|
|
|
|
|
|
|
|
<!DOCTYPE html> |
|
|
<html class="writer-html5" lang="en" > |
|
|
<head> |
|
|
<meta charset="utf-8" /> |
|
|
|
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0" /> |
|
|
|
|
|
<title>dscript.pretrained — D-SCRIPT v1.0-beta documentation</title> |
|
|
|
|
|
|
|
|
|
|
|
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" /> |
|
|
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script> |
|
|
<script src="../../_static/jquery.js"></script> |
|
|
<script src="../../_static/underscore.js"></script> |
|
|
<script src="../../_static/doctools.js"></script> |
|
|
|
|
|
<script type="text/javascript" src="../../_static/js/theme.js"></script> |
|
|
|
|
|
|
|
|
<link rel="index" title="Index" href="../../genindex.html" /> |
|
|
<link rel="search" title="Search" href="../../search.html" /> |
|
|
</head> |
|
|
|
|
|
<body class="wy-body-for-nav"> |
|
|
|
|
|
|
|
|
<div class="wy-grid-for-nav"> |
|
|
|
|
|
<nav data-toggle="wy-nav-shift" class="wy-nav-side"> |
|
|
<div class="wy-side-scroll"> |
|
|
<div class="wy-side-nav-search" > |
|
|
|
|
|
|
|
|
|
|
|
<a href="../../index.html" class="icon icon-home"> D-SCRIPT |
|
|
|
|
|
|
|
|
|
|
|
</a> |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<div role="search"> |
|
|
<form id="rtd-search-form" class="wy-form" action="../../search.html" method="get"> |
|
|
<input type="text" name="q" placeholder="Search docs" /> |
|
|
<input type="hidden" name="check_keywords" value="yes" /> |
|
|
<input type="hidden" name="area" value="default" /> |
|
|
</form> |
|
|
</div> |
|
|
|
|
|
|
|
|
</div> |
|
|
|
|
|
|
|
|
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<ul> |
|
|
<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li> |
|
|
<li class="toctree-l1"><a class="reference internal" href="../../usage.html">Usage</a></li> |
|
|
<li class="toctree-l1"><a class="reference internal" href="../../data.html">Data</a></li> |
|
|
<li class="toctree-l1"><a class="reference internal" href="../../api/index.html">API</a></li> |
|
|
</ul> |
|
|
|
|
|
|
|
|
|
|
|
</div> |
|
|
|
|
|
</div> |
|
|
</nav> |
|
|
|
|
|
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> |
|
|
|
|
|
|
|
|
<nav class="wy-nav-top" aria-label="top navigation"> |
|
|
|
|
|
<i data-toggle="wy-nav-top" class="fa fa-bars"></i> |
|
|
<a href="../../index.html">D-SCRIPT</a> |
|
|
|
|
|
</nav> |
|
|
|
|
|
|
|
|
<div class="wy-nav-content"> |
|
|
|
|
|
<div class="rst-content"> |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<div role="navigation" aria-label="breadcrumbs navigation"> |
|
|
|
|
|
<ul class="wy-breadcrumbs"> |
|
|
|
|
|
<li><a href="../../index.html" class="icon icon-home"></a> »</li> |
|
|
|
|
|
<li><a href="../index.html">Module code</a> »</li> |
|
|
|
|
|
<li>dscript.pretrained</li> |
|
|
|
|
|
|
|
|
<li class="wy-breadcrumbs-aside"> |
|
|
|
|
|
</li> |
|
|
|
|
|
</ul> |
|
|
|
|
|
|
|
|
<hr/> |
|
|
</div> |
|
|
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> |
|
|
<div itemprop="articleBody"> |
|
|
|
|
|
<h1>Source code for dscript.pretrained</h1><div class="highlight"><pre> |
|
|
<span></span><span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span> |
|
|
<span class="kn">import</span> <span class="nn">torch</span> |
|
|
|
|
|
<span class="kn">from</span> <span class="nn">.models.embedding</span> <span class="kn">import</span> <span class="n">FullyConnectedEmbed</span><span class="p">,</span> <span class="n">SkipLSTM</span> |
|
|
<span class="kn">from</span> <span class="nn">.models.contact</span> <span class="kn">import</span> <span class="n">ContactCNN</span> |
|
|
<span class="kn">from</span> <span class="nn">.models.interaction</span> <span class="kn">import</span> <span class="n">ModelInteraction</span> |
|
|
|
|
|
|
|
|
<span class="k">def</span> <span class="nf">build_lm_1</span><span class="p">(</span><span class="n">state_dict_path</span><span class="p">):</span> |
|
|
<span class="sd">"""</span> |
|
|
<span class="sd"> :meta private:</span> |
|
|
<span class="sd"> """</span> |
|
|
<span class="n">model</span> <span class="o">=</span> <span class="n">SkipLSTM</span><span class="p">(</span><span class="mi">21</span><span class="p">,</span> <span class="mi">100</span><span class="p">,</span> <span class="mi">1024</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span> |
|
|
<span class="n">state_dict</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">state_dict_path</span><span class="p">)</span> |
|
|
