deploy: b45af3a

about/license-faq/index.html

@@ -1125,8 +1125,8 @@ <h2 id="2-can-i-publish-research-papers-using-multimolecule">2. Can I publish re
 <p>As a special exemption under section 7 of the <em><a href="../license/">License</a></em>, we grant permission to publish research papers using MultiMolecule in fully open access journals, conferences, or preprint servers that do not charge any fee from authors, provided all published manuscripts are made available under the <a href="https://www.gnu.org/licenses/fdl.html">GNU Free Documentation License (GFDL)</a>, or a <a href="https://creativecommons.org">Creative Commons license</a>, or an <a href="https://opensource.org/licenses">OSI-approved license</a> that permits the sharing of manuscripts.</p>
 <p>As a special exemption under section 7 of the <em><a href="../license/">License</a></em>, we grant permission to publish research papers using MultiMolecule in certain non-profit journals, conferences, or preprint servers. Currently, the non-profit journals, conferences, or preprint servers we allow include:</p>
 <ul>
-<li>All journals published by American Association for the Advancement of Science (AAAS)</li>
-<li>eLife</li>
+<li><a href="https://www.aaas.org/journals">All journals published by American Association for the Advancement of Science (AAAS)</a></li>
+<li><a href="https://elifesciences.org">eLife</a></li>
 </ul>
 <p>For publishing in closed access journals or conferences, you must obtain a separate license from us. This typically involves co-authorship, a fee to support the project, or both. Contact us at <a href="mailto:[email protected]">[email protected]</a> for more information.</p>
 <p>While not mandatory, we recommend citing the MultiMolecule project in your research papers.</p>

data/dataset/index.html

@@ -2761,7 +2761,7 @@ <h3 id="multimolecule.data.Dataset(fingerprint)" class="doc doc-heading doc-head
 </span><span id="__span-0-459"><a id="__codelineno-0-459" name="__codelineno-0-459"></a>                <span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="n">fill_value</span><span class="p">)</span>
 </span><span id="__span-0-460"><a id="__codelineno-0-460" name="__codelineno-0-460"></a>            <span class="k">else</span><span class="p">:</span>
 </span><span id="__span-0-461"><a id="__codelineno-0-461" name="__codelineno-0-461"></a>                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Invalid nan_process: </span><span class="si">{</span><span class="n">nan_process</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="__span-0-462"><a id="__codelineno-0-462" name="__codelineno-0-462"></a>        <span class="k">return</span> <span class="n">pa</span><span class="o">.</span><span class="n">Table</span><span class="o">.</span><span class="n">from_pandas</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+</span><span id="__span-0-462"><a id="__codelineno-0-462" name="__codelineno-0-462"></a>        <span class="k">return</span> <span class="n">pa</span><span class="o">.</span><span class="n">Table</span><span class="o">.</span><span class="n">from_pandas</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">preserve_index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
 </span><span id="__span-0-463"><a id="__codelineno-0-463" name="__codelineno-0-463"></a>
 </span><span id="__span-0-464"><a id="__codelineno-0-464" name="__codelineno-0-464"></a>    <span class="nd">@property</span>
 </span><span id="__span-0-465"><a id="__codelineno-0-465" name="__codelineno-0-465"></a>    <span class="k">def</span> <span class="nf">id_cols</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">:</span>

index.html

@@ -1006,15 +1006,20 @@ <h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanen
 </span></code></pre></div></td></tr></table></div>
 <div class="admonition caution">
 <p class="admonition-title">Caution</p>
-<p>The MultiMolecule project uses a GNU Affero General Public License.
+<p>The MultiMolecule project uses a <a href="#license">GNU Affero General Public License</a>.
 Research papers are considered derivative works, and therefore must be licensed under the same terms.</p>
 <p>You can only publish your research papers in fully open-access journals, conference, or pre-print servers that do not charge fees to publish or read.
 You must obtain a waiver from the authors to publish in a closed-access / author-fee journal, conference, or pre-print server.</p>
+<p>You may receive auto-approval for waivers if you are submitting to the following non-profit journals:</p>
+<ul>
+<li><a href="https://www.aaas.org/journals">All journals published by American Association for the Advancement of Science (AAAS)</a></li>
+<li><a href="https://elifesciences.org">eLife</a></li>
+</ul>
 <p>Read more in the <a href="about/license-faq/#2-can-i-publish-research-papers-using-multimolecule">license faq</a>.</p>
 </div>
 <h2 id="license">License<a class="headerlink" href="#license" title="Permanent link">&para;</a></h2>
 <p>We believe openness is the Foundation of Research.</p>
-<p>MultiMolecule is licensed under the GNU Affero General Public License.</p>
+<p>MultiMolecule is licensed under the <a href="LICENSE.md">GNU Affero General Public License</a>.</p>
 <p>Please join us in building an open research community.</p>
 <p><code>SPDX-License-Identifier: AGPL-3.0-or-later</code></p>
 

