Skip to content

Commit b5f2395

Browse files
doc updated
1 parent 97335c6 commit b5f2395

46 files changed

Lines changed: 166 additions & 168 deletions

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

docs/.nojekyll

Whitespace-only changes.

docs/_sources/index.rst.txt

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -4,12 +4,8 @@
44
IDPET Documentation
55
===================
66

7-
Welcome to the documentation for **IDPET** – a Python package for analyzing
8-
intrinsically disordered protein ensembles.
9-
10-
Add your content using ``reStructuredText`` syntax.
11-
See the `reStructuredText guide <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
12-
for more details.
7+
**IDPET** (**I**\ntrinsically **D**\isordered **P**\rotein **E**\nsemble **T**\ools) is a Python package for comprehensively analyzing of the conformational ensembles of disordered proteins. It is built upon the mdtraj library for reading the ensemble files in various formats.
8+
**IDPET** provides informative visualizations based on multiple global and local features of the flexible regions of proteins. Additionally, it integrates various dimensionality reduction and statistical methods to facilitate the analysis of conformational ensembles.
139

1410
.. toctree::
1511
:maxdepth: 1

docs/comparison.html

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@
1919
<script src="_static/js/theme.js"></script>
2020
<link rel="index" title="Index" href="genindex.html" />
2121
<link rel="search" title="Search" href="search.html" />
22+
<link rel="next" title="dpet" href="modules.html" />
2223
<link rel="prev" title="visualization" href="visualization.html" />
2324
</head>
2425

@@ -72,6 +73,7 @@
7273
<li class="toctree-l2"><a class="reference internal" href="#dpet.comparison.sturges_rule"><code class="docutils literal notranslate"><span class="pre">sturges_rule()</span></code></a></li>
7374
</ul>
7475
</li>
76+
<li class="toctree-l1"><a class="reference internal" href="modules.html">dpet</a></li>
7577
</ul>
7678

7779
</div>
@@ -622,6 +624,7 @@ <h2>Returns<a class="headerlink" href="#id29" title="Link to this heading"></
622624
</div>
623625
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
624626
<a href="visualization.html" class="btn btn-neutral float-left" title="visualization" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
627+
<a href="modules.html" class="btn btn-neutral float-right" title="dpet" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
625628
</div>
626629

627630
<hr/>

docs/dpet.data.html

Lines changed: 33 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,9 @@
1818
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
1919
<script src="_static/js/theme.js"></script>
2020
<link rel="index" title="Index" href="genindex.html" />
21-
<link rel="search" title="Search" href="search.html" />
21+
<link rel="search" title="Search" href="search.html" />
22+
<link rel="next" title="dpet.featurization package" href="dpet.featurization.html" />
23+
<link rel="prev" title="dpet package" href="dpet.html" />
2224
</head>
2325

