docs

Author: mbarber

apidocs/build/doctrees/environment.pickle

@@ -7,9 +7,9 @@ PoET is a generative protein language model that allows controllable design of p
 Creating a prompt
 -------------------
 
-You can create a prompt either from an MSA (see below), or by directly uploading a *de novo* :py:meth:`openprotein.api.poet.PoetAPI.upload_prompt`. 
+You can create a prompt either from an MSA (see below), or by directly uploading a *de novo* prompt :py:meth:`openprotein.api.poet.PoetAPI.upload_prompt`. 
 
-To create an MSA based prompt, you can first request an MSA with :py:meth:`openprotein.api.poet.PoetAPI.create_msa` and then filter (sample) it with :py:meth:`openprotein.api.poet.MSAFuture.sample_prompt`.
+To create an MSA based prompt, you can first request an MSA with :py:meth:`openprotein.api.poet.PoetAPI.create_msa` and then filter it with :py:meth:`openprotein.api.poet.MSAFuture.sample_prompt`.
 
 Once you have a viable prompt, you can execute the PoET workflows:
 

apidocs/build/doctrees/poet_workflow.doctree

@@ -89,8 +89,8 @@ <h1>De Novo prediction &amp; generative models (PoET)<a class="headerlink" href=
 <p>PoET is a generative protein language model that allows controllable design of protein sequences and variant effect prediction. This model is controlled by providing it with a prompt, a set of sequences that represent homologues, family members, or some other grouping of related sequences that represent your protein of interest. We provide tools for creating these prompts from multiple sequence alignments (MSAs) and for using homology search to build MSAs from a seed sequence.</p>
 <section id="creating-a-prompt">
 <h2>Creating a prompt<a class="headerlink" href="#creating-a-prompt" title="Permalink to this heading"></a></h2>
-<p>You can create a prompt either from an MSA (see below), or by directly uploading a <em>de novo</em> <a class="reference internal" href="poet.html#openprotein.api.poet.PoetAPI.upload_prompt" title="openprotein.api.poet.PoetAPI.upload_prompt"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.PoetAPI.upload_prompt()</span></code></a>.</p>
-<p>To create an MSA based prompt, you can first request an MSA with <a class="reference internal" href="poet.html#openprotein.api.poet.PoetAPI.create_msa" title="openprotein.api.poet.PoetAPI.create_msa"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.PoetAPI.create_msa()</span></code></a> and then filter (sample) it with <a class="reference internal" href="poet.html#openprotein.api.poet.MSAFuture.sample_prompt" title="openprotein.api.poet.MSAFuture.sample_prompt"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.MSAFuture.sample_prompt()</span></code></a>.</p>
+<p>You can create a prompt either from an MSA (see below), or by directly uploading a <em>de novo</em> prompt <a class="reference internal" href="poet.html#openprotein.api.poet.PoetAPI.upload_prompt" title="openprotein.api.poet.PoetAPI.upload_prompt"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.PoetAPI.upload_prompt()</span></code></a>.</p>
+<p>To create an MSA based prompt, you can first request an MSA with <a class="reference internal" href="poet.html#openprotein.api.poet.PoetAPI.create_msa" title="openprotein.api.poet.PoetAPI.create_msa"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.PoetAPI.create_msa()</span></code></a> and then filter it with <a class="reference internal" href="poet.html#openprotein.api.poet.MSAFuture.sample_prompt" title="openprotein.api.poet.MSAFuture.sample_prompt"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.MSAFuture.sample_prompt()</span></code></a>.</p>
 <p>Once you have a viable prompt, you can execute the PoET workflows:</p>
 <ul class="simple">
 <li><p>Score arbitrary sequences you provide to predict sequence fitness and rank variants. This works for substitutions and indels and allows high order variants. (for example, <a class="reference internal" href="poet.html#openprotein.api.poet.PoetAPI.score" title="openprotein.api.poet.PoetAPI.score"><code class="xref py py-meth docutils literal notranslate"><span class="pre">openprotein.api.poet.PoetAPI.score()</span></code></a>)</p></li>

apidocs/build/html/_sources/poet_workflow.rst.txt

@@ -7,9 +7,9 @@ PoET is a generative protein language model that allows controllable design of p
 Creating a prompt
 -------------------
 
-You can create a prompt either from an MSA (see below), or by directly uploading a *de novo* :py:meth:`openprotein.api.poet.PoetAPI.upload_prompt`. 
+You can create a prompt either from an MSA (see below), or by directly uploading a *de novo* prompt :py:meth:`openprotein.api.poet.PoetAPI.upload_prompt`. 
 
-To create an MSA based prompt, you can first request an MSA with :py:meth:`openprotein.api.poet.PoetAPI.create_msa` and then filter (sample) it with :py:meth:`openprotein.api.poet.MSAFuture.sample_prompt`.
+To create an MSA based prompt, you can first request an MSA with :py:meth:`openprotein.api.poet.PoetAPI.create_msa` and then filter it with :py:meth:`openprotein.api.poet.MSAFuture.sample_prompt`.
 
 Once you have a viable prompt, you can execute the PoET workflows: