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@Zulko
Zulko committed Dec 16, 2024
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Showing 1 changed file with 45 additions and 34 deletions.
79 changes: 45 additions & 34 deletions _modules/ginkgo_ai_client/queries.html
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Expand Up @@ -407,7 +407,7 @@ <h1>Source code for ginkgo_ai_client.queries</h1><div class="highlight"><pre>
</span><span data-line="290"> <span class="n">promoter_sequence</span><span class="p">:</span> <span class="nb">str</span>
</span><span data-line="291"> <span class="n">orf_sequence</span><span class="p">:</span> <span class="nb">str</span>
</span><span data-line="292"> <span class="n">tissue_of_interest</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]]</span>
</span><span data-line="293"> <span class="n">source</span><span class="p">:</span> <span class="nb">str</span>
</span><span data-line="293"> <span class="n">source</span><span class="p">:</span> <span class="nb">str</span>
</span><span data-line="294"> <span class="n">model</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;borzoi-human-fold0&quot;</span>
</span><span data-line="295"> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
</span><span data-line="296">
Expand Down Expand Up @@ -702,41 +702,52 @@ <h1>Source code for ginkgo_ai_client.queries</h1><div class="highlight"><pre>
</span><span data-line="585"><span class="sd"> query_name: Optional[str] = None</span>
</span><span data-line="586"><span class="sd"> The name of the query. It will appear in the API response and can be used to</span>
</span><span data-line="587"><span class="sd"> handle exceptions.</span>
</span><span data-line="588"><span class="sd"> &quot;&quot;&quot;</span>
</span><span data-line="589">
</span><span data-line="590"> <span class="n">sequences</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Dict</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;protein&quot;</span><span class="p">,</span> <span class="s2">&quot;ligand&quot;</span><span class="p">],</span> <span class="n">Union</span><span class="p">[</span><span class="n">_Protein</span><span class="p">,</span> <span class="n">_CCD</span><span class="p">,</span> <span class="n">_Smiles</span><span class="p">]]]</span>
</span><span data-line="591"> <span class="n">model</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;boltz&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;boltz&quot;</span>
</span><span data-line="592"> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
</span><span data-line="588">
</span><span data-line="589"><span class="sd"> Examples</span>
</span><span data-line="590"><span class="sd"> --------</span>
</span><span data-line="591">
</span><span data-line="592"><span class="sd"> .. code:: python</span>
</span><span data-line="593">
</span><span data-line="594"> <span class="k">def</span> <span class="nf">to_request_params</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">:</span>
</span><span data-line="595"> <span class="k">return</span> <span class="p">{</span>
</span><span data-line="596"> <span class="s2">&quot;model&quot;</span><span class="p">:</span> <span class="s2">&quot;boltz&quot;</span><span class="p">,</span>
</span><span data-line="597"> <span class="s2">&quot;transforms&quot;</span><span class="p">:</span> <span class="p">[{</span><span class="s2">&quot;type&quot;</span><span class="p">:</span> <span class="s2">&quot;INFER_STRUCTURE&quot;</span><span class="p">}],</span>
</span><span data-line="598"> <span class="s2">&quot;text&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_dump</span><span class="p">(</span><span class="n">exclude</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;model&quot;</span><span class="p">,</span> <span class="s2">&quot;query_name&quot;</span><span class="p">],</span> <span class="n">mode</span><span class="o">=</span><span class="s2">&quot;json&quot;</span><span class="p">),</span>
</span><span data-line="599"> <span class="p">}</span>
</span><span data-line="594"><span class="sd"> query = BoltzStructurePredictionQuery.from_yaml_file(&quot;input.yaml&quot;) # or below:</span>
</span><span data-line="595"><span class="sd"> query = BoltzStructurePredictionQuery.from_protein_sequence(&quot;MLLKP&quot;)</span>
</span><span data-line="596"><span class="sd"> response = client.send_request(query)</span>
</span><span data-line="597"><span class="sd"> response.download_structure(&quot;structure.cif&quot;) # or below:</span>
</span><span data-line="598"><span class="sd"> response.download_structure(&quot;structure.pdb&quot;)</span>
</span><span data-line="599"><span class="sd"> &quot;&quot;&quot;</span>
</span><span data-line="600">
</span><span data-line="601"> <span class="k">def</span> <span class="nf">parse_response</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">results</span><span class="p">:</span> <span class="n">Dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">BoltzStructurePredictionResponse</span><span class="p">:</span>
</span><span data-line="602"> <span class="k">return</span> <span class="n">BoltzStructurePredictionResponse</span><span class="p">(</span>
</span><span data-line="603"> <span class="n">cif_file_url</span><span class="o">=</span><span class="n">results</span><span class="p">[</span><span class="s2">&quot;cif_file_url&quot;</span><span class="p">],</span>
</span><span data-line="604"> <span class="n">confidence_data</span><span class="o">=</span><span class="n">results</span><span class="p">[</span><span class="s2">&quot;confidence_data&quot;</span><span class="p">],</span>
</span><span data-line="605"> <span class="n">query_name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">query_name</span><span class="p">,</span>
</span><span data-line="606"> <span class="p">)</span>
</span><span data-line="607">
</span><span data-line="608"> <span class="nd">@classmethod</span>
</span><span data-line="609"> <span class="k">def</span> <span class="nf">from_yaml_file</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;auto&quot;</span><span class="p">):</span>
</span><span data-line="610"> <span class="n">path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
</span><span data-line="611"> <span class="k">if</span> <span class="n">query_name</span> <span class="o">==</span> <span class="s2">&quot;auto&quot;</span><span class="p">:</span>
</span><span data-line="612"> <span class="n">query_name</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">name</span>
</span><span data-line="613"> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
</span><span data-line="614"> <span class="n">data</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">yaml</span><span class="o">.</span><span class="n">SafeLoader</span><span class="p">)</span>
