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When it is not found, a full rebuild will be done. +config: 18efb40e970fb2c9b3465eeb13d835bc +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6754d9593a08b02cf9af8205533962ea6cab6d8 --- /dev/null +++ b/docs/_build/html/_sources/index.rst.txt @@ -0,0 +1,18 @@ +.. 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 `_ +documentation for details. + + +.. toctree:: + :maxdepth: 4 + :caption: Contents: + + source/modules \ No newline at end of file diff --git a/docs/_build/html/_sources/source/modules.rst.txt b/docs/_build/html/_sources/source/modules.rst.txt new file mode 100644 index 0000000000000000000000000000000000000000..cac44ec69b6a88537a027c4b3b28c1c4741c3b3d --- /dev/null +++ b/docs/_build/html/_sources/source/modules.rst.txt @@ -0,0 +1,7 @@ +protac_degradation_predictor +============================ + +.. toctree:: + :maxdepth: 4 + + protac_degradation_predictor diff --git a/docs/_build/html/_sources/source/protac_degradation_predictor.optuna.rst.txt b/docs/_build/html/_sources/source/protac_degradation_predictor.optuna.rst.txt new file mode 100644 index 0000000000000000000000000000000000000000..44e702e0ecad724cf16d55ffcda92bb3d03b4c38 --- /dev/null +++ b/docs/_build/html/_sources/source/protac_degradation_predictor.optuna.rst.txt @@ -0,0 +1,45 @@ +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: diff --git a/docs/_build/html/_sources/source/protac_degradation_predictor.rst.txt b/docs/_build/html/_sources/source/protac_degradation_predictor.rst.txt new file mode 100644 index 0000000000000000000000000000000000000000..c33a7d8875beafb9be7903ad95b444824660f9cf --- /dev/null +++ b/docs/_build/html/_sources/source/protac_degradation_predictor.rst.txt @@ -0,0 +1,85 @@ +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: diff --git a/docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js b/docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 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+ +/** + * 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); diff --git a/docs/_build/html/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js new file mode 100644 index 0000000000000000000000000000000000000000..8a96c69a1942318413af68fd459122b56edd8d69 --- /dev/null +++ b/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. 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2, "util": [1, 2], "val": 2, "val_d": 2, "val_dataload": [1, 2], "val_dataset": 2, "val_df": [2, 3], "valid": [2, 3], "validation_step": [1, 2], "valu": 2, "var": 2, "version": 2, "view": 2, "vote": [2, 3], "we": 2, "weight": 2, "well": 2, "when": 2, "whether": 2, "which": 2, "while": 2, "whole": 2, "whose": 2, "with_kwarg": 2, "within": 2, "without": 2, "won": 2, "work": 2, "would": 2, "wrap": 2, "xdoctest": 2, "xgboost": 2, "xgboost_hyperparameter_tuning_and_train": [0, 1, 2], "xgboost_model": [1, 2], "xgboost_model_object": [0, 1, 2], "xpu": [1, 2], "y": 2, "y_pred": 2, "yet": 2, "yield": 2, "you": 2, "your": [0, 2], "zero": 2, "zero_grad": [1, 2]}, "titles": ["PROTAC-Degradation-Predictor documentation", "protac_degradation_predictor", "protac_degradation_predictor package", "protac_degradation_predictor.optuna package"], "titleterms": {"config": 2, "content": [0, 2, 3], "data_util": 2, "degrad": 0, "document": 0, "modul": [2, 3], "optuna": 3, "optuna_util": 2, "optuna_utils_xgboost": 2, "packag": [2, 3], "predictor": 0, "protac": 0, "protac_dataset": 2, "protac_degradation_predictor": [1, 2, 3], "pytorch_model": [2, 3], "sklearn_model": [2, 3], "submodul": [2, 3], "subpackag": 2, "util": 3, "xgboost_model": 3}}) \ No newline at end of file diff --git a/docs/_build/html/source/modules.html b/docs/_build/html/source/modules.html new file mode 100644 index 0000000000000000000000000000000000000000..182838c853f1f702cc504e32d0db353b0aa46f32 --- /dev/null +++ b/docs/_build/html/source/modules.html @@ -0,0 +1,290 @@ + + + + + + + protac_degradation_predictor — PROTAC-Degradation-Predictor v1.0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
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+ +
+
+
+
+ +
+

protac_degradation_predictor

+
+ +
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+ + +
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+ +
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+ + + + \ No newline at end of file diff --git a/docs/_build/html/source/protac_degradation_predictor.html b/docs/_build/html/source/protac_degradation_predictor.html new file mode 100644 index 0000000000000000000000000000000000000000..e4a59b1edc6decb0b44ec4c50960ebad96947b9e --- /dev/null +++ b/docs/_build/html/source/protac_degradation_predictor.html @@ -0,0 +1,2620 @@ + + + + + + + protac_degradation_predictor package — PROTAC-Degradation-Predictor v1.0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

protac_degradation_predictor package

+
+

Subpackages

+ +
+
+

Submodules

+
+
+

protac_degradation_predictor.config module

+
+
+class protac_degradation_predictor.config.Config(morgan_radius: int = 10, fingerprint_size: int = 256, protein_embedding_size: int = 1024, cell_embedding_size: int = 768, dmax_threshold: float = 0.6, pdc50_threshold: float = 6.0, active_label: str = 'Active (Dmax 0.6, pDC50 6.0)', e3_ligase2uniprot: dict = <factory>)
+

Bases: object

+
+
Parameters:
+
    +
  • morgan_radius (int)

  • +
  • fingerprint_size (int)

  • +
  • protein_embedding_size (int)

  • +
  • cell_embedding_size (int)

  • +
  • dmax_threshold (float)

  • +
  • pdc50_threshold (float)

  • +
  • active_label (str)

  • +
  • e3_ligase2uniprot (dict)

  • +
+
+
+
+
+morgan_radius: int = 10
+
+ +
+
+fingerprint_size: int = 256
+
+ +
+
+protein_embedding_size: int = 1024
+
+ +
+
+cell_embedding_size: int = 768
+
+ +
+
+dmax_threshold: float = 0.6
+
+ +
+
+pdc50_threshold: float = 6.0
+
+ +
+
+active_label: str = 'Active (Dmax 0.6, pDC50 6.0)'
+
+ +
+
+e3_ligase2uniprot: dict
+
+ +
+ +
+
+

protac_degradation_predictor.data_utils module

+
+
+protac_degradation_predictor.data_utils.avail_e3_ligases()
+

Get the available E3 ligases.

+
+
Returns:
+

The available E3 ligases.

+
+
Return type:
+

List[str]

+
+
+
+ +
+
+protac_degradation_predictor.data_utils.avail_cell_lines()
+

Get the available cell lines.

+
+
Returns:
+

The available cell lines.

+
+
Return type:
+

List[str]

+
+
+
+ +
+
+protac_degradation_predictor.data_utils.avail_uniprots()
+

Get the available Uniprot IDs.

+
+
Returns:
+

The available Uniprot IDs.

+
+
Return type:
+

List[str]

+
+
+
+ +
+
+protac_degradation_predictor.data_utils.get_fingerprint(smiles, morgan_fpgen=None)
+

Get the Morgan fingerprint of a molecule.

+
+
Parameters:
+
    +
  • smiles (str) – The SMILES string of the molecule.

  • +
  • morgan_fpgen – The Morgan fingerprint generator.

  • +
+
+
Returns:
+

The Morgan fingerprint.

+
+
Return type:
+

np.ndarray

+
+
+
+ +
+
+protac_degradation_predictor.data_utils.is_active(DC50, Dmax, pDC50_threshold=7.0, Dmax_threshold=0.8, oring=False)
+

Check if a PROTAC is active based on DC50 and Dmax. +:param DC50: DC50 in nM +:type DC50: float +:param Dmax: Dmax in % +:type Dmax: float

+
+
Returns:
+

True if active, False if inactive, np.nan if either DC50 or Dmax is NaN

+
+
Return type:
+

bool

+
+
Parameters:
+
    +
  • DC50 (float)

  • +
  • Dmax (float)

  • +
  • pDC50_threshold (float)

  • +
  • Dmax_threshold (float)

  • +
  • oring (bool)

  • +
+
+
+
+ +
+
+protac_degradation_predictor.data_utils.load_curated_dataset()
+

Load the curated PROTAC dataset as described in the paper: https://arxiv.org/abs/2406.02637

+
+
Returns:
+

The curated PROTAC dataset.

+
+
Return type:
+

pd.DataFrame

+
+
+
+ +
+
+

protac_degradation_predictor.optuna_utils module

+
+
+protac_degradation_predictor.optuna_utils.get_dataframe_stats(train_df=None, val_df=None, test_df=None, active_label='Active')
+

Get some statistics from the dataframes.

+
+
Parameters:
+
    +
  • train_df (pd.DataFrame) – The training set.

  • +
  • val_df (pd.DataFrame) – The validation set.

  • +
  • test_df (pd.DataFrame) – The test set.

  • +
+
+
Return type:
+

Dict

+
+
+
+ +
+
+protac_degradation_predictor.optuna_utils.get_majority_vote_metrics(test_preds, test_df, active_label='Active')
+

Get the majority vote metrics.

