINX_HIGHLIGHT_ENABLED) return;  // bail if no highlight
+
+    // get and clear terms from localstorage
+    const url = new URL(window.location);
+    const highlight =
+        localStorage.getItem("sphinx_highlight_terms")
+        || url.searchParams.get("highlight")
+        || "";
+    localStorage.removeItem("sphinx_highlight_terms")
+    url.searchParams.delete("highlight");
+    window.history.replaceState({}, "", url);
+
+    // get individual terms from highlight string
+    const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
+    if (terms.length === 0) return; // nothing to do
+
+    // There should never be more than one element matching "div.body"
+    const divBody = document.querySelectorAll("div.body");
+    const body = divBody.length ? divBody[0] : document.querySelector("body");
+    window.setTimeout(() => {
+      terms.forEach((term) => _highlightText(body, term, "highlighted"));
+    }, 10);
+
+    const searchBox = document.getElementById("searchbox");
+    if (searchBox === null) return;
+    searchBox.appendChild(
+      document
+        .createRange()
+        .createContextualFragment(
+          '<p class="highlight-link">' +
+            '<a href="javascript:SphinxHighlight.hideSearchWords()">' +
+            _("Hide Search Matches") +
+            "</a></p>"
+        )
+    );
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords: () => {
+    document
+      .querySelectorAll("#searchbox .highlight-link")
+      .forEach((el) => el.remove());
+    document
+      .querySelectorAll("span.highlighted")
+      .forEach((el) => el.classList.remove("highlighted"));
+    localStorage.removeItem("sphinx_highlight_terms")
+  },
+
+  initEscapeListener: () => {
+    // only install a listener if it is really needed
+    if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return;
+
+    document.addEventListener("keydown", (event) => {
+      // bail for input elements
+      if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+      // bail with special keys
+      if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return;
+      if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) {
+        SphinxHighlight.hideSearchWords();
+        event.preventDefault();
+      }
+    });
+  },
+};
+
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});

docs/_build/html/genindex.html

@@ -0,0 +1,649 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Index &mdash; PROTAC-Degradation-Predictor v1.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+  
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=d29a5c0e"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></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">
+            PROTAC-Degradation-Predictor
+          </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" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="source/modules.html">protac_degradation_predictor</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">PROTAC-Degradation-Predictor</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">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#H"><strong>H</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#O"><strong>O</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#V"><strong>V</strong></a>
+ | <a href="#X"><strong>X</strong></a>
+ | <a href="#Z"><strong>Z</strong></a>
+ 
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.active_label">active_label (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.add_module">add_module() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.apply">apply() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.apply_scalers">apply_scalers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.apply_scaling">apply_scaling() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.apply_smote">apply_smote() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_cell_lines">avail_cell_lines() (in module protac_degradation_predictor.data_utils)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_e3_ligases">avail_e3_ligases() (in module protac_degradation_predictor.data_utils)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_uniprots">avail_uniprots() (in module protac_degradation_predictor.data_utils)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.bfloat16">bfloat16() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.buffers">buffers() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.call_super_init">call_super_init (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.cell_embedding_size">cell_embedding_size (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.children">children() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config">Config (class in protac_degradation_predictor.config)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.configure_optimizers">configure_optimizers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.cpu">cpu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.cuda">cuda() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.dmax_threshold">dmax_threshold (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.double">double() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.dump_patches">dump_patches (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.e3_ligase2uniprot">e3_ligase2uniprot (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.eval">eval() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.evaluate_model">evaluate_model() (in module protac_degradation_predictor.pytorch_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.extra_repr">extra_repr() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.fingerprint_size">fingerprint_size (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.fit_scaling">fit_scaling() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.float">float() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.forward">forward() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.forward">(protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_buffer">get_buffer() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_cell_emb_dim">get_cell_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.get_confidence_scores">get_confidence_scores() (in module protac_degradation_predictor.optuna_utils_xgboost)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.get_confidence_scores">(in module protac_degradation_predictor.pytorch_models)</a>
+</li>
+      </ul></li>