</span><span data-line="615"> <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">sequences</span><span class="o">=</span><span class="n">data</span><span class="p">[</span><span class="s2">&quot;sequences&quot;</span><span class="p">],</span> <span class="n">query_name</span><span class="o">=</span><span class="n">query_name</span><span class="p">)</span>
</span><span data-line="616">
</span><span data-line="617"> <span class="nd">@classmethod</span>
</span><span data-line="618"> <span class="k">def</span> <span class="nf">from_protein_sequence</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">sequence</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
</span><span data-line="619"> <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
</span><span data-line="620"> <span class="n">sequences</span><span class="o">=</span><span class="p">[{</span><span class="s2">&quot;protein&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;id&quot;</span><span class="p">:</span> <span class="s2">&quot;A&quot;</span><span class="p">,</span> <span class="s2">&quot;sequence&quot;</span><span class="p">:</span> <span class="n">sequence</span><span class="p">}}],</span>
</span><span data-line="621"> <span class="n">query_name</span><span class="o">=</span><span class="n">query_name</span><span class="p">,</span>
</span><span data-line="622"> <span class="p">)</span>
</span><span data-line="601"> <span class="n">sequences</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Dict</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;protein&quot;</span><span class="p">,</span> <span class="s2">&quot;ligand&quot;</span><span class="p">],</span> <span class="n">Union</span><span class="p">[</span><span class="n">_Protein</span><span class="p">,</span> <span class="n">_CCD</span><span class="p">,</span> <span class="n">_Smiles</span><span class="p">]]]</span>
</span><span data-line="602"> <span class="n">model</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;boltz&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;boltz&quot;</span>
</span><span data-line="603"> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
</span><span data-line="604">
</span><span data-line="605"> <span class="k">def</span> <span class="nf">to_request_params</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">:</span>
</span><span data-line="606"> <span class="k">return</span> <span class="p">{</span>
</span><span data-line="607"> <span class="s2">&quot;model&quot;</span><span class="p">:</span> <span class="s2">&quot;boltz&quot;</span><span class="p">,</span>
</span><span data-line="608"> <span class="s2">&quot;transforms&quot;</span><span class="p">:</span> <span class="p">[{</span><span class="s2">&quot;type&quot;</span><span class="p">:</span> <span class="s2">&quot;INFER_STRUCTURE&quot;</span><span class="p">}],</span>
</span><span data-line="609"> <span class="s2">&quot;text&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_dump</span><span class="p">(</span><span class="n">exclude</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;model&quot;</span><span class="p">,</span> <span class="s2">&quot;query_name&quot;</span><span class="p">],</span> <span class="n">mode</span><span class="o">=</span><span class="s2">&quot;json&quot;</span><span class="p">),</span>
</span><span data-line="610"> <span class="p">}</span>
</span><span data-line="611">
</span><span data-line="612"> <span class="k">def</span> <span class="nf">parse_response</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">results</span><span class="p">:</span> <span class="n">Dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">BoltzStructurePredictionResponse</span><span class="p">:</span>
</span><span data-line="613"> <span class="k">return</span> <span class="n">BoltzStructurePredictionResponse</span><span class="p">(</span>
</span><span data-line="614"> <span class="n">cif_file_url</span><span class="o">=</span><span class="n">results</span><span class="p">[</span><span class="s2">&quot;cif_file_url&quot;</span><span class="p">],</span>
</span><span data-line="615"> <span class="n">confidence_data</span><span class="o">=</span><span class="n">results</span><span class="p">[</span><span class="s2">&quot;confidence_data&quot;</span><span class="p">],</span>
</span><span data-line="616"> <span class="n">query_name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">query_name</span><span class="p">,</span>
</span><span data-line="617"> <span class="p">)</span>
</span><span data-line="618">
</span><span data-line="619"> <span class="nd">@classmethod</span>
</span><span data-line="620"> <span class="k">def</span> <span class="nf">from_yaml_file</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;auto&quot;</span><span class="p">):</span>
</span><span data-line="621"> <span class="n">path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
</span><span data-line="622"> <span class="k">if</span> <span class="n">query_name</span> <span class="o">==</span> <span class="s2">&quot;auto&quot;</span><span class="p">:</span>
</span><span data-line="623"> <span class="n">query_name</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">name</span>
</span><span data-line="624"> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
</span><span data-line="625"> <span class="n">data</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">yaml</span><span class="o">.</span><span class="n">SafeLoader</span><span class="p">)</span>
</span><span data-line="626"> <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">sequences</span><span class="o">=</span><span class="n">data</span><span class="p">[</span><span class="s2">&quot;sequences&quot;</span><span class="p">],</span> <span class="n">query_name</span><span class="o">=</span><span class="n">query_name</span><span class="p">)</span>
</span><span data-line="627">
</span><span data-line="628"> <span class="nd">@classmethod</span>
</span><span data-line="629"> <span class="k">def</span> <span class="nf">from_protein_sequence</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">sequence</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">query_name</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
</span><span data-line="630"> <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
</span><span data-line="631"> <span class="n">sequences</span><span class="o">=</span><span class="p">[{</span><span class="s2">&quot;protein&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;id&quot;</span><span class="p">:</span> <span class="s2">&quot;A&quot;</span><span class="p">,</span> <span class="s2">&quot;sequence&quot;</span><span class="p">:</span> <span class="n">sequence</span><span class="p">}}],</span>
</span><span data-line="632"> <span class="n">query_name</span><span class="o">=</span><span class="n">query_name</span><span class="p">,</span>
</span><span data-line="633"> <span class="p">)</span>
</span></pre></div>
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