+
+
Parameters:
+
    +
  • test_preds (List)

  • +
  • test_df (DataFrame)

  • +
  • active_label (str)

  • +
+
+
Return type:
+

Dict

+
+
+
+ +
+
+protac_degradation_predictor.optuna_utils.get_suggestion(trial, dtype, hparams_range)
+
+ +
+
+protac_degradation_predictor.optuna_utils.pytorch_model_objective(trial, protein2embedding, cell2embedding, smiles2fp, train_val_df, kf, groups=None, test_df=None, hparams_ranges=None, fast_dev_run=False, active_label='Active', disabled_embeddings=[], max_epochs=100, use_logger=False, logger_save_dir='logs', logger_name='cv_model', enable_checkpointing=False)
+

Objective function for hyperparameter optimization.

+
+
Parameters:
+
    +
  • trial (optuna.Trial) – The Optuna trial object.

  • +
  • train_df (pd.DataFrame) – The training set.

  • +
  • val_df (pd.DataFrame) – The validation set.

  • +
  • hparams_ranges (List[Dict[str, Any]]) – NOT IMPLEMENTED YET. Hyperparameters ranges. +The list must be of a tuple of the type of hparam to suggest (‘int’, ‘float’, or ‘categorical’), and the dictionary must contain the arguments of the corresponding trial.suggest method.

  • +
  • fast_dev_run (bool) – Whether to run a fast development run.

  • +
  • active_label (str) – The active label column.

  • +
  • disabled_embeddings (List[str]) – The list of disabled embeddings.

  • +
  • protein2embedding (Dict)

  • +
  • cell2embedding (Dict)

  • +
  • smiles2fp (Dict)

  • +
  • train_val_df (DataFrame)

  • +
  • kf (StratifiedKFold | StratifiedGroupKFold)

  • +
  • groups (array | None)

  • +
  • test_df (DataFrame | None)

  • +
  • max_epochs (int)

  • +
  • use_logger (bool)

  • +
  • logger_save_dir (str)

  • +
  • logger_name (str)

  • +
  • enable_checkpointing (bool)

  • +
+
+
Return type:
+

float

+
+
+
+ +
+
+protac_degradation_predictor.optuna_utils.hyperparameter_tuning_and_training(protein2embedding, cell2embedding, smiles2fp, train_val_df, test_df, kf, groups=None, split_type='standard', n_models_for_test=3, fast_dev_run=False, n_trials=50, logger_save_dir='logs', logger_name='protac_hparam_search', active_label='Active', max_epochs=100, study_filename=None, force_study=False)
+

Hyperparameter tuning and training of a PROTAC model.

+
+
Parameters:
+
    +
  • protein2embedding (Dict) – The protein to embedding dictionary.

  • +
  • cell2embedding (Dict) – The cell to embedding dictionary.

  • +
  • smiles2fp (Dict) – The SMILES to fingerprint dictionary.

  • +
  • train_val_df (pd.DataFrame) – The training and validation set.

  • +
  • test_df (pd.DataFrame) – The test set.

  • +
  • kf (StratifiedKFold | StratifiedGroupKFold) – The KFold object.

  • +
  • groups (np.array) – The groups for the StratifiedGroupKFold.

  • +
  • split_type (str) – The split type of the current study. Used for reporting.

  • +
  • n_models_for_test (int) – The number of models to train for the test set.

  • +
  • fast_dev_run (bool) – Whether to run a fast development run.

  • +
  • n_trials (int) – The number of trials for the hyperparameter search.

  • +
  • logger_save_dir (str) – The logger save directory.

  • +
  • logger_name (str) – The logger name.

  • +
  • active_label (str) – The active label column.

  • +
  • max_epochs (int) – The maximum number of epochs.

  • +
  • study_filename (str) – The study filename.

  • +
  • force_study (bool) – Whether to force the study.

  • +
+
+
Returns:
+

The trained model, the trainer, and the best metrics.

+
+
Return type:
+

tuple

+
+
+
+ +
+
+

protac_degradation_predictor.optuna_utils_xgboost module

+
+
+protac_degradation_predictor.optuna_utils_xgboost.get_confidence_scores(y, y_pred, threshold=0.5)
+
+ +
+
+protac_degradation_predictor.optuna_utils_xgboost.train_and_evaluate_xgboost(protein2embedding, cell2embedding, smiles2fp, train_df, val_df, params, test_df=None, active_label='Active', num_boost_round=100, shuffle_train_data=False)
+

Train and evaluate an XGBoost model with the given parameters.

+
+
Parameters:
+
    +
  • train_df (pd.DataFrame) – The training and validation data.

  • +
  • test_df (pd.DataFrame) – The test data.

  • +
  • params (dict) – Hyperparameters for the XGBoost model.

  • +
  • active_label (str) – The active label column.

  • +
  • num_boost_round (int) – Maximum number of epochs.

  • +
  • protein2embedding (Dict)

  • +
  • cell2embedding (Dict)

  • +
  • smiles2fp (Dict)

  • +
  • val_df (DataFrame)

  • +
  • shuffle_train_data (bool)

  • +
+
+
Returns:
+

The trained model, test predictions, and metrics.

+
+
Return type:
+

tuple

+
+
+
+ +
+
+protac_degradation_predictor.optuna_utils_xgboost.xgboost_model_objective(trial, protein2embedding, cell2embedding, smiles2fp, train_val_df, kf, groups=None, active_label='Active', num_boost_round=100, model_name=None)
+

Objective function for hyperparameter optimization with XGBoost.

+
+
Parameters:
+
    +
  • trial (optuna.Trial) – The Optuna trial object.

  • +
  • train_val_df (pd.DataFrame) – The training and validation data.

  • +
  • kf (StratifiedKFold) – Stratified K-Folds cross-validator.

  • +
  • test_df (Optional[pd.DataFrame]) – The test data.

  • +
  • active_label (str) – The active label column.

  • +
  • num_boost_round (int) – Maximum number of epochs.

  • +
  • model_name (Optional[str]) – The prefix name of the CV models to save, if supplied. Used as: f”{model_name}_fold_{k}.json”

  • +
  • protein2embedding (Dict)

  • +
  • cell2embedding (Dict)

  • +
  • smiles2fp (Dict)

  • +
  • groups (array | None)

  • +
+
+
Return type:
+

float

+
+
+
+ +
+
+protac_degradation_predictor.optuna_utils_xgboost.xgboost_hyperparameter_tuning_and_training(protein2embedding, cell2embedding, smiles2fp, train_val_df, test_df, kf, groups=None, split_type='random', n_models_for_test=3, n_trials=50, active_label='Active', num_boost_round=100, study_filename=None, force_study=False, model_name=None)
+

Hyperparameter tuning and training of an XGBoost model.

+
+
Parameters:
+
    +
  • train_val_df (pd.DataFrame) – The training and validation data.

  • +
  • test_df (pd.DataFrame) – The test data.

  • +
  • kf (StratifiedKFold) – Stratified K-Folds cross-validator.

  • +
  • groups (Optional[np.array]) – Group labels for the samples used while splitting the dataset into train/test set.

  • +
  • split_type (str) – Type of the data split. Used for reporting information.

  • +
  • n_models_for_test (int) – Number of models to train for testing.

  • +
  • fast_dev_run (bool) – Whether to run a fast development run.

  • +
  • n_trials (int) – Number of trials for hyperparameter optimization.

  • +
  • logger_save_dir (str) – Directory to save logs.

  • +
  • logger_name (str) – Name of the logger.

  • +
  • active_label (str) – The active label column.

  • +
  • num_boost_round (int) – Maximum number of epochs.

  • +
  • study_filename (Optional[str]) – File name to save/load the Optuna study.

  • +
  • force_study (bool) – Whether to force the study optimization even if the study file exists.

  • +
  • protein2embedding (Dict)

  • +
  • cell2embedding (Dict)

  • +
  • smiles2fp (Dict)

  • +
  • model_name (str | None)

  • +
+
+
Returns:
+

A dictionary containing reports from the CV and test.

+
+
Return type:
+

dict

+
+
+
+ +
+
+

protac_degradation_predictor.protac_dataset module

+
+
+class protac_degradation_predictor.protac_dataset.PROTAC_Dataset(protac_df, protein2embedding, cell2embedding, smiles2fp, use_smote=False, oversampler=None, active_label='Active', disabled_embeddings=[], scaler=None, use_single_scaler=None, shuffle_embedding_prob=0.0)
+

Bases: Dataset

+
+
Parameters:
+
    +
  • protac_df (DataFrame)

  • +
  • protein2embedding (Dict[str, ndarray])

  • +
  • cell2embedding (Dict[str, ndarray])

  • +
  • smiles2fp (Dict[str, ndarray])

  • +
  • use_smote (bool)

  • +
  • oversampler (SMOTE | ADASYN | None)

  • +
  • active_label (str)

  • +
  • disabled_embeddings (List[Literal['smiles', 'poi', 'e3', 'cell']])

  • +
  • scaler (StandardScaler | Dict[str, StandardScaler] | None)

  • +
  • use_single_scaler (bool | None)

  • +
  • shuffle_embedding_prob (float)

  • +
+
+
+
+
+get_smiles_emb_dim()
+
+ +
+
+get_protein_emb_dim()
+
+ +
+
+get_cell_emb_dim()
+
+ +
+
+apply_smote()
+
+ +
+
+fit_scaling(use_single_scaler=False, **scaler_kwargs)
+

Fit the scalers for the data and save them in the dataset class.