models/calm/index.html

@@ -3041,14 +3041,14 @@ <h4 id="multimolecule.models.calm.RnaTokenizer(do_upper_case)" class="doc doc-he
 </span><span id="__span-0-98"><a id="__codelineno-0-98" name="__codelineno-0-98"></a>        <span class="p">)</span>
 </span><span id="__span-0-99"><a id="__codelineno-0-99" name="__codelineno-0-99"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">replace_T_with_U</span> <span class="o">=</span> <span class="n">replace_T_with_U</span>
 </span><span id="__span-0-100"><a id="__codelineno-0-100" name="__codelineno-0-100"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">nmers</span> <span class="o">=</span> <span class="n">nmers</span>
-</span><span id="__span-0-101"><a id="__codelineno-0-101" name="__codelineno-0-101"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">condon</span> <span class="o">=</span> <span class="n">codon</span>
+</span><span id="__span-0-101"><a id="__codelineno-0-101" name="__codelineno-0-101"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">codon</span> <span class="o">=</span> <span class="n">codon</span>
 </span><span id="__span-0-102"><a id="__codelineno-0-102" name="__codelineno-0-102"></a>
 </span><span id="__span-0-103"><a id="__codelineno-0-103" name="__codelineno-0-103"></a>    <span class="k">def</span> <span class="nf">_tokenize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">text</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 </span><span id="__span-0-104"><a id="__codelineno-0-104" name="__codelineno-0-104"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">do_upper_case</span><span class="p">:</span>
 </span><span id="__span-0-105"><a id="__codelineno-0-105" name="__codelineno-0-105"></a>            <span class="n">text</span> <span class="o">=</span> <span class="n">text</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
 </span><span id="__span-0-106"><a id="__codelineno-0-106" name="__codelineno-0-106"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">replace_T_with_U</span><span class="p">:</span>
 </span><span id="__span-0-107"><a id="__codelineno-0-107" name="__codelineno-0-107"></a>            <span class="n">text</span> <span class="o">=</span> <span class="n">text</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;T&quot;</span><span class="p">,</span> <span class="s2">&quot;U&quot;</span><span class="p">)</span>
-</span><span id="__span-0-108"><a id="__codelineno-0-108" name="__codelineno-0-108"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">condon</span><span class="p">:</span>
+</span><span id="__span-0-108"><a id="__codelineno-0-108" name="__codelineno-0-108"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">codon</span><span class="p">:</span>
 </span><span id="__span-0-109"><a id="__codelineno-0-109" name="__codelineno-0-109"></a>            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">text</span><span class="p">)</span> <span class="o">%</span> <span class="mi">3</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
 </span><span id="__span-0-110"><a id="__codelineno-0-110" name="__codelineno-0-110"></a>                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
 </span><span id="__span-0-111"><a id="__codelineno-0-111" name="__codelineno-0-111"></a>                    <span class="sa">f</span><span class="s2">&quot;length of input sequence must be a multiple of 3 for codon tokenization, but got </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">text</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span>

