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<section id="overview-of-symmetry-in-rfd3">
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<h1>Overview of Symmetry in RFD3<a class="headerlink" href="#overview-of-symmetry-in-rfd3" title="Link to this heading">¶</a></h1>
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<section id="specifying-symmetry-in-your-input-specifications">
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<h2>Specifying symmetry in your input specifications<a class="headerlink" href="#specifying-symmetry-in-your-input-specifications" title="Link to this heading">¶</a></h2>
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<p>Symmetry configurations are specified within the input JSON or YAML file, nested under its own specific configuration. The symmetry specific config has the following:</p>
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<div class="highlight-json notranslate"><div class="highlight"><pre><span></span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
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<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C3"</span><span class="p">,</span>
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<span class="w"> </span><span class="nt">"is_unsym_motif"</span><span class="p">:</span><span class="w"> </span><span class="s2">"Y1-11,Z16-25"</span><span class="p">,</span>
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||
<span class="w"> </span><span class="nt">"is_symmetric_motif"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span>
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<span class="p">}</span>
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|
||
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="nt">symmetry</span><span class="p">:</span>
|
||
<span class="w"> </span><span class="nt">id</span><span class="p">:</span><span class="w"> </span><span class="s">"C3"</span>
|
||
<span class="w"> </span><span class="nt">is_unsym_motif</span><span class="p">:</span><span class="w"> </span><span class="s">"Y1-11,Z16-25"</span>
|
||
<span class="w"> </span><span class="nt">is_symmetric_motif</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
|
||
</pre></div>
|
||
</div>
|
||
<ul class="simple">
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">id</span></code> : Symmetry group ID; e.g. “C3” for a cyclic protein with 3 subunits, “D2” for a dihedral protein with 2 subunits. Note that only C and D symmetry types are supported currently.</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">is_unsym_motif</span></code> : Comma separated string list of contig/ligand names that should NOT be symmetrized (e.g. DNA strands). If not provided, all motifs are assumed to be symmetrized. See <a class="reference internal" href="#designs-with-motifs"><span class="xref myst">Designs with motifs</span></a> section for details.</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">is_symmetric_motif</span></code>: Boolean value whether the input motif is symmetric. Currently only symmetric input motifs are supported, therefore, <code class="docutils literal notranslate"><span class="pre">true</span></code> by default.</p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="example-command">
|
||
<h2>Example command<a class="headerlink" href="#example-command" title="Link to this heading">¶</a></h2>
|
||
<p>You can run the following example command:</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>./src/modelhub/inference.py inference_sampler.kind=symmetry out_dir=logs/inference_outs/sym_demo/0 ckpt_path=$cur_ckpt inputs=./projects/aa_design/tests/test_data/sym_tests.json diffusion_batch_size=1
|
||
</pre></div>
|
||
</div>
|
||
<ul class="simple">
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">inference_sampler.kind</span></code>: Set <code class="docutils literal notranslate"><span class="pre">symmetry</span></code> to tern on symmetry mode.</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">diffusion_batch_size</span></code> : <code class="docutils literal notranslate"><span class="pre">8</span></code> by default, but it is recommended to set it to <code class="docutils literal notranslate"><span class="pre">1</span></code> for symmetry due to memory limitations.</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">low_memory_mode</span></code> : Additionally you can set this to <code class="docutils literal notranslate"><span class="pre">True</span></code> if you have memory constraints (e.g. “CUDA error: out of memory”). However, this will significantly slow the inference.</p></li>
|
||
</ul>
|
||
</section>
|
||
<section id="unconditional-multimer-design">
|
||
<h2>Unconditional multimer design<a class="headerlink" href="#unconditional-multimer-design" title="Link to this heading">¶</a></h2>
|
||
<p>As mentioned above, we currently only support C and D symmetry types.
|
||
The following provides a general overview of the types of symmetry and examples of how to run:</p>
|
||
<section id="cyclic">
|
||
<h3>Cyclic<a class="headerlink" href="#cyclic" title="Link to this heading">¶</a></h3>
|
||
<p><strong>Defaults:</strong></p>
|
||
<div class="highlight-json notranslate"><div class="highlight"><pre><span></span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"uncond_C5"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"length"</span><span class="p">:</span><span class="w"> </span><span class="mi">100</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_non_loopy"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C5"</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
<section id="dihedrals">
|
||
<h3>Dihedrals<a class="headerlink" href="#dihedrals" title="Link to this heading">¶</a></h3>
|
||
<p><strong>Defaults:</strong></p>
|
||
<div class="highlight-json notranslate"><div class="highlight"><pre><span></span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"uncond_D4"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="w"> </span>
|
||
<span class="w"> </span><span class="nt">"length"</span><span class="p">:</span><span class="w"> </span><span class="mi">50</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_non_loopy"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"D4"</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="designs-with-motifs">
|
||
<h2>Designs with motifs<a class="headerlink" href="#designs-with-motifs" title="Link to this heading">¶</a></h2>
|
||
<p>As mentioned above, symmetry sampling currently only supports pre-symmetrized motifs around the origin. Therefore, <code class="docutils literal notranslate"><span class="pre">is_symmetric_motif</span></code> is set to <code class="docutils literal notranslate"><span class="pre">true</span></code> by default.