+
+
Parameters:
+
    +
  • use_single_scaler (bool) – Whether to use a single scaler for all features.

  • +
  • scaler_kwargs – Keyword arguments for the StandardScaler.

  • +
+
+
Returns:
+

The fitted scalers.

+
+
Return type:
+

dict

+
+
+
+ +
+
+apply_scaling(scalers, use_single_scaler=False)
+

Apply scaling to the data.

+
+
Parameters:
+
    +
  • scalers (dict) – The scalers for each feature.

  • +
  • use_single_scaler (bool) – Whether to use a single scaler for all features.

  • +
+
+
+
+ +
+
+get_numpy_arrays(component=None)
+

Get the numpy arrays for the dataset.

+
+
Parameters:
+

component (str) – The component to get the numpy arrays for. Defaults to None, i.e., get a single stacked array.

+
+
Returns:
+

The numpy arrays for the dataset. The first element is the input array, and the second element is the output array.

+
+
Return type:
+

tuple

+
+
+
+ +
+ +
+
+protac_degradation_predictor.protac_dataset.get_datasets(train_df, val_df, test_df=None, protein2embedding=None, cell2embedding=None, smiles2fp=None, smote_k_neighbors=5, active_label='Active', disabled_embeddings=[], scaler=None, use_single_scaler=None, apply_scaling=False, shuffle_embedding_prob=0.0)
+

Get the datasets for training the PROTAC model.

+
+
Parameters:
+
    +
  • train_df (pd.DataFrame) – The training data.

  • +
  • val_df (pd.DataFrame) – The validation data.

  • +
  • test_df (pd.DataFrame) – The test data.

  • +
  • protein2embedding (dict) – Dictionary of protein embeddings.

  • +
  • cell2embedding (dict) – Dictionary of cell line embeddings.

  • +
  • smiles2fp (dict) – Dictionary of SMILES to fingerprint.

  • +
  • use_smote (bool) – Whether to use SMOTE for oversampling.

  • +
  • smote_k_neighbors (int) – The number of neighbors to use for SMOTE.

  • +
  • active_label (str) – The active label column.

  • +
  • disabled_embeddings (list) – The list of embeddings to disable.

  • +
  • scaler (StandardScaler | dict) – The scaler to use for the embeddings.

  • +
  • use_single_scaler (bool) – Whether to use a single scaler for all features.

  • +
  • apply_scaling (bool) – Whether to apply scaling to the data now. Defaults to False (the Pytorch Lightning model does that).

  • +
  • shuffle_embedding_prob (float)

  • +
+
+
Return type:
+

Tuple[PROTAC_Dataset, PROTAC_Dataset, PROTAC_Dataset | None]

+
+
+
+ +
+
+class protac_degradation_predictor.protac_dataset.PROTAC_DataModule(*args, **kwargs)
+

Bases: LightningDataModule

+

PyTorch Lightning DataModule for the PROTAC dataset.

+

TODO: Work in progress. It would be nice to wrap all information into a +single class, but it is not clear how to do it yet due to cross-validation +and the need to split the data into training, validation, and test sets +accordingly.

+
+
Parameters:
+
    +
  • protac_csv_filepath (str) – The path to the PROTAC CSV file.

  • +
  • protein2embedding_filepath (str) – The path to the protein to embedding dictionary.

  • +
  • cell2embedding_filepath (str) – The path to the cell line to embedding dictionary.

  • +
  • pDC50_threshold (float) – The threshold for the pDC50 value to consider a PROTAC active.

  • +
  • Dmax_threshold (float) – The threshold for the Dmax value to consider a PROTAC active.

  • +
  • use_smote (bool) – Whether to use SMOTE for oversampling.

  • +
  • smote_k_neighbors (int) – The number of neighbors to use for SMOTE.

  • +
  • active_label (str) – The column containing the active/inactive information.

  • +
  • disabled_embeddings (list) – The list of embeddings to disable.

  • +
  • scaler (StandardScaler | dict) – The scaler to use for the embeddings.

  • +
  • use_single_scaler (bool) – Whether to use a single scaler for all features.

  • +
+
+
+
+
+setup(stage)
+
+
Parameters:
+

stage (str)

+
+
+
+ +
+
+train_dataloader()
+
+ +
+
+val_dataloader()
+
+ +
+
+test_dataloader()
+
+ +
+
+static get_random_split_indices(active_df, test_split)
+

Get the indices of the test set using a random split.

+
+
Parameters:
+
    +
  • active_df (pd.DataFrame) – The DataFrame containing the active PROTACs.

  • +
  • test_split (float) – The percentage of the active PROTACs to use as the test set.

  • +
+
+
Returns:
+

The indices of the test set.

+
+
Return type:
+

pd.Index

+
+
+
+ +
+
+static get_e3_ligase_split_indices(active_df)
+

Get the indices of the test set using the E3 ligase split.

+
+
Parameters:
+

active_df (pd.DataFrame) – The DataFrame containing the active PROTACs.

+
+
Returns:
+

The indices of the test set.

+
+
Return type:
+

pd.Index

+
+
+
+ +
+
+static get_smiles2fp_and_avg_tanimoto(protac_df)
+

Get the SMILES to fingerprint dictionary and the average Tanimoto similarity.

+
+
Parameters:
+

protac_df (pd.DataFrame) – The DataFrame containing the PROTACs.

+
+
Returns:
+

The SMILES to fingerprint dictionary and the average Tanimoto similarity.

+
+
Return type:
+

tuple

+
+
+
+ +
+
+static get_tanimoto_split_indices(active_df, active_label, test_split, n_bins_tanimoto=200)
+

Get the indices of the test set using the Tanimoto-based split.

+
+
Parameters:
+
    +
  • active_df (pd.DataFrame) – The DataFrame containing the active PROTACs.

  • +
  • n_bins_tanimoto (int) – The number of bins to use for the Tanimoto similarity.

  • +
  • active_label (str)

  • +
  • test_split (float)

  • +
+
+
Returns:
+

The indices of the test set.

+
+
Return type:
+

pd.Index

+
+
+
+ +
+
+static get_target_split_indices(active_df, active_label, test_split)
+

Get the indices of the test set using the target-based split.

+
+
Parameters:
+
    +
  • active_df (pd.DataFrame) – The DataFrame containing the active PROTACs.

  • +
  • active_label (str) – The column containing the active/inactive information.

  • +
  • test_split (float) – The percentage of the active PROTACs to use as the test set.

  • +
+
+
Returns:
+

The indices of the test set.

+
+
Return type:
+

pd.Index

+
+
+
+ +
+ +
+
+

protac_degradation_predictor.protac_degradation_predictor module

+
+
+protac_degradation_predictor.protac_degradation_predictor.get_protac_active_proba(protac_smiles, e3_ligase, target_uniprot, cell_line, device='cpu', use_models_from_cv=False, use_xgboost_models=False, study_type='standard')
+

Predict the probability of a PROTAC being active.

+
+
Parameters:
+
    +
  • protac_smiles (str | List[str]) – The SMILES of the PROTAC.

  • +
  • e3_ligase (str | List[str]) – The Uniprot ID of the E3 ligase.

  • +
  • target_uniprot (str | List[str]) – The Uniprot ID of the target protein.

  • +
  • cell_line (str | List[str]) – The cell line identifier.

  • +
  • device (str) – The device to run the model on.

  • +
  • use_models_from_cv (bool) – Whether to use the models from cross-validation.

  • +
  • use_xgb_models (bool) – Whether to use the XGBoost models.

  • +
  • study_type (str) – Use models trained on the specified study. Options are ‘standard’, ‘similarity’, ‘target’.

  • +
  • use_xgboost_models (bool)

  • +
+
+
Returns:
+

The predictions of the model. The dictionary contains the following: ‘preds’, ‘mean’, ‘majority_vote’. The ‘preds’ key contains the predictions of all models with shape: (n_models, batch_size), ‘mean’ contains the mean prediction, and ‘majority_vote’ contains the majority vote.

+
+
Return type:
+

Dict[str, np.ndarray]

+
+
+
+ +
+
+protac_degradation_predictor.protac_degradation_predictor.is_protac_active(protac_smiles, e3_ligase, target_uniprot, cell_line, device='cpu', proba_threshold=0.5, use_majority_vote=False, use_models_from_cv=False, use_xgboost_models=False, study_type='standard')
+

Predict whether a PROTAC is active or not.

+
+
Parameters:
+
    +
  • protac_smiles (str) – The SMILES of the PROTAC.

  • +
  • e3_ligase (str) – The Uniprot ID of the E3 ligase.

  • +
  • target_uniprot (str) – The Uniprot ID of the target protein.

  • +
  • cell_line (str) – The cell line identifier.

  • +
  • device (str) – The device to run the model on.

  • +
  • proba_threshold (float) – The probability threshold.

