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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> |
55 | 58 | </ul> |
56 | 59 | </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> |
63 | 69 | </ul> |
64 | 70 | </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> |
68 | 71 | </ul> |
69 | 72 | </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> |
75 | 73 | </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> |
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@@ -634,7 +624,9 @@ <h3>Notes<a class="headerlink" href="#id33" title="Link to this heading"></a> |
634 | 624 |
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