|
||
The following are example JSON specifications for different symmetric motif scaffolding. You can also find the corresponding input PDBs in <code class="docutils literal notranslate"><span class="pre">docs/input_pdbs/symmetry_examples</span></code>. Although we only give JSON examples, you can also use YAML for everything shown below.</p>
|
||
<p>The tasks that these examples describe are as follows:</p>
|
||
<ul class="simple">
|
||
<li><p>unindexed_C2_1j79, unindexed_C2_1e3v:
|
||
Unindexed motif scaffolding for symmetric enzyme active sites. The motifs are located within a subunit; no inter-subunit motifs.</p></li>
|
||
<li><p>indexed_unsym_C2_1bfr:
|
||
Indexed motif scaffolding for a single active site held by a symmetric enzyme. <code class="docutils literal notranslate"><span class="pre">is_unsym_motif</span></code> specifies the ligand that shouldn’t be symmetrized.</p></li>
|
||
<li><p>uncond_unsym_C3_6t8h:
|
||
Unconditional generation of C3 proteins around a DNA helix. The DNA chains are the motifs. <code class="docutils literal notranslate"><span class="pre">is_unsym_motif</span></code> specifies the DNA strands that shouldn’t be symmetrized.</p></li>
|
||
</ul>
|
||
<div class="highlight-json notranslate"><div class="highlight"><pre><span></span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"unindexed_C2_1j79"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C2"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_symmetric_motif"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"input"</span><span class="p">:</span><span class="w"> </span><span class="s2">"../input_pdbs/symmetry_examples/1j79_C2.pdb"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"ligand"</span><span class="p">:</span><span class="w"> </span><span class="s2">"ORO,ZN"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"unindex"</span><span class="p">:</span><span class="w"> </span><span class="s2">"A250"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"length"</span><span class="p">:</span><span class="w"> </span><span class="mi">130</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"select_fixed_atoms"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"A250"</span><span class="p">:</span><span class="w"> </span><span class="s2">"OD1,CG"</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"unindexed_C2_1e3v"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C2"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_symmetric_motif"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"input"</span><span class="p">:</span><span class="w"> </span><span class="s2">"../input_pdbs/symmetry_examples/1e3v_C2.pdb"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"ligand"</span><span class="p">:</span><span class="w"> </span><span class="s2">"DXC"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"unindex"</span><span class="p">:</span><span class="w"> </span><span class="s2">"A16,A40,A100,A103"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"length"</span><span class="p">:</span><span class="w"> </span><span class="mi">80</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"select_fixed_atoms"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"A16"</span><span class="p">:</span><span class="w"> </span><span class="s2">"OH,CZ,CE1,CE2"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"A40"</span><span class="p">:</span><span class="w"> </span><span class="s2">"OD2,CG"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"A100"</span><span class="p">:</span><span class="w"> </span><span class="s2">"N,CA,C,CB"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"A103"</span><span class="p">:</span><span class="w"> </span><span class="s2">"OD2,CG"</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"indexed_unsym_C2_1bfr"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C2"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_symmetric_motif"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_unsym_motif"</span><span class="p">:</span><span class="w"> </span><span class="s2">"HEM"</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"input"</span><span class="p">:</span><span class="w"> </span><span class="s2">"../input_pdbs/symmetry_examples/1bfr_C2.pdb"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"ligand"</span><span class="p">:</span><span class="w"> </span><span class="s2">"HEM"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"contig"</span><span class="p">:</span><span class="w"> </span><span class="s2">"51,M52,80"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"length"</span><span class="p">:</span><span class="w"> </span><span class="kc">null</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"select_fixed_atoms"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"M52"</span><span class="p">:</span><span class="w"> </span><span class="s2">"CG,SD,CE"</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"unsym_C3_6t8h"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"symmetry"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="nt">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C3"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_symmetric_motif"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_unsym_motif"</span><span class="p">:</span><span class="w"> </span><span class="s2">"Y1-11,Z16-25"</span>
|
||
<span class="w"> </span><span class="p">},</span>
|
||
<span class="w"> </span><span class="nt">"input"</span><span class="p">:</span><span class="w"> </span><span class="s2">"../input_pdbs/symmetry_examples/6t8h_C3.pdb"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"contig"</span><span class="p">:</span><span class="w"> </span><span class="s2">"150-150,/0,Y1-11,/0,Z16-25"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"length"</span><span class="p">:</span><span class="w"> </span><span class="kc">null</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="nt">"is_non_loopy"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
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|
||
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<div class="toc-tree-container">
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<div class="toc-tree">
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<ul>
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<li><a class="reference internal" href="#">Overview of Symmetry in RFD3</a><ul>
|
||
<li><a class="reference internal" href="#specifying-symmetry-in-your-input-specifications">Specifying symmetry in your input specifications</a></li>
|
||
<li><a class="reference internal" href="#example-command">Example command</a></li>
|
||
<li><a class="reference internal" href="#unconditional-multimer-design">Unconditional multimer design</a><ul>
|
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<li><a class="reference internal" href="#cyclic">Cyclic</a></li>
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<li><a class="reference internal" href="#dihedrals">Dihedrals</a></li>
|
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</ul>
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</li>
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<li><a class="reference internal" href="#designs-with-motifs">Designs with motifs</a></li>
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