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4 changes: 2 additions & 2 deletions README.rst
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Expand Up @@ -27,8 +27,8 @@ The ``rstoolbox`` is a python library aimed to the analysis and management of bi
:target: https://doi.org/10.1101/428045
:alt: bioRxiv

.. image:: https://img.shields.io/badge/BMC%20Bioinformatics-submitted-green.svg
:target: https://doi.org/10.1101/428045
.. image:: https://img.shields.io/badge/BMC%20Bioinformatics-doi.org/10.1186/s12859--019--2796--3-green.svg
:target: https://doi.org/10.1186/s12859-019-2796-3
:alt: BMC Bioinformatics

Although inspired by the output of the protein design tool **ROSETTA**, the library aims to be of a wider applicability, and can be
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2 changes: 1 addition & 1 deletion docs/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 31d5c52e3e895d896deaa0d25f684a2f
config: 59155d77beb3cd6d68e48c586ec86886
tags: 645f666f9bcd5a90fca523b33c5a78b7
2 changes: 1 addition & 1 deletion docs/_static/documentation_options.js
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var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '0.9.3',
VERSION: '0.9.4',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
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21 changes: 12 additions & 9 deletions docs/api.html
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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>API reference &#8212; rstoolbox 0.9.3 documentation</title>
<title>API reference &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/style.css" />
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</button>
<a class="navbar-brand" href="index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
Expand Down Expand Up @@ -388,25 +388,28 @@ <h2>Utils: Plot<a class="headerlink" href="#utils-plot" title="Permalink to this
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.format_Ipython.html#rstoolbox.utils.format_Ipython" title="rstoolbox.utils.format_Ipython"><code class="xref py py-obj docutils literal notranslate"><span class="pre">format_Ipython</span></code></a>()</td>
<td>Ensure <code class="docutils literal notranslate"><span class="pre">monospace</span></code> representation of <a class="reference external" href="http://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html#pandas.DataFrame" title="(in pandas v0.24.2)"><code class="xref py py-class docutils literal notranslate"><span class="pre">DataFrame</span></code></a> in <strong>Jupyter Notebooks</strong>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.use_qgrid.html#rstoolbox.utils.use_qgrid" title="rstoolbox.utils.use_qgrid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">use_qgrid</span></code></a>(df,&nbsp;**kwargs)</td>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.highlight.html#rstoolbox.utils.highlight" title="rstoolbox.utils.highlight"><code class="xref py py-obj docutils literal notranslate"><span class="pre">highlight</span></code></a>(row,&nbsp;selection[,&nbsp;color,&nbsp;…])</td>
<td>Highlight rows in <strong>Jupyter Notebooks</strong> that match the given index.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.use_qgrid.html#rstoolbox.utils.use_qgrid" title="rstoolbox.utils.use_qgrid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">use_qgrid</span></code></a>(df,&nbsp;**kwargs)</td>
<td>Create a <code class="docutils literal notranslate"><span class="pre">QgridWidget</span></code> object from the <a class="reference external" href="https://qgrid.readthedocs.io/en/latest/">qgrid library</a> in <strong>Jupyter Notebooks</strong>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.add_left_title.html#rstoolbox.utils.add_left_title" title="rstoolbox.utils.add_left_title"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_left_title</span></code></a>(ax,&nbsp;title,&nbsp;**kwargs)</td>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.add_left_title.html#rstoolbox.utils.add_left_title" title="rstoolbox.utils.add_left_title"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_left_title</span></code></a>(ax,&nbsp;title,&nbsp;**kwargs)</td>
<td>Add a centered title on the left of the selected axis.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.add_right_title.html#rstoolbox.utils.add_right_title" title="rstoolbox.utils.add_right_title"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_right_title</span></code></a>(ax,&nbsp;title,&nbsp;**kwargs)</td>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.add_right_title.html#rstoolbox.utils.add_right_title" title="rstoolbox.utils.add_right_title"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_right_title</span></code></a>(ax,&nbsp;title,&nbsp;**kwargs)</td>
<td>Add a centered title on rigth of the selected axis.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.add_top_title.html#rstoolbox.utils.add_top_title" title="rstoolbox.utils.add_top_title"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_top_title</span></code></a>(ax,&nbsp;title,&nbsp;**kwargs)</td>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.add_top_title.html#rstoolbox.utils.add_top_title" title="rstoolbox.utils.add_top_title"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_top_title</span></code></a>(ax,&nbsp;title,&nbsp;**kwargs)</td>
<td>Add a centered title on top of the selected axis.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.edit_legend_text.html#rstoolbox.utils.edit_legend_text" title="rstoolbox.utils.edit_legend_text"><code class="xref py py-obj docutils literal notranslate"><span class="pre">edit_legend_text</span></code></a>(ax,&nbsp;labels[,&nbsp;title])</td>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.edit_legend_text.html#rstoolbox.utils.edit_legend_text" title="rstoolbox.utils.edit_legend_text"><code class="xref py py-obj docutils literal notranslate"><span class="pre">edit_legend_text</span></code></a>(ax,&nbsp;labels[,&nbsp;title])</td>
<td>Change the labels and title of a legend.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.add_white_to_cmap.html#rstoolbox.utils.add_white_to_cmap" title="rstoolbox.utils.add_white_to_cmap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_white_to_cmap</span></code></a>([color,&nbsp;cmap,&nbsp;n_colors])</td>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.add_white_to_cmap.html#rstoolbox.utils.add_white_to_cmap" title="rstoolbox.utils.add_white_to_cmap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_white_to_cmap</span></code></a>([color,&nbsp;cmap,&nbsp;n_colors])</td>
<td>Generate a new colormap with white as first instance.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="generated/rstoolbox.utils.color_variant.html#rstoolbox.utils.color_variant" title="rstoolbox.utils.color_variant"><code class="xref py py-obj docutils literal notranslate"><span class="pre">color_variant</span></code></a>(color[,&nbsp;brightness_offset])</td>
<tr class="row-odd"><td><a class="reference internal" href="generated/rstoolbox.utils.color_variant.html#rstoolbox.utils.color_variant" title="rstoolbox.utils.color_variant"><code class="xref py py-obj docutils literal notranslate"><span class="pre">color_variant</span></code></a>(color[,&nbsp;brightness_offset])</td>
<td>Make a color darker or lighter.</td>
</tr>
</tbody>
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4 changes: 2 additions & 2 deletions docs/contributing.html
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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Contributing &#8212; rstoolbox 0.9.3 documentation</title>
<title>Contributing &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/style.css" />
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</button>
<a class="navbar-brand" href="index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
</div>