  • +
  • use_majority_vote (bool) – Whether to use the majority vote.

  • +
  • use_models_from_cv (bool) – Whether to use the models from cross-validation.

  • +
  • use_xgboost_models (bool) – Whether to use the XGBoost models.

  • +
  • study_type (str) – Use models trained on the specified study. Options are ‘standard’, ‘similarity’, ‘target’.

  • +
+
+
Returns:
+

Whether the PROTAC is active or not.

+
+
Return type:
+

bool

+
+
+
+ +
+
+protac_degradation_predictor.protac_degradation_predictor.get_protac_embedding(protac_smiles, e3_ligase, target_uniprot, cell_line, device='cpu', use_models_from_cv=False, study_type='standard')
+

Get the embeddings of a PROTAC or a list of PROTACs.

+
+
Parameters:
+
    +
  • protac_smiles (str | List[str]) – The SMILES of the PROTAC.

  • +
  • e3_ligase (str | List[str]) – The Uniprot ID of the E3 ligase.

  • +
  • target_uniprot (str | List[str]) – The Uniprot ID of the target protein.

  • +
  • cell_line (str | List[str]) – The cell line identifier.

  • +
  • device (str) – The device to run the model on.

  • +
  • use_models_from_cv (bool) – Whether to use the models from cross-validation.

  • +
  • study_type (str) – Use models trained on the specified study. Options are ‘standard’, ‘similarity’, ‘target’.

  • +
+
+
Returns:
+

The embeddings of the given PROTAC. Each key is the name of the model and the value is the embedding, of shape: (batch_size, model_hidden_size). NOTE: Each model has its own hidden size, so the embeddings might have different dimensions.

+
+
Return type:
+

Dict[str, np.ndarray]

+
+
+
+ +
+
+

protac_degradation_predictor.pytorch_models module

+
+
+class protac_degradation_predictor.pytorch_models.PROTAC_Predictor(hidden_dim, smiles_emb_dim=256, poi_emb_dim=1024, e3_emb_dim=1024, cell_emb_dim=768, dropout=0.2, join_embeddings='sum', use_batch_norm=False, disabled_embeddings=[])
+

Bases: Module

+
+
Parameters:
+
    +
  • hidden_dim (int)

  • +
  • smiles_emb_dim (int)

  • +
  • poi_emb_dim (int)

  • +
  • e3_emb_dim (int)

  • +
  • cell_emb_dim (int)

  • +
  • dropout (float)

  • +
  • join_embeddings (Literal['beginning', 'concat', 'sum'])

  • +
  • use_batch_norm (bool)

  • +
  • disabled_embeddings (List[Literal['smiles', 'poi', 'e3', 'cell']])

  • +
+
+
+
+
+forward(poi_emb, e3_emb, cell_emb, smiles_emb, return_embeddings=False)
+

Defines the computation performed at every call.

+

Should be overridden by all subclasses.

+
+

Note

+

Although the recipe for forward pass needs to be defined within +this function, one should call the Module instance afterwards +instead of this since the former takes care of running the +registered hooks while the latter silently ignores them.

+
+
+ +
+
+T_destination = ~T_destination
+
+ +
+
+add_module(name, module)
+

Adds a child module to the current module.

+

The module can be accessed as an attribute using the given name.

+
+
Parameters:
+
    +
  • name (str) – name of the child module. The child module can be +accessed from this module using the given name

  • +
  • module (Module) – child module to be added to the module.

  • +
+
+
Return type:
+

None

+
+
+
+ +
+
+apply(fn)
+

Applies fn recursively to every submodule (as returned by .children()) +as well as self. Typical use includes initializing the parameters of a model +(see also nn-init-doc).

+
+
Parameters:
+
    +
  • fn (Module -> None) – function to be applied to each submodule

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+

Example:

+
>>> @torch.no_grad()
+>>> def init_weights(m):
+>>>     print(m)
+>>>     if type(m) == nn.Linear:
+>>>         m.weight.fill_(1.0)
+>>>         print(m.weight)
+>>> net = nn.Sequential(nn.Linear(2, 2), nn.Linear(2, 2))
+>>> net.apply(init_weights)
+Linear(in_features=2, out_features=2, bias=True)
+Parameter containing:
+tensor([[1., 1.],
+        [1., 1.]], requires_grad=True)
+Linear(in_features=2, out_features=2, bias=True)
+Parameter containing:
+tensor([[1., 1.],
+        [1., 1.]], requires_grad=True)
+Sequential(
+  (0): Linear(in_features=2, out_features=2, bias=True)
+  (1): Linear(in_features=2, out_features=2, bias=True)
+)
+
+
+
+ +
+
+bfloat16()
+

Casts all floating point parameters and buffers to bfloat16 datatype.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
Parameters:
+

self (T)

+
+
+
+ +
+
+buffers(recurse=True)
+

Returns an iterator over module buffers.

+
+
Parameters:
+

recurse (bool) – if True, then yields buffers of this module +and all submodules. Otherwise, yields only buffers that +are direct members of this module.

+
+
Yields:
+

torch.Tensor – module buffer

+
+
Return type:
+

Iterator[Tensor]

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> for buf in model.buffers():
+>>>     print(type(buf), buf.size())
+<class 'torch.Tensor'> (20L,)
+<class 'torch.Tensor'> (20L, 1L, 5L, 5L)
+
+
+
+ +
+
+call_super_init: bool = False
+
+ +
+
+children()
+

Returns an iterator over immediate children modules.

+
+
Yields:
+

Module – a child module

+
+
Return type:
+

Iterator[Module]

+
+
+
+ +
+
+cpu()
+

Moves all model parameters and buffers to the CPU.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
Parameters:
+

self (T)

+
+
+
+ +
+
+cuda(device=None)
+

Moves all model parameters and buffers to the GPU.

+

This also makes associated parameters and buffers different objects. So +it should be called before constructing optimizer if the module will +live on GPU while being optimized.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Parameters:
+
    +
  • device (int, optional) – if specified, all parameters will be +copied to that device

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+double()
+

Casts all floating point parameters and buffers to double datatype.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
Parameters:
+

self (T)

+
+
+
+ +
+
+dump_patches: bool = False
+
+ +
+
+eval()
+

Sets the module in evaluation mode.

+

This has any effect only on certain modules. See documentations of +particular modules for details of their behaviors in training/evaluation +mode, if they are affected, e.g. Dropout, BatchNorm, +etc.

+

This is equivalent with self.train(False).

+

See locally-disable-grad-doc for a comparison between +.eval() and several similar mechanisms that may be confused with it.

+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
Parameters:
+

self (T)

+
+
+
+ +
+
+extra_repr()
+

Set the extra representation of the module

+

To print customized extra information, you should re-implement +this method in your own modules. Both single-line and multi-line +strings are acceptable.

+
+
Return type:
+

str

+
+
+
+ +
+
+float()
+

Casts all floating point parameters and buffers to float datatype.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
Parameters:
+

self (T)

+
+
+
+ +
+
+get_buffer(target)
+

Returns the buffer given by target if it exists, +otherwise throws an error.

+

See the docstring for get_submodule for a more detailed +explanation of this method’s functionality as well as how to +correctly specify target.

+
+
Parameters:
+

target (str) – The fully-qualified string name of the buffer +to look for. (See get_submodule for how to specify a +fully-qualified string.)

+
+
Returns:
+

The buffer referenced by target

+
+
Return type:
+

torch.Tensor

+
+
Raises:
+

AttributeError – If the target string references an invalid + path or resolves to something that is not a + buffer

+
+
+
+ +
+
+get_extra_state()
+

Returns any extra state to include in the module’s state_dict. +Implement this and a corresponding set_extra_state() for your module +if you need to store extra state. This function is called when building the +module’s state_dict().

+

Note that extra state should be picklable to ensure working serialization +of the state_dict. We only provide provide backwards compatibility guarantees +for serializing Tensors; other objects may break backwards compatibility if +their serialized pickled form changes.

+
+
Returns:
+

Any extra state to store in the module’s state_dict

+
+
Return type:
+

object

+
+
+
+ +
+
+get_parameter(target)
+

Returns the parameter given by target if it exists, +otherwise throws an error.

+

See the docstring for get_submodule for a more detailed +explanation of this method’s functionality as well as how to +correctly specify target.

+
+
Parameters:
+

target (str) – The fully-qualified string name of the Parameter +to look for. (See get_submodule for how to specify a +fully-qualified string.)

+
+
Returns:
+

The Parameter referenced by target

+
+
Return type:
+

torch.nn.Parameter

+
+
Raises:
+

AttributeError – If the target string references an invalid + path or resolves to something that is not an + nn.Parameter

+
+
+
+ +
+
+get_submodule(target)
+

Returns the submodule given by target if it exists, +otherwise throws an error.

+

For example, let’s say you have an nn.Module A that +looks like this:

+
A(
+    (net_b): Module(
+        (net_c): Module(
+            (conv): Conv2d(16, 33, kernel_size=(3, 3), stride=(2, 2))
+        )
+        (linear): Linear(in_features=100, out_features=200, bias=True)
+    )
+)
+
+
+

(The diagram shows an nn.Module A. A has a nested +submodule net_b, which itself has two submodules net_c +and linear. net_c then has a submodule conv.)