+      <li><a href="source/protac_degradation_predictor.optuna.html#protac_degradation_predictor.optuna.utils.get_dataframe_stats">get_dataframe_stats() (in module protac_degradation_predictor.optuna.utils)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_dataframe_stats">(in module protac_degradation_predictor.optuna_utils)</a>
+</li>
+      </ul></li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.get_datasets">get_datasets() (in module protac_degradation_predictor.protac_dataset)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_e3_ligase_split_indices">get_e3_ligase_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_extra_state">get_extra_state() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.get_fingerprint">get_fingerprint() (in module protac_degradation_predictor.data_utils)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.optuna.html#protac_degradation_predictor.optuna.utils.get_majority_vote_metrics">get_majority_vote_metrics() (in module protac_degradation_predictor.optuna.utils)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_majority_vote_metrics">(in module protac_degradation_predictor.optuna_utils)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_numpy_arrays">get_numpy_arrays() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_parameter">get_parameter() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_active_proba">get_protac_active_proba() (in module protac_degradation_predictor.protac_degradation_predictor)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_embedding">get_protac_embedding() (in module protac_degradation_predictor.protac_degradation_predictor)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_protein_emb_dim">get_protein_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_random_split_indices">get_random_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_smiles2fp_and_avg_tanimoto">get_smiles2fp_and_avg_tanimoto() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset.get_smiles_emb_dim">get_smiles_emb_dim() (protac_degradation_predictor.protac_dataset.PROTAC_Dataset method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.get_submodule">get_submodule() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_suggestion">get_suggestion() (in module protac_degradation_predictor.optuna_utils)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_tanimoto_split_indices">get_tanimoto_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.get_target_split_indices">get_target_split_indices() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule static method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="H">H</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.half">half() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.hyperparameter_tuning_and_training">hyperparameter_tuning_and_training() (in module protac_degradation_predictor.optuna_utils)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.initialize_scalers">initialize_scalers() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.ipu">ipu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.is_active">is_active() (in module protac_degradation_predictor.data_utils)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.is_protac_active">is_protac_active() (in module protac_degradation_predictor.protac_degradation_predictor)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.load_curated_dataset">load_curated_dataset() (in module protac_degradation_predictor.data_utils)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.load_model">load_model() (in module protac_degradation_predictor.pytorch_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.load_state_dict">load_state_dict() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    module
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor">protac_degradation_predictor</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.config">protac_degradation_predictor.config</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.data_utils">protac_degradation_predictor.data_utils</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna">protac_degradation_predictor.optuna</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna.utils">protac_degradation_predictor.optuna.utils</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils">protac_degradation_predictor.optuna_utils</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils_xgboost">protac_degradation_predictor.optuna_utils_xgboost</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_dataset">protac_degradation_predictor.protac_dataset</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_degradation_predictor">protac_degradation_predictor.protac_degradation_predictor</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.pytorch_models">protac_degradation_predictor.pytorch_models</a>
+</li>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.sklearn_models">protac_degradation_predictor.sklearn_models</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.modules">modules() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.morgan_radius">morgan_radius (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_buffers">named_buffers() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_children">named_children() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_modules">named_modules() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.named_parameters">named_parameters() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="O">O</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.on_load_checkpoint">on_load_checkpoint() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.on_save_checkpoint">on_save_checkpoint() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.parameters">parameters() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.pdc50_threshold">pdc50_threshold (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.predict_step">predict_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule">PROTAC_DataModule (class in protac_degradation_predictor.protac_dataset)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset">PROTAC_Dataset (class in protac_degradation_predictor.protac_dataset)</a>
+</li>
+      <li>
+    protac_degradation_predictor
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.config
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.config">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.data_utils
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.data_utils">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.optuna
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.optuna.utils
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.optuna.html#module-protac_degradation_predictor.optuna.utils">module</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    protac_degradation_predictor.optuna_utils