2426
<body class="wy-body-for-nav">
@@ -40,34 +42,37 @@
4042
</form>
4143
</div>
4244
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
43-
<!-- Local TOC -->
44-
<div class="local-toc"><ul>
45-
<li><a class="reference internal" href="#">dpet.data package</a><ul>
46-
<li><a class="reference internal" href="#submodules">Submodules</a></li>
47-
<li><a class="reference internal" href="#module-dpet.data.api_client">dpet.data.api_client module</a><ul>
48-
<li><a class="reference internal" href="#dpet.data.api_client.APIClient"><code class="docutils literal notranslate"><span class="pre">APIClient</span></code></a><ul>
49-
<li><a class="reference internal" href="#dpet.data.api_client.APIClient.close_session"><code class="docutils literal notranslate"><span class="pre">APIClient.close_session()</span></code></a></li>
50-
<li><a class="reference internal" href="#dpet.data.api_client.APIClient.download_response_content"><code class="docutils literal notranslate"><span class="pre">APIClient.download_response_content()</span></code></a></li>
51-
<li><a class="reference internal" href="#dpet.data.api_client.APIClient.perform_get_request"><code class="docutils literal notranslate"><span class="pre">APIClient.perform_get_request()</span></code></a></li>
45+
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
46+
<ul class="current">
47+
<li class="toctree-l1"><a class="reference internal" href="overview.html">Overview</a></li>
48+
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
49+
<li class="toctree-l1"><a class="reference internal" href="demo.html">Demo</a></li>
50+
<li class="toctree-l1"><a class="reference internal" href="ensemble_analysis.html">ensemble_analysis</a></li>
51+
<li class="toctree-l1"><a class="reference internal" href="ensemble.html">ensemble</a></li>
52+
<li class="toctree-l1"><a class="reference internal" href="visualization.html">visualization</a></li>
53+
<li class="toctree-l1"><a class="reference internal" href="comparison.html">ensemble_compariosn</a></li>
54+
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">dpet</a><ul class="current">
55+
<li class="toctree-l2 current"><a class="reference internal" href="dpet.html">dpet package</a><ul class="current">
56+
<li class="toctree-l3 current"><a class="reference internal" href="dpet.html#subpackages">Subpackages</a><ul class="current">
57+
<li class="toctree-l4 current"><a class="current reference internal" href="#">dpet.data package</a></li>
58+
<li class="toctree-l4"><a class="reference internal" href="dpet.featurization.html">dpet.featurization package</a></li>
5259
</ul>
5360
</li>
61+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#submodules">Submodules</a></li>
62+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.comparison">dpet.comparison module</a></li>
63+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.coord">dpet.coord module</a></li>
64+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.dimensionality_reduction">dpet.dimensionality_reduction module</a></li>
65+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.ensemble">dpet.ensemble module</a></li>
66+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.ensemble_analysis">dpet.ensemble_analysis module</a></li>
67+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.utils">dpet.utils module</a></li>
68+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.visualization">dpet.visualization module</a></li>
69+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet">Module contents</a></li>
5470
</ul>
5571
</li>
56-
<li><a class="reference internal" href="#module-dpet.data.io_utils">dpet.data.io_utils module</a><ul>
57-
<li><a class="reference internal" href="#dpet.data.io_utils.extract_tar_gz"><code class="docutils literal notranslate"><span class="pre">extract_tar_gz()</span></code></a></li>
58-
<li><a class="reference internal" href="#dpet.data.io_utils.setup_data_dir"><code class="docutils literal notranslate"><span class="pre">setup_data_dir()</span></code></a></li>
5972
</ul>
6073
</li>
61-
<li><a class="reference internal" href="#module-dpet.data.topology">dpet.data.topology module</a><ul>
62-
<li><a class="reference internal" href="#dpet.data.topology.get_ca_topology"><code class="docutils literal notranslate"><span class="pre">get_ca_topology()</span></code></a></li>
63-
<li><a class="reference internal" href="#dpet.data.topology.slice_traj_to_com"><code class="docutils literal notranslate"><span class="pre">slice_traj_to_com()</span></code></a></li>
6474
</ul>
65-
</li>
66-
<li><a class="reference internal" href="#module-dpet.data">Module contents</a></li>
67-
</ul>
68-
</li>
69-
</ul>
70-
</div>
75+
7176
</div>
7277
</div>
7378
</nav>
@@ -82,6 +87,8 @@
8287
<div role="navigation" aria-label="Page navigation">
8388
<ul class="wy-breadcrumbs">
8489
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
90+
<li class="breadcrumb-item"><a href="modules.html">dpet</a></li>
91+
<li class="breadcrumb-item"><a href="dpet.html">dpet package</a></li>
8592
<li class="breadcrumb-item active">dpet.data package</li>
8693
<li class="wy-breadcrumbs-aside">
8794
<a href="_sources/dpet.data.rst.txt" rel="nofollow"> View page source</a>
@@ -168,7 +175,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
168175

169176
</div>
170177
</div>
171-
<footer>
178+
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
179+
<a href="dpet.html" class="btn btn-neutral float-left" title="dpet package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
180+
<a href="dpet.featurization.html" class="btn btn-neutral float-right" title="dpet.featurization package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
181+
</div>
172182

173183
<hr/>
174184

docs/dpet.featurization.html

Lines changed: 31 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,8 @@
1818
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
1919
<script src="_static/js/theme.js"></script>
2020
<link rel="index" title="Index" href="genindex.html" />
21-
<link rel="search" title="Search" href="search.html" />
21+
<link rel="search" title="Search" href="search.html" />
22+
<link rel="prev" title="dpet.data package" href="dpet.data.html" />
2223
</head>
2324