+

To check whether or not we have the linear submodule, we +would call get_submodule("net_b.linear"). To check whether +we have the conv submodule, we would call +get_submodule("net_b.net_c.conv").

+

The runtime of get_submodule is bounded by the degree +of module nesting in target. A query against +named_modules achieves the same result, but it is O(N) in +the number of transitive modules. So, for a simple check to see +if some submodule exists, get_submodule should always be +used.

+
+
Parameters:
+

target (str) – The fully-qualified string name of the submodule +to look for. (See above example for how to specify a +fully-qualified string.)

+
+
Returns:
+

The submodule referenced by target

+
+
Return type:
+

torch.nn.Module

+
+
Raises:
+

AttributeError – If the target string references an invalid + path or resolves to something that is not an + nn.Module

+
+
+
+ +
+
+half()
+

Casts all floating point parameters and buffers to half datatype.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
Parameters:
+

self (T)

+
+
+
+ +
+
+ipu(device=None)
+

Moves all model parameters and buffers to the IPU.

+

This also makes associated parameters and buffers different objects. So +it should be called before constructing optimizer if the module will +live on IPU while being optimized.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Parameters:
+
    +
  • device (int, optional) – if specified, all parameters will be +copied to that device

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+load_state_dict(state_dict, strict=True)
+

Copies parameters and buffers from state_dict into +this module and its descendants. If strict is True, then +the keys of state_dict must exactly match the keys returned +by this module’s state_dict() function.

+
+
Parameters:
+
    +
  • state_dict (dict) – a dict containing parameters and +persistent buffers.

  • +
  • strict (bool, optional) – whether to strictly enforce that the keys +in state_dict match the keys returned by this module’s +state_dict() function. Default: True

  • +
+
+
Returns:
+

    +
  • missing_keys is a list of str containing the missing keys

  • +
  • unexpected_keys is a list of str containing the unexpected keys

  • +
+

+
+
Return type:
+

NamedTuple with missing_keys and unexpected_keys fields

+
+
+
+

Note

+

If a parameter or buffer is registered as None and its corresponding key +exists in state_dict, load_state_dict() will raise a +RuntimeError.

+
+
+ +
+
+modules()
+

Returns an iterator over all modules in the network.

+
+
Yields:
+

Module – a module in the network

+
+
Return type:
+

Iterator[Module]

+
+
+
+

Note

+

Duplicate modules are returned only once. In the following +example, l will be returned only once.

+
+

Example:

+
>>> l = nn.Linear(2, 2)
+>>> net = nn.Sequential(l, l)
+>>> for idx, m in enumerate(net.modules()):
+...     print(idx, '->', m)
+
+0 -> Sequential(
+  (0): Linear(in_features=2, out_features=2, bias=True)
+  (1): Linear(in_features=2, out_features=2, bias=True)
+)
+1 -> Linear(in_features=2, out_features=2, bias=True)
+
+
+
+ +
+
+named_buffers(prefix='', recurse=True, remove_duplicate=True)
+

Returns an iterator over module buffers, yielding both the +name of the buffer as well as the buffer itself.

+
+
Parameters:
+
    +
  • prefix (str) – prefix to prepend to all buffer names.

  • +
  • recurse (bool, optional) – if True, then yields buffers of this module +and all submodules. Otherwise, yields only buffers that +are direct members of this module. Defaults to True.

  • +
  • remove_duplicate (bool, optional) – whether to remove the duplicated buffers in the result. Defaults to True.

  • +
+
+
Yields:
+

(str, torch.Tensor) – Tuple containing the name and buffer

+
+
Return type:
+

Iterator[Tuple[str, Tensor]]

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> for name, buf in self.named_buffers():
+>>>     if name in ['running_var']:
+>>>         print(buf.size())
+
+
+
+ +
+
+named_children()
+

Returns an iterator over immediate children modules, yielding both +the name of the module as well as the module itself.

+
+
Yields:
+

(str, Module) – Tuple containing a name and child module

+
+
Return type:
+

Iterator[Tuple[str, Module]]

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> for name, module in model.named_children():
+>>>     if name in ['conv4', 'conv5']:
+>>>         print(module)
+
+
+
+ +
+
+named_modules(memo=None, prefix='', remove_duplicate=True)
+

Returns an iterator over all modules in the network, yielding +both the name of the module as well as the module itself.

+
+
Parameters:
+
    +
  • memo (Set[Module] | None) – a memo to store the set of modules already added to the result

  • +
  • prefix (str) – a prefix that will be added to the name of the module

  • +
  • remove_duplicate (bool) – whether to remove the duplicated module instances in the result +or not

  • +
+
+
Yields:
+

(str, Module) – Tuple of name and module

+
+
+
+

Note

+

Duplicate modules are returned only once. In the following +example, l will be returned only once.

+
+

Example:

+
>>> l = nn.Linear(2, 2)
+>>> net = nn.Sequential(l, l)
+>>> for idx, m in enumerate(net.named_modules()):
+...     print(idx, '->', m)
+
+0 -> ('', Sequential(
+  (0): Linear(in_features=2, out_features=2, bias=True)
+  (1): Linear(in_features=2, out_features=2, bias=True)
+))
+1 -> ('0', Linear(in_features=2, out_features=2, bias=True))
+
+
+
+ +
+
+named_parameters(prefix='', recurse=True, remove_duplicate=True)
+

Returns an iterator over module parameters, yielding both the +name of the parameter as well as the parameter itself.

+
+
Parameters:
+
    +
  • prefix (str) – prefix to prepend to all parameter names.

  • +
  • recurse (bool) – if True, then yields parameters of this module +and all submodules. Otherwise, yields only parameters that +are direct members of this module.

  • +
  • remove_duplicate (bool, optional) – whether to remove the duplicated +parameters in the result. Defaults to True.

  • +
+
+
Yields:
+

(str, Parameter) – Tuple containing the name and parameter

+
+
Return type:
+

Iterator[Tuple[str, Parameter]]

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> for name, param in self.named_parameters():
+>>>     if name in ['bias']:
+>>>         print(param.size())
+
+
+
+ +
+
+parameters(recurse=True)
+

Returns an iterator over module parameters.

+

This is typically passed to an optimizer.

+
+
Parameters:
+

recurse (bool) – if True, then yields parameters of this module +and all submodules. Otherwise, yields only parameters that +are direct members of this module.

+
+
Yields:
+

Parameter – module parameter

+
+
Return type:
+

Iterator[Parameter]

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> for param in model.parameters():
+>>>     print(type(param), param.size())
+<class 'torch.Tensor'> (20L,)
+<class 'torch.Tensor'> (20L, 1L, 5L, 5L)
+
+
+
+ +
+
+register_backward_hook(hook)
+

Registers a backward hook on the module.

+

This function is deprecated in favor of register_full_backward_hook() and +the behavior of this function will change in future versions.

+
+
Returns:
+

a handle that can be used to remove the added hook by calling +handle.remove()

+
+
Return type:
+

torch.utils.hooks.RemovableHandle

+
+
Parameters:
+

hook (Callable[[Module, Tuple[Tensor, ...] | Tensor, Tuple[Tensor, ...] | Tensor], None | Tuple[Tensor, ...] | Tensor])

+
+
+
+ +
+
+register_buffer(name, tensor, persistent=True)
+

Adds a buffer to the module.

+

This is typically used to register a buffer that should not to be +considered a model parameter. For example, BatchNorm’s running_mean +is not a parameter, but is part of the module’s state. Buffers, by +default, are persistent and will be saved alongside parameters. This +behavior can be changed by setting persistent to False. The +only difference between a persistent buffer and a non-persistent buffer +is that the latter will not be a part of this module’s +state_dict.

+

Buffers can be accessed as attributes using given names.

+
+
Parameters:
+
    +
  • name (str) – name of the buffer. The buffer can be accessed +from this module using the given name

  • +
  • tensor (Tensor or None) – buffer to be registered. If None, then operations +that run on buffers, such as cuda, are ignored. If None, +the buffer is not included in the module’s state_dict.

  • +
  • persistent (bool) – whether the buffer is part of this module’s +state_dict.

  • +
+
+
Return type:
+

None

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> self.register_buffer('running_mean', torch.zeros(num_features))
+
+
+
+ +
+
+register_forward_hook(hook, *, prepend=False, with_kwargs=False)
+

Registers a forward hook on the module.

+

The hook will be called every time after forward() has computed an output.

+

If with_kwargs is False or not specified, the input contains only +the positional arguments given to the module. Keyword arguments won’t be +passed to the hooks and only to the forward. The hook can modify the +output. It can modify the input inplace but it will not have effect on +forward since this is called after forward() is called. The hook +should have the following signature:

+
hook(module, args, output) -> None or modified output
+
+
+

If with_kwargs is True, the forward hook will be passed the +kwargs given to the forward function and be expected to return the +output possibly modified. The hook should have the following signature:

+
hook(module, args, kwargs, output) -> None or modified output
+
+
+
+
Parameters:
+
    +
  • hook (Callable) – The user defined hook to be registered.