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.optuna_utils_xgboost
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils_xgboost">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.protac_dataset
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_dataset">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.protac_degradation_predictor
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_degradation_predictor">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.pytorch_models
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.pytorch_models">module</a>
+</li>
+      </ul></li>
+      <li>
+    protac_degradation_predictor.sklearn_models
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.sklearn_models">module</a>
+</li>
+      </ul></li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model">PROTAC_Model (class in protac_degradation_predictor.pytorch_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor">PROTAC_Predictor (class in protac_degradation_predictor.pytorch_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config.protein_embedding_size">protein_embedding_size (protac_degradation_predictor.config.Config attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.pytorch_model_objective">pytorch_model_objective() (in module protac_degradation_predictor.optuna_utils)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_backward_hook">register_backward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_buffer">register_buffer() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_forward_hook">register_forward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_forward_pre_hook">register_forward_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_full_backward_hook">register_full_backward_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_full_backward_pre_hook">register_full_backward_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_load_state_dict_post_hook">register_load_state_dict_post_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_module">register_module() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_parameter">register_parameter() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.register_state_dict_pre_hook">register_state_dict_pre_hook() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.requires_grad_">requires_grad_() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.scale_tensor">scale_tensor() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.set_extra_state">set_extra_state() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.setup">setup() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.share_memory">share_memory() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.state_dict">state_dict() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.step">step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_gradient_boosting">suggest_gradient_boosting() (in module protac_degradation_predictor.sklearn_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_logistic_regression">suggest_logistic_regression() (in module protac_degradation_predictor.sklearn_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_random_forest">suggest_random_forest() (in module protac_degradation_predictor.sklearn_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_svc">suggest_svc() (in module protac_degradation_predictor.sklearn_models)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.T_destination">T_destination (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.test_dataloader">test_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.test_dataloader">(protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      </ul></li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.test_step">test_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.to">to() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.to_empty">to_empty() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.train">train() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.train_and_evaluate_xgboost">train_and_evaluate_xgboost() (in module protac_degradation_predictor.optuna_utils_xgboost)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.train_dataloader">train_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.train_dataloader">(protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      </ul></li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.train_model">train_model() (in module protac_degradation_predictor.pytorch_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.train_sklearn_model">train_sklearn_model() (in module protac_degradation_predictor.sklearn_models)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.training">training (protac_degradation_predictor.pytorch_models.PROTAC_Predictor attribute)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.training_step">training_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.type">type() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule.val_dataloader">val_dataloader() (protac_degradation_predictor.protac_dataset.PROTAC_DataModule method)</a>
+
+      <ul>
+        <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.val_dataloader">(protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model.validation_step">validation_step() (protac_degradation_predictor.pytorch_models.PROTAC_Model method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="X">X</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_hyperparameter_tuning_and_training">xgboost_hyperparameter_tuning_and_training() (in module protac_degradation_predictor.optuna_utils_xgboost)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_model_objective">xgboost_model_objective() (in module protac_degradation_predictor.optuna_utils_xgboost)</a>
+</li>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.xpu">xpu() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Z">Z</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor.zero_grad">zero_grad() (protac_degradation_predictor.pytorch_models.PROTAC_Predictor method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+
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+<h1>PROTAC-Degradation-Predictor documentation<a class="headerlink" href="#protac-degradation-predictor-documentation" title="Link to this heading"></a></h1>