2425
<body class="wy-body-for-nav">
@@ -40,50 +41,37 @@
4041
</form>
4142
</div>
4243
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
43-
<!-- Local TOC -->
44-
<div class="local-toc"><ul>
45-
<li><a class="reference internal" href="#">dpet.featurization package</a><ul>
46-
<li><a class="reference internal" href="#submodules">Submodules</a></li>
47-
<li><a class="reference internal" href="#module-dpet.featurization.angles">dpet.featurization.angles module</a><ul>
48-
<li><a class="reference internal" href="#dpet.featurization.angles.featurize_a_angle"><code class="docutils literal notranslate"><span class="pre">featurize_a_angle()</span></code></a></li>
49-
<li><a class="reference internal" href="#dpet.featurization.angles.featurize_phi_psi"><code class="docutils literal notranslate"><span class="pre">featurize_phi_psi()</span></code></a></li>
50-
<li><a class="reference internal" href="#dpet.featurization.angles.featurize_tr_angle"><code class="docutils literal notranslate"><span class="pre">featurize_tr_angle()</span></code></a></li>
51-
<li><a class="reference internal" href="#dpet.featurization.angles.featurize_tr_omega"><code class="docutils literal notranslate"><span class="pre">featurize_tr_omega()</span></code></a></li>
52-
<li><a class="reference internal" href="#dpet.featurization.angles.featurize_tr_phi"><code class="docutils literal notranslate"><span class="pre">featurize_tr_phi()</span></code></a></li>
53-
<li><a class="reference internal" href="#dpet.featurization.angles.get_angles"><code class="docutils literal notranslate"><span class="pre">get_angles()</span></code></a></li>
54-
<li><a class="reference internal" href="#dpet.featurization.angles.get_dihedrals"><code class="docutils literal notranslate"><span class="pre">get_dihedrals()</span></code></a></li>
44+
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
45+
<ul class="current">
46+
<li class="toctree-l1"><a class="reference internal" href="overview.html">Overview</a></li>
47+
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
48+
<li class="toctree-l1"><a class="reference internal" href="demo.html">Demo</a></li>
49+
<li class="toctree-l1"><a class="reference internal" href="ensemble_analysis.html">ensemble_analysis</a></li>
50+
<li class="toctree-l1"><a class="reference internal" href="ensemble.html">ensemble</a></li>
51+
<li class="toctree-l1"><a class="reference internal" href="visualization.html">visualization</a></li>
52+
<li class="toctree-l1"><a class="reference internal" href="comparison.html">ensemble_compariosn</a></li>
53+
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">dpet</a><ul class="current">
54+
<li class="toctree-l2 current"><a class="reference internal" href="dpet.html">dpet package</a><ul class="current">
55+
<li class="toctree-l3 current"><a class="reference internal" href="dpet.html#subpackages">Subpackages</a><ul class="current">
56+
<li class="toctree-l4"><a class="reference internal" href="dpet.data.html">dpet.data package</a></li>
57+
<li class="toctree-l4 current"><a class="current reference internal" href="#">dpet.featurization package</a></li>
5558
</ul>
5659
</li>
57-
<li><a class="reference internal" href="#module-dpet.featurization.distances">dpet.featurization.distances module</a><ul>
58-
<li><a class="reference internal" href="#dpet.featurization.distances.calc_ca_dmap"><code class="docutils literal notranslate"><span class="pre">calc_ca_dmap()</span></code></a></li>
59-
<li><a class="reference internal" href="#dpet.featurization.distances.calc_com_dmap"><code class="docutils literal notranslate"><span class="pre">calc_com_dmap()</span></code></a></li>
60-
<li><a class="reference internal" href="#dpet.featurization.distances.featurize_ca_dist"><code class="docutils literal notranslate"><span class="pre">featurize_ca_dist()</span></code></a></li>
61-
<li><a class="reference internal" href="#dpet.featurization.distances.featurize_com_dist"><code class="docutils literal notranslate"><span class="pre">featurize_com_dist()</span></code></a></li>
62-
<li><a class="reference internal" href="#dpet.featurization.distances.rmsd"><code class="docutils literal notranslate"><span class="pre">rmsd()</span></code></a></li>
60+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#submodules">Submodules</a></li>
61+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.comparison">dpet.comparison module</a></li>
62+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.coord">dpet.coord module</a></li>
63+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.dimensionality_reduction">dpet.dimensionality_reduction module</a></li>
64+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.ensemble">dpet.ensemble module</a></li>
65+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.ensemble_analysis">dpet.ensemble_analysis module</a></li>
66+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.utils">dpet.utils module</a></li>
67+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet.visualization">dpet.visualization module</a></li>
68+
<li class="toctree-l3"><a class="reference internal" href="dpet.html#module-dpet">Module contents</a></li>
6369
</ul>
6470
</li>
65-
<li><a class="reference internal" href="#module-dpet.featurization.ensemble_level">dpet.featurization.ensemble_level module</a><ul>
66-
<li><a class="reference internal" href="#dpet.featurization.ensemble_level.calc_flory_scaling_exponent"><code class="docutils literal notranslate"><span class="pre">calc_flory_scaling_exponent()</span></code></a></li>
67-
<li><a class="reference internal" href="#dpet.featurization.ensemble_level.calc_flory_scaling_exponent_cg"><code class="docutils literal notranslate"><span class="pre">calc_flory_scaling_exponent_cg()</span></code></a></li>
6871
</ul>
6972
</li>
70-
<li><a class="reference internal" href="#module-dpet.featurization.glob">dpet.featurization.glob module</a><ul>
71-
<li><a class="reference internal" href="#dpet.featurization.glob.compute_asphericity"><code class="docutils literal notranslate"><span class="pre">compute_asphericity()</span></code></a></li>
72-
<li><a class="reference internal" href="#dpet.featurization.glob.compute_end_to_end_distances"><code class="docutils literal notranslate"><span class="pre">compute_end_to_end_distances()</span></code></a></li>
73-
<li><a class="reference internal" href="#dpet.featurization.glob.compute_ensemble_sasa"><code class="docutils literal notranslate"><span class="pre">compute_ensemble_sasa()</span></code></a></li>
74-
<li><a class="reference internal" href="#dpet.featurization.glob.compute_prolateness"><code class="docutils literal notranslate"><span class="pre">compute_prolateness()</span></code></a></li>
7573
</ul>
76-
</li>
77-
<li><a class="reference internal" href="#module-dpet.featurization.utils">dpet.featurization.utils module</a><ul>
78-
<li><a class="reference internal" href="#dpet.featurization.utils.get_max_sep"><code class="docutils literal notranslate"><span class="pre">get_max_sep()</span></code></a></li>
79-
<li><a class="reference internal" href="#dpet.featurization.utils.get_triu_indices"><code class="docutils literal notranslate"><span class="pre">get_triu_indices()</span></code></a></li>
80-
</ul>
81-
</li>
82-
<li><a class="reference internal" href="#module-dpet.featurization">Module contents</a></li>
83-
</ul>
84-
</li>
85-
</ul>
86-
</div>
74+
8775
</div>
8876
</div>
8977
</nav>
@@ -98,6 +86,8 @@
9886
<div role="navigation" aria-label="Page navigation">
9987
<ul class="wy-breadcrumbs">
10088
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
89+
<li class="breadcrumb-item"><a href="modules.html">dpet</a></li>
90+
<li class="breadcrumb-item"><a href="dpet.html">dpet package</a></li>
10191
<li class="breadcrumb-item active">dpet.featurization package</li>
10292
<li class="wy-breadcrumbs-aside">
10393
<a href="_sources/dpet.featurization.rst.txt" rel="nofollow"> View page source</a>
@@ -634,7 +624,9 @@ <h3>Notes<a class="headerlink" href="#id33" title="Link to this heading"></a>
634624

