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hanjinliu · Oct 28, 2024 · d94cf69 · d94cf69
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diff --git a/404.html b/404.html
@@ -14,15 +14,15 @@
 
 
       <link rel="icon" href="/assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="/assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="/assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="/assets/stylesheets/palette.06af60db.min.css">
@@ -1955,7 +1955,7 @@ <h1>404 - Not found</h1>
     <script id="__config" type="application/json">{"base": "/", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "/assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="/assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="/assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
 

diff --git a/alignment/conventional/index.html b/alignment/conventional/index.html
@@ -18,15 +18,15 @@
 
 
       <link rel="icon" href="../../assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>Conventional Methods in Cryo-ET Studies - Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="../../assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="../../assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="../../assets/stylesheets/palette.06af60db.min.css">
@@ -2294,7 +2294,7 @@ <h2 id="pcak-means-classification">PCA/K-means Classification</h2>
     <script id="__config" type="application/json">{"base": "../..", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "../../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../../assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
 

diff --git a/alignment/index.html b/alignment/index.html
@@ -18,15 +18,15 @@
 
 
       <link rel="icon" href="../assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>Subtomogram Alignment and Averaging - Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="../assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="../assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="../assets/stylesheets/palette.06af60db.min.css">
@@ -2067,7 +2067,7 @@ <h2 id="index">Index</h2>
     <script id="__config" type="application/json">{"base": "..", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="../assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
 

diff --git a/alignment/landscape/index.html b/alignment/landscape/index.html
@@ -18,15 +18,15 @@
 
 
       <link rel="icon" href="../../assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>Build Correlation Landscapes - Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="../../assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="../../assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="../../assets/stylesheets/palette.06af60db.min.css">
@@ -2142,7 +2142,7 @@ <h2 id="visualizing-the-landscape">Visualizing the Landscape</h2>
     <script id="__config" type="application/json">{"base": "../..", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "../../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../../assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
 

diff --git a/alignment/rma/index.html b/alignment/rma/index.html
@@ -18,15 +18,15 @@
 
 
       <link rel="icon" href="../../assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>Restricted Mesh Annealing (RMA) - Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="../../assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="../../assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="../../assets/stylesheets/palette.06af60db.min.css">
@@ -2139,7 +2139,7 @@ <h2 id="run-rma-without-constructing-a-landscape">Run RMA without Constructing a
     <script id="__config" type="application/json">{"base": "../..", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "../../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../../assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
 

diff --git a/alignment/viterbi/index.html b/alignment/viterbi/index.html
@@ -18,15 +18,15 @@
 
 
       <link rel="icon" href="../../assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>Viterbi Alignment - Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="../../assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="../../assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="../../assets/stylesheets/palette.06af60db.min.css">
@@ -2133,7 +2133,7 @@ <h2 id="run-viterbi-alignment-without-constructing-a-landscape">Run Viterbi Alig
     <script id="__config" type="application/json">{"base": "../..", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "../../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../../assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
 

diff --git a/api/builtins/imod/index.html b/api/builtins/imod/index.html
@@ -18,15 +18,15 @@
 
 
       <link rel="icon" href="../../../assets/images/favicon.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.38">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.42">
 
 
 
         <title>cylindra_builtins.imod - Cylindra</title>
 
 
 
-      <link rel="stylesheet" href="../../../assets/stylesheets/main.8c3ca2c6.min.css">
+      <link rel="stylesheet" href="../../../assets/stylesheets/main.0253249f.min.css">
 
 
         <link rel="stylesheet" href="../../../assets/stylesheets/palette.06af60db.min.css">
@@ -2101,6 +2101,11 @@ <h1 id="cylindra_builtinsimod">cylindra_builtins.imod</h1>
 
 
 