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+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="source/modules.html">protac_degradation_predictor</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="source/protac_degradation_predictor.html">protac_degradation_predictor package</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#subpackages">Subpackages</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.optuna.html">protac_degradation_predictor.optuna package</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#submodules">Submodules</a></li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.config">protac_degradation_predictor.config module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.config.Config"><code class="docutils literal notranslate"><span class="pre">Config</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.data_utils">protac_degradation_predictor.data_utils module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_e3_ligases"><code class="docutils literal notranslate"><span class="pre">avail_e3_ligases()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_cell_lines"><code class="docutils literal notranslate"><span class="pre">avail_cell_lines()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.avail_uniprots"><code class="docutils literal notranslate"><span class="pre">avail_uniprots()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.get_fingerprint"><code class="docutils literal notranslate"><span class="pre">get_fingerprint()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.is_active"><code class="docutils literal notranslate"><span class="pre">is_active()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.data_utils.load_curated_dataset"><code class="docutils literal notranslate"><span class="pre">load_curated_dataset()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils">protac_degradation_predictor.optuna_utils module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_dataframe_stats"><code class="docutils literal notranslate"><span class="pre">get_dataframe_stats()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_majority_vote_metrics"><code class="docutils literal notranslate"><span class="pre">get_majority_vote_metrics()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.get_suggestion"><code class="docutils literal notranslate"><span class="pre">get_suggestion()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.pytorch_model_objective"><code class="docutils literal notranslate"><span class="pre">pytorch_model_objective()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils.hyperparameter_tuning_and_training"><code class="docutils literal notranslate"><span class="pre">hyperparameter_tuning_and_training()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.optuna_utils_xgboost">protac_degradation_predictor.optuna_utils_xgboost module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.get_confidence_scores"><code class="docutils literal notranslate"><span class="pre">get_confidence_scores()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.train_and_evaluate_xgboost"><code class="docutils literal notranslate"><span class="pre">train_and_evaluate_xgboost()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_model_objective"><code class="docutils literal notranslate"><span class="pre">xgboost_model_objective()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.optuna_utils_xgboost.xgboost_hyperparameter_tuning_and_training"><code class="docutils literal notranslate"><span class="pre">xgboost_hyperparameter_tuning_and_training()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_dataset">protac_degradation_predictor.protac_dataset module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_Dataset"><code class="docutils literal notranslate"><span class="pre">PROTAC_Dataset</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.get_datasets"><code class="docutils literal notranslate"><span class="pre">get_datasets()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_dataset.PROTAC_DataModule"><code class="docutils literal notranslate"><span class="pre">PROTAC_DataModule</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.protac_degradation_predictor">protac_degradation_predictor.protac_degradation_predictor module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_active_proba"><code class="docutils literal notranslate"><span class="pre">get_protac_active_proba()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.is_protac_active"><code class="docutils literal notranslate"><span class="pre">is_protac_active()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.protac_degradation_predictor.get_protac_embedding"><code class="docutils literal notranslate"><span class="pre">get_protac_embedding()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.pytorch_models">protac_degradation_predictor.pytorch_models module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Predictor"><code class="docutils literal notranslate"><span class="pre">PROTAC_Predictor</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.PROTAC_Model"><code class="docutils literal notranslate"><span class="pre">PROTAC_Model</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.get_confidence_scores"><code class="docutils literal notranslate"><span class="pre">get_confidence_scores()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.train_model"><code class="docutils literal notranslate"><span class="pre">train_model()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.evaluate_model"><code class="docutils literal notranslate"><span class="pre">evaluate_model()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.pytorch_models.load_model"><code class="docutils literal notranslate"><span class="pre">load_model()</span></code></a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="source/protac_degradation_predictor.html#module-protac_degradation_predictor.sklearn_models">protac_degradation_predictor.sklearn_models module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.train_sklearn_model"><code class="docutils literal notranslate"><span class="pre">train_sklearn_model()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_random_forest"><code class="docutils literal notranslate"><span class="pre">suggest_random_forest()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_logistic_regression"><code class="docutils literal notranslate"><span class="pre">suggest_logistic_regression()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="source/protac_degradation_predictor.html#protac_degradation_predictor.sklearn_models.suggest_svc"><code class="docutils literal notranslate"><span class="pre">suggest_svc()</span></code></a></li>
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