  • +
  • prepend (bool) – If True, the provided hook will be fired +before all existing forward hooks on this +torch.nn.modules.Module. Otherwise, the provided +hook will be fired after all existing forward hooks on +this torch.nn.modules.Module. Note that global +forward hooks registered with +register_module_forward_hook() will fire before all hooks +registered by this method. +Default: False

  • +
  • with_kwargs (bool) – If True, the hook will be passed the +kwargs given to the forward function. +Default: False

  • +
+
+
Returns:
+

a handle that can be used to remove the added hook by calling +handle.remove()

+
+
Return type:
+

torch.utils.hooks.RemovableHandle

+
+
+
+ +
+
+register_forward_pre_hook(hook, *, prepend=False, with_kwargs=False)
+

Registers a forward pre-hook on the module.

+

The hook will be called every time before forward() is invoked.

+

If with_kwargs is false or not specified, the input contains only +the positional arguments given to the module. Keyword arguments won’t be +passed to the hooks and only to the forward. The hook can modify the +input. User can either return a tuple or a single modified value in the +hook. We will wrap the value into a tuple if a single value is returned +(unless that value is already a tuple). The hook should have the +following signature:

+
hook(module, args) -> None or modified input
+
+
+

If with_kwargs is true, the forward pre-hook will be passed the +kwargs given to the forward function. And if the hook modifies the +input, both the args and kwargs should be returned. The hook should have +the following signature:

+
hook(module, args, kwargs) -> None or a tuple of modified input and kwargs
+
+
+
+
Parameters:
+
    +
  • hook (Callable) – The user defined hook to be registered.

  • +
  • prepend (bool) – If true, the provided hook will be fired before +all existing forward_pre hooks on this +torch.nn.modules.Module. Otherwise, the provided +hook will be fired after all existing forward_pre hooks +on this torch.nn.modules.Module. Note that global +forward_pre hooks registered with +register_module_forward_pre_hook() will fire before all +hooks registered by this method. +Default: False

  • +
  • with_kwargs (bool) – If true, the hook will be passed the kwargs +given to the forward function. +Default: False

  • +
+
+
Returns:
+

a handle that can be used to remove the added hook by calling +handle.remove()

+
+
Return type:
+

torch.utils.hooks.RemovableHandle

+
+
+
+ +
+
+register_full_backward_hook(hook, prepend=False)
+

Registers a backward hook on the module.

+

The hook will be called every time the gradients with respect to a module +are computed, i.e. the hook will execute if and only if the gradients with +respect to module outputs are computed. The hook should have the following +signature:

+
hook(module, grad_input, grad_output) -> tuple(Tensor) or None
+
+
+

The grad_input and grad_output are tuples that contain the gradients +with respect to the inputs and outputs respectively. The hook should +not modify its arguments, but it can optionally return a new gradient with +respect to the input that will be used in place of grad_input in +subsequent computations. grad_input will only correspond to the inputs given +as positional arguments and all kwarg arguments are ignored. Entries +in grad_input and grad_output will be None for all non-Tensor +arguments.

+

For technical reasons, when this hook is applied to a Module, its forward function will +receive a view of each Tensor passed to the Module. Similarly the caller will receive a view +of each Tensor returned by the Module’s forward function.

+
+

Warning

+

Modifying inputs or outputs inplace is not allowed when using backward hooks and +will raise an error.

+
+
+
Parameters:
+
    +
  • hook (Callable) – The user-defined hook to be registered.

  • +
  • prepend (bool) – If true, the provided hook will be fired before +all existing backward hooks on this +torch.nn.modules.Module. Otherwise, the provided +hook will be fired after all existing backward hooks on +this torch.nn.modules.Module. Note that global +backward hooks registered with +register_module_full_backward_hook() will fire before +all hooks registered by this method.

  • +
+
+
Returns:
+

a handle that can be used to remove the added hook by calling +handle.remove()

+
+
Return type:
+

torch.utils.hooks.RemovableHandle

+
+
+
+ +
+
+register_full_backward_pre_hook(hook, prepend=False)
+

Registers a backward pre-hook on the module.

+

The hook will be called every time the gradients for the module are computed. +The hook should have the following signature:

+
hook(module, grad_output) -> Tensor or None
+
+
+

The grad_output is a tuple. The hook should +not modify its arguments, but it can optionally return a new gradient with +respect to the output that will be used in place of grad_output in +subsequent computations. Entries in grad_output will be None for +all non-Tensor arguments.

+

For technical reasons, when this hook is applied to a Module, its forward function will +receive a view of each Tensor passed to the Module. Similarly the caller will receive a view +of each Tensor returned by the Module’s forward function.

+
+

Warning

+

Modifying inputs inplace is not allowed when using backward hooks and +will raise an error.

+
+
+
Parameters:
+
    +
  • hook (Callable) – The user-defined hook to be registered.

  • +
  • prepend (bool) – If true, the provided hook will be fired before +all existing backward_pre hooks on this +torch.nn.modules.Module. Otherwise, the provided +hook will be fired after all existing backward_pre hooks +on this torch.nn.modules.Module. Note that global +backward_pre hooks registered with +register_module_full_backward_pre_hook() will fire before +all hooks registered by this method.

  • +
+
+
Returns:
+

a handle that can be used to remove the added hook by calling +handle.remove()

+
+
Return type:
+

torch.utils.hooks.RemovableHandle

+
+
+
+ +
+
+register_load_state_dict_post_hook(hook)
+

Registers a post hook to be run after module’s load_state_dict +is called.

+
+
It should have the following signature::

hook(module, incompatible_keys) -> None

+
+
+

The module argument is the current module that this hook is registered +on, and the incompatible_keys argument is a NamedTuple consisting +of attributes missing_keys and unexpected_keys. missing_keys +is a list of str containing the missing keys and +unexpected_keys is a list of str containing the unexpected keys.

+

The given incompatible_keys can be modified inplace if needed.

+

Note that the checks performed when calling load_state_dict() with +strict=True are affected by modifications the hook makes to +missing_keys or unexpected_keys, as expected. Additions to either +set of keys will result in an error being thrown when strict=True, and +clearing out both missing and unexpected keys will avoid an error.

+
+
Returns:
+

a handle that can be used to remove the added hook by calling +handle.remove()

+
+
Return type:
+

torch.utils.hooks.RemovableHandle

+
+
+
+ +
+
+register_module(name, module)
+

Alias for add_module().

+
+
Parameters:
+
    +
  • name (str)

  • +
  • module (Module | None)

  • +
+
+
Return type:
+

None

+
+
+
+ +
+
+register_parameter(name, param)
+

Adds a parameter to the module.

+

The parameter can be accessed as an attribute using given name.

+
+
Parameters:
+
    +
  • name (str) – name of the parameter. The parameter can be accessed +from this module using the given name

  • +
  • param (Parameter or None) – parameter to be added to the module. If +None, then operations that run on parameters, such as cuda, +are ignored. If None, the parameter is not included in the +module’s state_dict.

  • +
+
+
Return type:
+

None

+
+
+
+ +
+
+register_state_dict_pre_hook(hook)
+

These hooks will be called with arguments: self, prefix, +and keep_vars before calling state_dict on self. The registered +hooks can be used to perform pre-processing before the state_dict +call is made.

+
+ +
+
+requires_grad_(requires_grad=True)
+

Change if autograd should record operations on parameters in this +module.

+

This method sets the parameters’ requires_grad attributes +in-place.

+

This method is helpful for freezing part of the module for finetuning +or training parts of a model individually (e.g., GAN training).

+

See locally-disable-grad-doc for a comparison between +.requires_grad_() and several similar mechanisms that may be confused with it.

+
+
Parameters:
+
    +
  • requires_grad (bool) – whether autograd should record operations on +parameters in this module. Default: True.

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+set_extra_state(state)
+

This function is called from load_state_dict() to handle any extra state +found within the state_dict. Implement this function and a corresponding +get_extra_state() for your module if you need to store extra state within its +state_dict.

+
+
Parameters:
+

state (dict) – Extra state from the state_dict

+
+
+
+ +
+
+share_memory()
+

See torch.Tensor.share_memory_()

+
+
Parameters:
+

self (T)

+
+
Return type:
+

T

+
+
+
+ +
+
+state_dict(*args, destination=None, prefix='', keep_vars=False)
+

Returns a dictionary containing references to the whole state of the module.

+

Both parameters and persistent buffers (e.g. running averages) are +included. Keys are corresponding parameter and buffer names. +Parameters and buffers set to None are not included.

+
+

Note

+

The returned object is a shallow copy. It contains references +to the module’s parameters and buffers.

+
+
+

Warning

+

Currently state_dict() also accepts positional arguments for +destination, prefix and keep_vars in order. However, +this is being deprecated and keyword arguments will be enforced in +future releases.

+
+
+

Warning

+

Please avoid the use of argument destination as it is not +designed for end-users.

+
+
+
Parameters:
+
    +
  • destination (dict, optional) – If provided, the state of module will +be updated into the dict and the same object is returned. +Otherwise, an OrderedDict will be created and returned. +Default: None.

  • +
  • prefix (str, optional) – a prefix added to parameter and buffer +names to compose the keys in state_dict. Default: ''.

