Skip to content

Commit

Permalink
deploy: c3f8099
Browse files Browse the repository at this point in the history
  • Loading branch information
github-actions committed Dec 24, 2023
1 parent 1b2bd08 commit 981e808
Show file tree
Hide file tree
Showing 35 changed files with 136 additions and 86 deletions.
Binary file modified .doctrees/api.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/bootstrap.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/clustering.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/confdistmatrix.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/covariance.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/dimensionality_reduction.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/similarity.doctree
View file
Binary file not shown.
Binary file modified .doctrees/encore/utils.doctree
View file
Binary file not shown.
Binary file modified .doctrees/environment.pickle
View file
Binary file not shown.
Binary file modified .doctrees/getting_started.doctree
View file
Binary file not shown.
Binary file modified .doctrees/index.doctree
View file
Binary file not shown.
8 changes: 5 additions & 3 deletions _modules/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/bootstrap.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.bootstrap &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/clustering/ClusterCollection.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.clustering.ClusterCollection &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/clustering/ClusteringMethod.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.clustering.ClusteringMethod &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/clustering/cluster.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.clustering.cluster &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/confdistmatrix.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.confdistmatrix &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/covariance.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.covariance &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/dimensionality_reduction/DimensionalityReductionMethod.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.dimensionality_reduction.DimensionalityReductionMethod &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/dimensionality_reduction/reduce_dimensionality.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.dimensionality_reduction.reduce_dimensionality &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/similarity.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.similarity &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
8 changes: 5 additions & 3 deletions _modules/mdaencore/utils.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,15 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mdaencore.utils &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../../_static/site.css" />


<!--[if lt IE 9]>
<script src="../../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
10 changes: 6 additions & 4 deletions api.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="./">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>API Documentation &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="_static/site.css" />


<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
10 changes: 6 additions & 4 deletions encore/bootstrap.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Bootstrap procedures — mdaencore.bootstrap &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
10 changes: 6 additions & 4 deletions encore/clustering.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Clustering &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
10 changes: 6 additions & 4 deletions encore/confdistmatrix.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Distance matrix calculations — mdaencore.confdistmatrix &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
10 changes: 6 additions & 4 deletions encore/covariance.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Covariance calculation — mdaencore.covariance &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
10 changes: 6 additions & 4 deletions encore/dimensionality_reduction.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Dimensionality reduction &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
15 changes: 9 additions & 6 deletions encore/similarity.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Ensemble Similarity Calculations — mdaencore.similarity &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down Expand Up @@ -545,11 +547,12 @@ <h2>Functions for ensemble comparisons<a class="headerlink" href="#functions-for
<h2>Function reference<a class="headerlink" href="#function-reference" title="Link to this heading"></a></h2>
<p class="rubric">References</p>
<div class="docutils container" id="id7">
<aside class="footnote brackets" id="footcite-lindorfflarsen2009" role="note">
<aside class="footnote-list brackets">
<aside class="footnote brackets" id="footcite-lindorfflarsen2009" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
<p>Kresten Lindorff-Larsen and Jesper Ferkinghoff-Borg. Similarity measures for protein ensembles. <em>PLOS ONE</em>, 4(1):1–13, 01 2009. <a class="reference external" href="https://doi.org/10.1371/journal.pone.0004203">doi:10.1371/journal.pone.0004203</a>.</p>
</aside>
<aside class="footnote brackets" id="footcite-tiberti2015" role="note">
<aside class="footnote brackets" id="footcite-tiberti2015" role="doc-footnote">
<span class="label"><span class="fn-bracket">[</span>2<span class="fn-bracket">]</span></span>
<span class="backrefs">(<a role="doc-backlink" href="#id2">1</a>,<a role="doc-backlink" href="#id3">2</a>,<a role="doc-backlink" href="#id4">3</a>,<a role="doc-backlink" href="#id5">4</a>,<a role="doc-backlink" href="#id6">5</a>,<a role="doc-backlink" href="#id8">6</a>,<a role="doc-backlink" href="#id9">7</a>,<a role="doc-backlink" href="#id10">8</a>,<a role="doc-backlink" href="#id11">9</a>)</span>
<p>Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen. Encore: software for quantitative ensemble comparison. <em>PLOS Computational Biology</em>, 11(10):1–16, 10 2015. <a class="reference external" href="https://doi.org/10.1371/journal.pcbi.1004415">doi:10.1371/journal.pcbi.1004415</a>.</p>
Expand Down
10 changes: 6 additions & 4 deletions encore/utils.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,16 @@
</head>

<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en" data-content_root="../">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Utility functions for ENCORE &mdash; mdaencore documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/site.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
<link rel="stylesheet" type="text/css" href="../_static/site.css" />


<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand Down
Loading

0 comments on commit 981e808

Please sign in to comment.