models/ernierna/index.html

@@ -2953,14 +2953,14 @@ <h4 id="multimolecule.models.ernierna.RnaTokenizer(do_upper_case)" class="doc do
 </span><span id="__span-0-98"><a id="__codelineno-0-98" name="__codelineno-0-98"></a>        <span class="p">)</span>
 </span><span id="__span-0-99"><a id="__codelineno-0-99" name="__codelineno-0-99"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">replace_T_with_U</span> <span class="o">=</span> <span class="n">replace_T_with_U</span>
 </span><span id="__span-0-100"><a id="__codelineno-0-100" name="__codelineno-0-100"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">nmers</span> <span class="o">=</span> <span class="n">nmers</span>
-</span><span id="__span-0-101"><a id="__codelineno-0-101" name="__codelineno-0-101"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">condon</span> <span class="o">=</span> <span class="n">codon</span>
+</span><span id="__span-0-101"><a id="__codelineno-0-101" name="__codelineno-0-101"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">codon</span> <span class="o">=</span> <span class="n">codon</span>
 </span><span id="__span-0-102"><a id="__codelineno-0-102" name="__codelineno-0-102"></a>
 </span><span id="__span-0-103"><a id="__codelineno-0-103" name="__codelineno-0-103"></a>    <span class="k">def</span> <span class="nf">_tokenize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">text</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 </span><span id="__span-0-104"><a id="__codelineno-0-104" name="__codelineno-0-104"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">do_upper_case</span><span class="p">:</span>
 </span><span id="__span-0-105"><a id="__codelineno-0-105" name="__codelineno-0-105"></a>            <span class="n">text</span> <span class="o">=</span> <span class="n">text</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
 </span><span id="__span-0-106"><a id="__codelineno-0-106" name="__codelineno-0-106"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">replace_T_with_U</span><span class="p">:</span>
 </span><span id="__span-0-107"><a id="__codelineno-0-107" name="__codelineno-0-107"></a>            <span class="n">text</span> <span class="o">=</span> <span class="n">text</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;T&quot;</span><span class="p">,</span> <span class="s2">&quot;U&quot;</span><span class="p">)</span>
-</span><span id="__span-0-108"><a id="__codelineno-0-108" name="__codelineno-0-108"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">condon</span><span class="p">:</span>
+</span><span id="__span-0-108"><a id="__codelineno-0-108" name="__codelineno-0-108"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">codon</span><span class="p">:</span>
 </span><span id="__span-0-109"><a id="__codelineno-0-109" name="__codelineno-0-109"></a>            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">text</span><span class="p">)</span> <span class="o">%</span> <span class="mi">3</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
 </span><span id="__span-0-110"><a id="__codelineno-0-110" name="__codelineno-0-110"></a>                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
 </span><span id="__span-0-111"><a id="__codelineno-0-111" name="__codelineno-0-111"></a>                    <span class="sa">f</span><span class="s2">&quot;length of input sequence must be a multiple of 3 for codon tokenization, but got </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">text</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span>

models/rinalmo/index.html

@@ -2995,14 +2995,14 @@ <h4 id="multimolecule.models.rinalmo.RnaTokenizer(do_upper_case)" class="doc doc
 </span><span id="__span-0-98"><a id="__codelineno-0-98" name="__codelineno-0-98"></a>        <span class="p">)</span>
 </span><span id="__span-0-99"><a id="__codelineno-0-99" name="__codelineno-0-99"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">replace_T_with_U</span> <span class="o">=</span> <span class="n">replace_T_with_U</span>
 </span><span id="__span-0-100"><a id="__codelineno-0-100" name="__codelineno-0-100"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">nmers</span> <span class="o">=</span> <span class="n">nmers</span>
-</span><span id="__span-0-101"><a id="__codelineno-0-101" name="__codelineno-0-101"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">condon</span> <span class="o">=</span> <span class="n">codon</span>
+</span><span id="__span-0-101"><a id="__codelineno-0-101" name="__codelineno-0-101"></a>        <span class="bp">self</span><span class="o">.</span><span class="n">codon</span> <span class="o">=</span> <span class="n">codon</span>
 </span><span id="__span-0-102"><a id="__codelineno-0-102" name="__codelineno-0-102"></a>
 </span><span id="__span-0-103"><a id="__codelineno-0-103" name="__codelineno-0-103"></a>    <span class="k">def</span> <span class="nf">_tokenize</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">text</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 </span><span id="__span-0-104"><a id="__codelineno-0-104" name="__codelineno-0-104"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">do_upper_case</span><span class="p">:</span>
 </span><span id="__span-0-105"><a id="__codelineno-0-105" name="__codelineno-0-105"></a>            <span class="n">text</span> <span class="o">=</span> <span class="n">text</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
 </span><span id="__span-0-106"><a id="__codelineno-0-106" name="__codelineno-0-106"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">replace_T_with_U</span><span class="p">:</span>
 </span><span id="__span-0-107"><a id="__codelineno-0-107" name="__codelineno-0-107"></a>            <span class="n">text</span> <span class="o">=</span> <span class="n">text</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;T&quot;</span><span class="p">,</span> <span class="s2">&quot;U&quot;</span><span class="p">)</span>
-</span><span id="__span-0-108"><a id="__codelineno-0-108" name="__codelineno-0-108"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">condon</span><span class="p">:</span>
+</span><span id="__span-0-108"><a id="__codelineno-0-108" name="__codelineno-0-108"></a>        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">codon</span><span class="p">:</span>
 </span><span id="__span-0-109"><a id="__codelineno-0-109" name="__codelineno-0-109"></a>            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">text</span><span class="p">)</span> <span class="o">%</span> <span class="mi">3</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
 </span><span id="__span-0-110"><a id="__codelineno-0-110" name="__codelineno-0-110"></a>                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
 </span><span id="__span-0-111"><a id="__codelineno-0-111" name="__codelineno-0-111"></a>                    <span class="sa">f</span><span class="s2">&quot;length of input sequence must be a multiple of 3 for codon tokenization, but got </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">text</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span>