<span class="n">model</span><span class="o">.</span><span class="n">load_state_dict</span><span class="p">(</span><span class="n">state_dict</span><span class="p">)</span> |
|
|
<span class="n">model</span><span class="o">.</span><span class="n">eval</span><span class="p">()</span> |
|
|
<span class="k">return</span> <span class="n">model</span> |
|
|
|
|
|
|
|
|
<span class="k">def</span> <span class="nf">build_human_1</span><span class="p">(</span><span class="n">state_dict_path</span><span class="p">):</span> |
|
|
<span class="sd">"""</span> |
|
|
<span class="sd"> :meta private:</span> |
|
|
<span class="sd"> """</span> |
|
|
<span class="n">embModel</span> <span class="o">=</span> <span class="n">FullyConnectedEmbed</span><span class="p">(</span><span class="mi">6165</span><span class="p">,</span> <span class="mi">100</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span> |
|
|
<span class="n">conModel</span> <span class="o">=</span> <span class="n">ContactCNN</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span> <span class="mi">50</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span> |
|
|
<span class="n">model</span> <span class="o">=</span> <span class="n">ModelInteraction</span><span class="p">(</span><span class="n">embModel</span><span class="p">,</span> <span class="n">conModel</span><span class="p">,</span> <span class="n">use_W</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">pool_size</span><span class="o">=</span><span class="mi">9</span><span class="p">)</span> |
|
|
<span class="n">state_dict</span> <span class="o">=</span> <span class="n">torch</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">state_dict_path</span><span class="p">)</span> |
|
|
<span class="n">model</span><span class="o">.</span><span class="n">load_state_dict</span><span class="p">(</span><span class="n">state_dict</span><span class="p">)</span> |
|
|
<span class="n">model</span><span class="o">.</span><span class="n">eval</span><span class="p">()</span> |
|
|
<span class="k">return</span> <span class="n">model</span> |
|
|
|
|
|
|
|
|
<span class="n">VALID_MODELS</span> <span class="o">=</span> <span class="p">{</span> |
|
|
<span class="s2">"lm_v1"</span><span class="p">:</span> <span class="n">build_lm_1</span><span class="p">,</span> |
|
|
<span class="s2">"human_v1"</span><span class="p">:</span> <span class="n">build_human_1</span> |
|
|
<span class="p">}</span> |
|
|
|
|
|
|
|
|
<div class="viewcode-block" id="get_state_dict"><a class="viewcode-back" href="../../api/index.html#dscript.pretrained.get_state_dict">[docs]</a><span class="k">def</span> <span class="nf">get_state_dict</span><span class="p">(</span><span class="n">version</span><span class="o">=</span><span class="s2">"human_v1"</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span> |
|
|
<span class="sd">"""</span> |
|
|
<span class="sd"> Download a pre-trained model if not already exists on local device.</span> |
|
|
|
|
|
<span class="sd"> :param version: Version of trained model to download [default: human_1]</span> |
|
|
<span class="sd"> :type version: str</span> |
|
|
<span class="sd"> :param verbose: Print model download status on stdout [default: True]</span> |
|
|
<span class="sd"> :type verbose: bool</span> |
|
|
<span class="sd"> :return: Path to state dictionary for pre-trained language model</span> |
|
|
<span class="sd"> :rtype: str</span> |
|
|
<span class="sd"> """</span> |
|
|
<span class="n">state_dict_basename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"dscript_</span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">.pt"</span> |
|
|
<span class="n">state_dict_basedir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">realpath</span><span class="p">(</span><span class="vm">__file__</span><span class="p">))</span> |
|
|
<span class="n">state_dict_fullname</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">state_dict_basedir</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">state_dict_basename</span><span class="si">}</span><span class="s2">"</span> |
|
|
<span class="n">state_dict_url</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"http://cb.csail.mit.edu/cb/dscript/data/models/</span><span class="si">{</span><span class="n">state_dict_basename</span><span class="si">}</span><span class="s2">"</span> |
|
|
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">state_dict_fullname</span><span class="p">):</span> |
|
|
<span class="k">try</span><span class="p">:</span> |
|
|
<span class="kn">import</span> <span class="nn">urllib.request</span> |
|