  • +
  • keep_vars (bool, optional) – by default the Tensor s +returned in the state dict are detached from autograd. If it’s +set to True, detaching will not be performed. +Default: False.

  • +
+
+
Returns:
+

a dictionary containing a whole state of the module

+
+
Return type:
+

dict

+
+
+

Example:

+
>>> # xdoctest: +SKIP("undefined vars")
+>>> module.state_dict().keys()
+['bias', 'weight']
+
+
+
+ +
+
+to(*args, **kwargs)
+

Moves and/or casts the parameters and buffers.

+

This can be called as

+
+
+to(device=None, dtype=None, non_blocking=False)
+
+ +
+
+to(dtype, non_blocking=False)
+
+ +
+
+to(tensor, non_blocking=False)
+
+ +
+
+to(memory_format=torch.channels_last)
+
+ +

Its signature is similar to torch.Tensor.to(), but only accepts +floating point or complex dtypes. In addition, this method will +only cast the floating point or complex parameters and buffers to dtype +(if given). The integral parameters and buffers will be moved +device, if that is given, but with dtypes unchanged. When +non_blocking is set, it tries to convert/move asynchronously +with respect to the host if possible, e.g., moving CPU Tensors with +pinned memory to CUDA devices.

+

See below for examples.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Parameters:
+
    +
  • device (torch.device) – the desired device of the parameters +and buffers in this module

  • +
  • dtype (torch.dtype) – the desired floating point or complex dtype of +the parameters and buffers in this module

  • +
  • tensor (torch.Tensor) – Tensor whose dtype and device are the desired +dtype and device for all parameters and buffers in this module

  • +
  • memory_format (torch.memory_format) – the desired memory +format for 4D parameters and buffers in this module (keyword +only argument)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+

Examples:

+
>>> # xdoctest: +IGNORE_WANT("non-deterministic")
+>>> linear = nn.Linear(2, 2)
+>>> linear.weight
+Parameter containing:
+tensor([[ 0.1913, -0.3420],
+        [-0.5113, -0.2325]])
+>>> linear.to(torch.double)
+Linear(in_features=2, out_features=2, bias=True)
+>>> linear.weight
+Parameter containing:
+tensor([[ 0.1913, -0.3420],
+        [-0.5113, -0.2325]], dtype=torch.float64)
+>>> # xdoctest: +REQUIRES(env:TORCH_DOCTEST_CUDA1)
+>>> gpu1 = torch.device("cuda:1")
+>>> linear.to(gpu1, dtype=torch.half, non_blocking=True)
+Linear(in_features=2, out_features=2, bias=True)
+>>> linear.weight
+Parameter containing:
+tensor([[ 0.1914, -0.3420],
+        [-0.5112, -0.2324]], dtype=torch.float16, device='cuda:1')
+>>> cpu = torch.device("cpu")
+>>> linear.to(cpu)
+Linear(in_features=2, out_features=2, bias=True)
+>>> linear.weight
+Parameter containing:
+tensor([[ 0.1914, -0.3420],
+        [-0.5112, -0.2324]], dtype=torch.float16)
+
+>>> linear = nn.Linear(2, 2, bias=None).to(torch.cdouble)
+>>> linear.weight
+Parameter containing:
+tensor([[ 0.3741+0.j,  0.2382+0.j],
+        [ 0.5593+0.j, -0.4443+0.j]], dtype=torch.complex128)
+>>> linear(torch.ones(3, 2, dtype=torch.cdouble))
+tensor([[0.6122+0.j, 0.1150+0.j],
+        [0.6122+0.j, 0.1150+0.j],
+        [0.6122+0.j, 0.1150+0.j]], dtype=torch.complex128)
+
+
+
+ +
+
+to_empty(*, device)
+

Moves the parameters and buffers to the specified device without copying storage.

+
+
Parameters:
+
    +
  • device (torch.device) – The desired device of the parameters +and buffers in this module.

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+train(mode=True)
+

Sets the module in training mode.

+

This has any effect only on certain modules. See documentations of +particular modules for details of their behaviors in training/evaluation +mode, if they are affected, e.g. Dropout, BatchNorm, +etc.

+
+
Parameters:
+
    +
  • mode (bool) – whether to set training mode (True) or evaluation +mode (False). Default: True.

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+type(dst_type)
+

Casts all parameters and buffers to dst_type.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Parameters:
+
    +
  • dst_type (type or string) – the desired type

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+xpu(device=None)
+

Moves all model parameters and buffers to the XPU.

+

This also makes associated parameters and buffers different objects. So +it should be called before constructing optimizer if the module will +live on XPU while being optimized.

+
+

Note

+

This method modifies the module in-place.

+
+
+
Parameters:
+
    +
  • device (int, optional) – if specified, all parameters will be +copied to that device

  • +
  • self (T)

  • +
+
+
Returns:
+

self

+
+
Return type:
+

Module

+
+
+
+ +
+
+zero_grad(set_to_none=True)
+

Sets gradients of all model parameters to zero. See similar function +under torch.optim.Optimizer for more context.

+
+
Parameters:
+

set_to_none (bool) – instead of setting to zero, set the grads to None. +See torch.optim.Optimizer.zero_grad() for details.

+
+
Return type:
+

None

+
+
+
+ +
+
+training: bool
+
+ +
+ +
+
+class protac_degradation_predictor.pytorch_models.PROTAC_Model(*args, **kwargs)
+

Bases: LightningModule

+
+
Parameters:
+
    +
  • hidden_dim (int)

  • +
  • smiles_emb_dim (int)

  • +
  • poi_emb_dim (int)

  • +
  • e3_emb_dim (int)

  • +
  • cell_emb_dim (int)

  • +
  • batch_size (int)

  • +
  • learning_rate (float)

  • +
  • dropout (float)

  • +
  • use_batch_norm (bool)

  • +
  • join_embeddings (Literal['beginning', 'concat', 'sum'])

  • +
  • train_dataset (PROTAC_Dataset)

  • +
  • val_dataset (PROTAC_Dataset)

  • +
  • test_dataset (PROTAC_Dataset)

  • +
  • disabled_embeddings (List[Literal['smiles', 'poi', 'e3', 'cell']])

  • +
  • apply_scaling (bool)

  • +
  • extra_optim_params (dict | None)

  • +
+
+
+
+
+initialize_scalers()
+

Initialize or reinitialize scalers based on dataset properties.

+
+ +
+
+apply_scalers()
+

Apply scalers to all datasets.

+
+ +
+
+scale_tensor(tensor, scaler, alpha=1e-10)
+

Scale a tensor using a scaler. This is done to avoid using numpy +arrays (and stay on the same device).

+
+
Parameters:
+
    +
  • tensor (torch.Tensor) – The tensor to scale.

  • +
  • scaler (StandardScaler) – The scaler to use.

  • +
  • alpha (float)

  • +
+
+
Returns:
+

The scaled tensor.

+
+
Return type:
+

torch.Tensor

+
+
+
+ +
+
+forward(poi_emb, e3_emb, cell_emb, smiles_emb, prescaled_embeddings=True, return_embeddings=False)
+
+ +
+
+step(batch, batch_idx, stage)
+
+ +
+
+training_step(batch, batch_idx)
+
+ +
+
+validation_step(batch, batch_idx)
+
+ +
+
+test_step(batch, batch_idx)
+
+ +
+
+configure_optimizers()
+
+ +
+
+predict_step(batch, batch_idx)
+
+ +
+
+train_dataloader()
+
+ +
+
+val_dataloader()
+
+ +
+
+test_dataloader()
+
+ +
+
+on_save_checkpoint(checkpoint)
+

Serialize the scalers to the checkpoint.

+
+ +
+
+on_load_checkpoint(checkpoint)
+

Deserialize the scalers from the checkpoint.

+
+ +
+ +
+
+protac_degradation_predictor.pytorch_models.get_confidence_scores(true_ds, y_preds, threshold=0.5)
+
+ +
+
+protac_degradation_predictor.pytorch_models.train_model(protein2embedding, cell2embedding, smiles2fp, train_df, val_df, test_df=None, hidden_dim=768, batch_size=128, learning_rate=2e-05, beta1=0.9, beta2=0.999, eps=1e-08, dropout=0.2, max_epochs=50, use_batch_norm=False, join_embeddings='sum', smote_k_neighbors=5, apply_scaling=True, active_label='Active', fast_dev_run=False, use_logger=True, logger_save_dir='../logs', logger_name='protac', enable_checkpointing=False, checkpoint_model_name='protac', disabled_embeddings=[], return_predictions=False, shuffle_embedding_prob=0.0, use_smote=False)
+

Train a PROTAC model using the given datasets and hyperparameters.

+
+
Parameters:
+
    +
  • protein2embedding (dict) – A dictionary mapping protein identifiers to embeddings.

  • +
  • cell2embedding (dict) – A dictionary mapping cell line identifiers to embeddings.

  • +
  • smiles2fp (dict) – A dictionary mapping SMILES strings to fingerprints.

  • +
  • train_df (pd.DataFrame) – The training dataframe.

  • +
  • val_df (pd.DataFrame) – The validation dataframe.

  • +
  • test_df (Optional[pd.DataFrame]) – The test dataframe.