+
+
+
+
+
   <div class="doc doc-children">
 
 
@@ -2139,7 +2144,9 @@ <h4 id="cylindra_builtins.imod.export_project" class="doc doc-heading">
       </thead>
       <tbody>
           <tr class="doc-section-item">
-            <td><code>layer</code></td>
+            <td>
+                <code>layer</code>
+            </td>
             <td>
                   <code>MoleculesLayer</code>
             </td>
@@ -2153,7 +2160,9 @@ <h4 id="cylindra_builtins.imod.export_project" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>save_dir</code></td>
+            <td>
+                <code>save_dir</code>
+            </td>
             <td>
                   <code><span title="magicclass.types.Path">Path</span></code>
             </td>
@@ -2167,7 +2176,9 @@ <h4 id="cylindra_builtins.imod.export_project" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>template_path</code></td>
+            <td>
+                <code>template_path</code>
+            </td>
             <td>
                   <code><a class="autorefs autorefs-external" href="https://docs.python.org/3/library/stdtypes.html#str">str</a></code>
             </td>
@@ -2181,7 +2192,9 @@ <h4 id="cylindra_builtins.imod.export_project" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>mask_params</code></td>
+            <td>
+                <code>mask_params</code>
+            </td>
             <td>
                   <code><a class="autorefs autorefs-external" title="typing.Any" href="https://docs.python.org/3/library/typing.html#typing.Any">Any</a></code>
             </td>
@@ -2195,7 +2208,9 @@ <h4 id="cylindra_builtins.imod.export_project" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>project_name</code></td>
+            <td>
+                <code>project_name</code>
+            </td>
             <td>
                   <code><a class="autorefs autorefs-external" href="https://docs.python.org/3/library/stdtypes.html#str">str</a></code>
             </td>
@@ -2394,7 +2409,9 @@ <h4 id="cylindra_builtins.imod.load_molecules" class="doc doc-heading">
       </thead>
       <tbody>
           <tr class="doc-section-item">
-            <td><code>mod_path</code></td>
+            <td>
+                <code>mod_path</code>
+            </td>
             <td>
                   <code><span title="magicclass.types.Path">Path</span></code>
             </td>
@@ -2408,7 +2425,9 @@ <h4 id="cylindra_builtins.imod.load_molecules" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>ang_path</code></td>
+            <td>
+                <code>ang_path</code>
+            </td>
             <td>
                   <code><span title="magicclass.types.Path">Path</span></code>
             </td>
@@ -2422,7 +2441,9 @@ <h4 id="cylindra_builtins.imod.load_molecules" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>shift_mol</code></td>
+            <td>
+                <code>shift_mol</code>
+            </td>
             <td>
                   <code><a class="autorefs autorefs-external" href="https://docs.python.org/3/library/functions.html#bool">bool</a></code>
             </td>
@@ -2584,7 +2605,9 @@ <h4 id="cylindra_builtins.imod.save_molecules" class="doc doc-heading">
       </thead>
       <tbody>
           <tr class="doc-section-item">
-            <td><code>save_dir</code></td>
+            <td>
+                <code>save_dir</code>
+            </td>
             <td>
                   <code><span title="magicclass.types.Path">Path</span></code>
             </td>
@@ -2598,7 +2621,9 @@ <h4 id="cylindra_builtins.imod.save_molecules" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>layers</code></td>
+            <td>
+                <code>layers</code>
+            </td>
             <td>
                   <code>sequence of MoleculesLayer</code>
             </td>
@@ -2686,7 +2711,9 @@ <h4 id="cylindra_builtins.imod.save_splines" class="doc doc-heading">
       </thead>
       <tbody>
           <tr class="doc-section-item">
-            <td><code>save_path</code></td>
+            <td>
+                <code>save_path</code>
+            </td>
             <td>
                   <code><span title="magicclass.types.Path">Path</span></code>
             </td>
@@ -2700,7 +2727,9 @@ <h4 id="cylindra_builtins.imod.save_splines" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>interval</code></td>
+            <td>
+                <code>interval</code>
+            </td>
             <td>
                   <code><a class="autorefs autorefs-external" href="https://docs.python.org/3/library/functions.html#float">float</a></code>
             </td>
@@ -2906,7 +2935,7 @@ <h4 id="cylindra_builtins.imod.save_splines" class="doc doc-heading">
     <script id="__config" type="application/json">{"base": "../../..", "features": ["content.code.annotate", "content.code.copy", "navigation.sections", "navigation.indexes", "navigation.footer", "toc.follow", "search.suggest", "search.share"], "search": "../../../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../../../assets/javascripts/bundle.d6f25eb3.min.js"></script>
+      <script src="../../../assets/javascripts/bundle.83f73b43.min.js"></script>
 
         <script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>