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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>rstoolbox.components.DesignFrame.add_reference &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.add_reference &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="../../_static/style.css" />
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
</div>

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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>rstoolbox.components.DesignFrame.add_reference_sequence &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.add_reference_sequence &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
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<link rel="stylesheet" type="text/css" href="../../_static/style.css" />
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
</div>

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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>rstoolbox.components.DesignFrame.add_reference_shift &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.add_reference_shift &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
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<link rel="stylesheet" type="text/css" href="../../_static/style.css" />
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
</div>

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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>rstoolbox.components.DesignFrame.add_reference_structure &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.add_reference_structure &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
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<link rel="stylesheet" type="text/css" href="../../_static/style.css" />
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
</div>

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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>rstoolbox.components.DesignFrame.add_source_file &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.add_source_file &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
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<title>rstoolbox.components.DesignFrame.add_source_files &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.add_source_files &#8212; rstoolbox 0.9.4 documentation</title>
<link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>rstoolbox.components.DesignFrame.apply_resfile &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.apply_resfile &#8212; rstoolbox 0.9.4 documentation</title>
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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<head>
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<title>rstoolbox.components.DesignFrame.clean_rosetta_suffix &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.clean_rosetta_suffix &#8212; rstoolbox 0.9.4 documentation</title>
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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<title>rstoolbox.components.DesignFrame.delete_reference &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.delete_reference &#8212; rstoolbox 0.9.4 documentation</title>
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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<head>
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<title>rstoolbox.components.DesignFrame.generate_mutant_variants &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.generate_mutant_variants &#8212; rstoolbox 0.9.4 documentation</title>
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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<title>rstoolbox.components.DesignFrame.generate_mutants_from_matrix &#8212; rstoolbox 0.9.3 documentation</title>
<title>rstoolbox.components.DesignFrame.generate_mutants_from_matrix &#8212; rstoolbox 0.9.4 documentation</title>
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</button>
<a class="navbar-brand" href="../../index.html">
rstoolbox</a>
<span class="navbar-text navbar-version pull-left"><b>0.9.3</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.9.4</b></span>
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