|
<span class="kn">import</span> <span class="nn">shutil</span> |
|
|
<span class="k">if</span> <span class="n">verbose</span><span class="p">:</span> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Downloading model </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2"> from </span><span class="si">{</span><span class="n">state_dict_url</span><span class="si">}</span><span class="s2">..."</span><span class="p">)</span> |
|
|
<span class="k">with</span> <span class="n">urllib</span><span class="o">.</span><span class="n">request</span><span class="o">.</span><span class="n">urlopen</span><span class="p">(</span><span class="n">state_dict_url</span><span class="p">)</span> <span class="k">as</span> <span class="n">response</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">state_dict_fullname</span><span class="p">,</span> <span class="s1">'wb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">out_file</span><span class="p">:</span> |
|
|
<span class="n">shutil</span><span class="o">.</span><span class="n">copyfileobj</span><span class="p">(</span><span class="n">response</span><span class="p">,</span> <span class="n">out_file</span><span class="p">)</span> |
|
|
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span> |
|
|
<span class="nb">print</span><span class="p">(</span><span class="s2">"Unable to download model - </span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">e</span><span class="p">))</span> |
|
|
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> |
|
|
<span class="k">return</span> <span class="n">state_dict_fullname</span></div> |
|
|
|
|
|
|
|
|
<div class="viewcode-block" id="get_pretrained"><a class="viewcode-back" href="../../api/index.html#dscript.pretrained.get_pretrained">[docs]</a><span class="k">def</span> <span class="nf">get_pretrained</span><span class="p">(</span><span class="n">version</span><span class="o">=</span><span class="s2">"human_v1"</span><span class="p">):</span> |
|
|
<span class="sd">"""</span> |
|
|
<span class="sd"> Get pre-trained model object.</span> |
|
|
|
|
|
<span class="sd"> Currently Available Models</span> |
|
|
<span class="sd"> ==========================</span> |
|
|
|
|
|
<span class="sd"> See the `documentation <https://d-script.readthedocs.io/en/main/data.html#trained-models>`_ for most up-to-date list.</span> |
|
|
|
|
|
<span class="sd"> - ``lm_v1`` - Language model from `Bepler & Berger <https://github.com/tbepler/protein-sequence-embedding-iclr2019>`_.</span> |
|
|
<span class="sd"> - ``human_v1`` - Human trained model from D-SCRIPT manuscript.</span> |
|
|
|
|
|
<span class="sd"> Default: ``human_v1``</span> |
|
|
|
|
|
<span class="sd"> :param version: Version of pre-trained model to get</span> |
|
|
<span class="sd"> :type version: str</span> |
|
|
<span class="sd"> :return: Pre-trained model</span> |
|
|
<span class="sd"> :rtype: dscript.models.*</span> |
|
|
<span class="sd"> """</span> |
|
|
<span class="k">if</span> <span class="ow">not</span> <span class="n">version</span> <span class="ow">in</span> <span class="n">VALID_MODELS</span><span class="p">:</span> |
|
|
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Model </span><span class="si">{}</span><span class="s2"> does not exist"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">version</span><span class="p">))</span> |
|
|
|
|
|
<span class="n">state_dict_path</span> <span class="o">=</span> <span class="n">get_state_dict</span><span class="p">(</span><span class="n">version</span><span class="p">)</span> |
|
|
<span class="k">return</span> <span class="n">VALID_MODELS</span><span class="p">[</span><span class="n">version</span><span class="p">](</span><span class="n">state_dict_path</span><span class="p">)</span></div> |
|
|
</pre></div> |
|
|
|
|
|
</div> |
|
|
|
|
|
</div> |
|
|
<footer> |
|
|
|
|
|
<hr/> |
|
|
|
|
|
<div role="contentinfo"> |
|
|
<p> |
|
|
© Copyright 2020, Samuel Sledzieski, Rohit Singh. |
|
|
|
|
|
</p> |
|
|
</div> |
|
|
|
|
|
|
|
|
|
|
|
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a |
|
|
|
|
|
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> |
|
|
|
|
|
provided by <a href="https://readthedocs.org">Read the Docs</a>. |
|
|
|
|
|
</footer> |
|
|
</div> |
|
|
</div> |
|
|
|
|
|
</section> |
|
|
|
|
|
</div> |
|
|
|
|
|
|
|
|
<script type="text/javascript"> |
|
|
jQuery(function () { |
|
|
SphinxRtdTheme.Navigation.enable(true); |
|
|
}); |
|
|
</script> |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</body> |
|
|
</html> |