  • +
  • hidden_dim (int) – The hidden dimension of the model

  • +
  • batch_size (int) – The batch size

  • +
  • learning_rate (float) – The learning rate

  • +
  • dropout (float) – The dropout rate

  • +
  • max_epochs (int) – The maximum number of epochs

  • +
  • use_batch_norm (bool) – Whether to use batch normalization

  • +
  • join_embeddings (Literal['beginning', 'concat', 'sum']) – How to join the embeddings

  • +
  • smote_k_neighbors (int) – The number of neighbors to use in SMOTE

  • +
  • use_smote (bool) – Whether to use SMOTE

  • +
  • apply_scaling (bool) – Whether to apply scaling to the embeddings

  • +
  • active_label (str) – The name of the active label. Default: ‘Active’

  • +
  • fast_dev_run (bool) – Whether to run a fast development run (see PyTorch Lightning documentation)

  • +
  • use_logger (bool) – Whether to use a logger

  • +
  • logger_save_dir (str) – The directory to save the logs

  • +
  • logger_name (str) – The name of the logger

  • +
  • enable_checkpointing (bool) – Whether to enable checkpointing

  • +
  • checkpoint_model_name (str) – The name of the model for checkpointing

  • +
  • disabled_embeddings (list) – List of disabled embeddings. Can be ‘poi’, ‘e3’, ‘cell’, ‘smiles’

  • +
  • return_predictions (bool) – Whether to return predictions on the validation and test sets

  • +
  • beta1 (float)

  • +
  • beta2 (float)

  • +
  • eps (float)

  • +
  • shuffle_embedding_prob (float)

  • +
+
+
Returns:
+

The trained model, the trainer, and the metrics over the validation and test sets.

+
+
Return type:
+

tuple

+
+
+
+ +
+
+protac_degradation_predictor.pytorch_models.evaluate_model(model, trainer, val_ds, test_ds=None, batch_size=128)
+

Evaluate a PROTAC model using the given datasets.

+
+
Parameters:
+
+
+
Return type:
+

tuple

+
+
+
+ +
+
+protac_degradation_predictor.pytorch_models.load_model(ckpt_path)
+

Load a PROTAC model from a checkpoint.

+
+
Parameters:
+

ckpt_path (str) – The path to the checkpoint.

+
+
Returns:
+

The loaded model.

+
+
Return type:
+

PROTAC_Model

+
+
+
+ +
+
+

protac_degradation_predictor.sklearn_models module

+
+
+protac_degradation_predictor.sklearn_models.train_sklearn_model(clf, protein2embedding, cell2embedding, smiles2fp, train_df, val_df, test_df=None, active_label='Active', use_single_scaler=True)
+

Train a classifier model on train and val sets and evaluate it on a test set.

+
+
Parameters:
+
    +
  • clf (ClassifierMixin) – The classifier model to train and evaluate.

  • +
  • train_df (pd.DataFrame) – The training set.

  • +
  • val_df (pd.DataFrame) – The validation set.

  • +
  • test_df (Optional[pd.DataFrame]) – The test set.

  • +
  • protein2embedding (Dict)

  • +
  • cell2embedding (Dict)

  • +
  • smiles2fp (Dict)

  • +
  • active_label (str)

  • +
  • use_single_scaler (bool)

  • +
+
+
Returns:
+

The trained model and the metrics.

+
+
Return type:
+

Tuple[ClassifierMixin, nn.ModuleDict]

+
+
+
+ +
+
+protac_degradation_predictor.sklearn_models.suggest_random_forest(trial)
+

Suggest hyperparameters for a Random Forest classifier.

+
+
Parameters:
+

trial (optuna.Trial) – The Optuna trial object.

+
+
Returns:
+

The Random Forest classifier with the suggested hyperparameters.

+
+
Return type:
+

ClassifierMixin

+
+
+
+ +
+
+protac_degradation_predictor.sklearn_models.suggest_logistic_regression(trial)
+

Suggest hyperparameters for a Logistic Regression classifier.

+
+
Parameters:
+

trial (optuna.Trial) – The Optuna trial object.

+
+
Returns:
+

The Logistic Regression classifier with the suggested hyperparameters.

+
+
Return type:
+

ClassifierMixin

+
+
+
+ +
+
+protac_degradation_predictor.sklearn_models.suggest_svc(trial)
+

Suggest hyperparameters for an SVC classifier.

+
+
Parameters:
+

trial (optuna.Trial) – The Optuna trial object.

+
+
Returns:
+

The SVC classifier with the suggested hyperparameters.

+
+
Return type:
+

ClassifierMixin

+
+
+
+ +
+
+protac_degradation_predictor.sklearn_models.suggest_gradient_boosting(trial)
+

Suggest hyperparameters for a Gradient Boosting classifier.

+
+
Parameters:
+

trial (optuna.Trial) – The Optuna trial object.

+
+
Returns:
+

The Gradient Boosting classifier with the suggested hyperparameters.

+
+
Return type:
+

ClassifierMixin

+
+
+
+ +
+
+

Module contents

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/_build/html/source/protac_degradation_predictor.optuna.html b/docs/_build/html/source/protac_degradation_predictor.optuna.html new file mode 100644 index 0000000000000000000000000000000000000000..eabfdda71807ad02bb9190a6a8fe80f5acaf4d7a --- /dev/null +++ b/docs/_build/html/source/protac_degradation_predictor.optuna.html @@ -0,0 +1,184 @@ + + + + + + + protac_degradation_predictor.optuna package — PROTAC-Degradation-Predictor v1.0.1 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

protac_degradation_predictor.optuna package

+
+

Submodules

+
+
+

protac_degradation_predictor.optuna.pytorch_models module

+
+
+

protac_degradation_predictor.optuna.sklearn_models module

+
+
+

protac_degradation_predictor.optuna.utils module

+
+
+protac_degradation_predictor.optuna.utils.get_dataframe_stats(train_df=None, val_df=None, test_df=None, active_label='Active')
+

Get some statistics from the dataframes.

+
+
Parameters:
+
    +
  • train_df (pd.DataFrame) – The training set.

  • +
  • val_df (pd.DataFrame) – The validation set.

  • +
  • test_df (pd.DataFrame) – The test set.

  • +
+
+
Return type:
+

Dict

+
+
+
+ +
+
+protac_degradation_predictor.optuna.utils.get_majority_vote_metrics(test_preds, test_df, active_label='Active')
+

Get the majority vote metrics.

+
+
Parameters:
+
    +
  • test_preds (List)

  • +
  • test_df (DataFrame)

  • +
  • active_label (str)

  • +
+
+
Return type:
+

Dict

+
+
+
+ +
+
+

protac_degradation_predictor.optuna.xgboost_models module

+
+
+

Module contents

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 8a814789547c20d2040b9f3a2315250f35c7aa37..7b1ab7ea57ea3cf89c2d045c14b203c059cdf122 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -35,6 +35,14 @@ autodoc_mock_imports = [ 'pytorch_lightning', ] +autodoc_default_options = { + 'members': True, + 'undoc-members': True, + 'show-inheritance': True, + 'inherited-members': True, + 'member-order': 'bysource', + } + # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output diff --git a/tests/test_degradation_prediction.py b/tests/test_degradation_prediction.py index 416f851bbcb04d15246455219ec444ae2c8ad738..9fc40105c1872ec953fc4443fff92743ee274142 100644 --- a/tests/test_degradation_prediction.py +++ b/tests/test_degradation_prediction.py @@ -8,6 +8,7 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) from protac_degradation_predictor import ( get_protac_active_proba, is_protac_active, + get_protac_embedding, ) import torch @@ -114,4 +115,38 @@ def test_active_proba_xgboost(): study_type='similarity', ) - print(f'[XGBoost] Active probability: {active_prob} (CPU)') \ No newline at end of file + print(f'[XGBoost] Active probability: {active_prob} (CPU)') + + +def test_embeddings(): + protac_smiles = 'Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)CN2C(=O)[C@@H](NC(=O)CC(=O)N2CCN(CC[C@H](CSc3ccccc3)Nc3ccc(S(=O)(=O)NC(=O)c4ccc(N5CCN(CC6=C(c7ccc(Cl)cc7)CCC(C)(C)C6)CC5)cc4)cc3S(=O)(=O)C(F)(F)F)CC2)C(C)(C)C)cc1' + e3_ligase = 'VHL' + target_uniprot = 'Q07817' + cell_line = 'MOLT-4' + device = 'cpu' + + protac_emb = get_protac_embedding( + protac_smiles=protac_smiles, + e3_ligase=e3_ligase, + target_uniprot=target_uniprot, + cell_line=cell_line, + device=device, + study_type='similarity', + ) + + print(f'Embeddings: {protac_emb}') + for model, emb in protac_emb.items(): + print(f'\t- shape: {emb.shape}') + + protac_emb = get_protac_embedding( + protac_smiles=[protac_smiles] * 8, + e3_ligase=[e3_ligase] * 8, + target_uniprot=[target_uniprot] * 8, + cell_line=[cell_line] * 8, + device=device, + study_type='similarity', + ) + + print(f'Embeddings (batched): {protac_emb}') + for model, emb in protac_emb.items(): + print(f'\t- shape: {emb.shape}') \ No newline at end of file