635625
</div>
636626
</div>
637-
<footer>
627+
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
628+
<a href="dpet.data.html" class="btn btn-neutral float-left" title="dpet.data package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
629+
</div>
638630

639631
<hr/>
640632

docs/dr_phipsi.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@
1919
<script src="_static/js/theme.js"></script>
2020
<link rel="index" title="Index" href="genindex.html" />
2121
<link rel="search" title="Search" href="search.html" />
22-
<link rel="next" title="Methods overview" href="method_overview.html" />
22+
<link rel="next" title="Methods overview" href="method_overview.html" />
2323
<link rel="prev" title="Dimensionality Reduction Analysis" href="dimensional_reduction.html" />
2424
</head>
2525

@@ -51,7 +51,7 @@
5151
<li class="toctree-l2"><a class="reference internal" href="local_analysis.html">Local analysis</a></li>
5252
<li class="toctree-l2 current"><a class="reference internal" href="dimensional_reduction.html">Dimensionality Reduction Analysis</a><ul class="current">
5353
<li class="toctree-l3 current"><a class="current reference internal" href="#">Dimensionality reduction based on angular-based features</a></li>
54-
<li class="toctree-l3"><a class="reference internal" href="method_overview.html">Methods overview</a></li>
54+
<li class="toctree-l3"><a class="reference internal" href="method_overview.html">Methods overview</a></li>
5555
<li class="toctree-l3"><a class="reference internal" href="dr_cadist.html">Dimensionality reduction based on distance-based features</a></li>
5656
</ul>
5757
</li>
@@ -201,7 +201,7 @@ <h1>Dimensionality reduction based on angular-based features<a class="headerlink
201201
</div>
202202
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
203203
<a href="dimensional_reduction.html" class="btn btn-neutral float-left" title="Dimensionality Reduction Analysis" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
204-
<a href="method_overview.html" class="btn btn-neutral float-right" title="Methods overview" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
204+
<a href="method_overview.html" class="btn btn-neutral float-right" title="Methods overview" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
205205
</div>
206206

207207
<hr/>

docs/ensemble.html

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -67,6 +67,7 @@
6767
</li>
6868
<li class="toctree-l1"><a class="reference internal" href="visualization.html">visualization</a></li>
6969
<li class="toctree-l1"><a class="reference internal" href="comparison.html">ensemble_compariosn</a></li>
70+
<li class="toctree-l1"><a class="reference internal" href="modules.html">dpet</a></li>
7071
</ul>
7172

7273
</div>

0 commit comments

Comments
 (0)