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fix: commit renderd docs #391

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Feb 27, 2024
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fix: commit renderd docs #391

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b0a82d0
fix: commit renderd docs
jmbuhr Feb 27, 2024
e36fab8
chore(docs): render docs
github-actions[bot] Feb 27, 2024
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3 changes: 3 additions & 0 deletions .github/workflows/build-docs.yml
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Expand Up @@ -34,7 +34,10 @@ jobs:
commit_user_name: "github-actions[bot]"
commit_user_email: "github-actions[bot]@users.noreply.github.com"
commit_author: "github-actions[bot] <github-actions[bot]@users.noreply.github.com>"
file_pattern: "docs/ _inv/ _reference/ _freeze/"
push_options: "--force"
- uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: docs

2 changes: 1 addition & 1 deletion _reference/kmc.qmd
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Expand Up @@ -18,7 +18,7 @@ and because we have one reactant molecule

### KMCResult { #kimmdy.kmc.KMCResult }

`kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)`
`kmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)`

The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.

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16 changes: 8 additions & 8 deletions _reference/topology.atomic.qmd
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Expand Up @@ -26,8 +26,8 @@ See [gromacs manual](https://manual.gromacs.org/current/reference-manual/topolog
| [PositionRestraint](#kimmdy.topology.atomic.PositionRestraint) | Information about one position restraint. |
| [ResidueAtomSpec](#kimmdy.topology.atomic.ResidueAtomSpec) | Information about one atom in a residue |
| [ResidueBondSpec](#kimmdy.topology.atomic.ResidueBondSpec) | Information about one bond in a residue |
| [ResidueImproperSpec](#kimmdy.topology.atomic.ResidueImproperSpec) | Information about one imroper dihedral in a residue |
| [ResidueProperSpec](#kimmdy.topology.atomic.ResidueProperSpec) | Information about one imroper dihedral in a residue |
| [ResidueImproperSpec](#kimmdy.topology.atomic.ResidueImproperSpec) | Information about one improper dihedral in a residue |
| [ResidueProperSpec](#kimmdy.topology.atomic.ResidueProperSpec) | Information about one proper dihedral in a residue |
| [ResidueType](#kimmdy.topology.atomic.ResidueType) | Information about one residuetype from aminoacids.rtp |
| [Settle](#kimmdy.topology.atomic.Settle) | Information about one settles |

Expand Down Expand Up @@ -215,19 +215,19 @@ Information about one bond in a residue

### ResidueImproperSpec { #kimmdy.topology.atomic.ResidueImproperSpec }

`topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, q0, cq)`
`topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)`

Information about one imroper dihedral in a residue
Information about one improper dihedral in a residue

; atom1 atom2 atom3 atom4 q0 cq
; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)

### ResidueProperSpec { #kimmdy.topology.atomic.ResidueProperSpec }

`topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, q0)`
`topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)`

Information about one imroper dihedral in a residue
Information about one proper dihedral in a residue

; atom1 atom2 atom3 atom4 q0 cq
; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2

### ResidueType { #kimmdy.topology.atomic.ResidueType }

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2 changes: 1 addition & 1 deletion docs/_reference/kmc.html
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Expand Up @@ -511,7 +511,7 @@ <h2 class="anchored" data-anchor-id="classes">Classes</h2>
</table>
<section id="kimmdy.kmc.KMCResult" class="level3">
<h3 class="anchored" data-anchor-id="kimmdy.kmc.KMCResult">KMCResult</h3>
<p><code>kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)</code></p>
<p><code>kmc.KMCResult(recipe=field(default_factory=lambda: Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)</code></p>
<p>The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.</p>
<section id="attributes" class="level4">
<h4 class="anchored" data-anchor-id="attributes">Attributes</h4>
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16 changes: 8 additions & 8 deletions docs/_reference/topology.atomic.html
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Expand Up @@ -563,11 +563,11 @@ <h2 class="anchored" data-anchor-id="classes">Classes</h2>
</tr>
<tr class="odd">
<td><a href="#kimmdy.topology.atomic.ResidueImproperSpec">ResidueImproperSpec</a></td>
<td>Information about one imroper dihedral in a residue</td>
<td>Information about one improper dihedral in a residue</td>
</tr>
<tr class="even">
<td><a href="#kimmdy.topology.atomic.ResidueProperSpec">ResidueProperSpec</a></td>
<td>Information about one imroper dihedral in a residue</td>
<td>Information about one proper dihedral in a residue</td>
</tr>
<tr class="odd">
<td><a href="#kimmdy.topology.atomic.ResidueType">ResidueType</a></td>
Expand Down Expand Up @@ -689,15 +689,15 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueBondSpec">Res
</section>
<section id="kimmdy.topology.atomic.ResidueImproperSpec" class="level3">
<h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueImproperSpec">ResidueImproperSpec</h3>
<p><code>topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, q0, cq)</code></p>
<p>Information about one imroper dihedral in a residue</p>
<p>; atom1 atom2 atom3 atom4 q0 cq</p>
<p><code>topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)</code></p>
<p>Information about one improper dihedral in a residue</p>
<p>; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)</p>
</section>
<section id="kimmdy.topology.atomic.ResidueProperSpec" class="level3">
<h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueProperSpec">ResidueProperSpec</h3>
<p><code>topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, q0)</code></p>
<p>Information about one imroper dihedral in a residue</p>
<p>; atom1 atom2 atom3 atom4 q0 cq</p>
<p><code>topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)</code></p>
<p>Information about one proper dihedral in a residue</p>
<p>; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2</p>
</section>
<section id="kimmdy.topology.atomic.ResidueType" class="level3">
<h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueType">ResidueType</h3>
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2 changes: 1 addition & 1 deletion docs/guide/explanation/index.html
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Expand Up @@ -537,7 +537,7 @@ <h1 class="title">Explanations</h1>
</tr>
</thead>
<tbody class="list">
<tr data-index="0" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
<tr data-index="0" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
<td>
<a href="../../guide/explanation/topology.html" class="title listing-title">Visualize Topologies</a>
</td>
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10 changes: 5 additions & 5 deletions docs/guide/how-to/index.html
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Expand Up @@ -537,39 +537,39 @@ <h1 class="title">How-To</h1>
</tr>
</thead>
<tbody class="list">
<tr data-index="0" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
<tr data-index="0" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
<td>
<a href="../../guide/how-to/contribute.html" class="title listing-title">Contribute</a>
</td>
<td>
<span class="listing-author">&nbsp;</span>
</td>
</tr>
<tr data-index="1" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
<tr data-index="1" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
<td>
<a href="../../guide/how-to/examples.html" class="title listing-title">Examples</a>
</td>
<td>
<span class="listing-author">&nbsp;</span>
</td>
</tr>
<tr data-index="2" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
<tr data-index="2" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
<td>
<a href="../../guide/how-to/hcp.html" class="title listing-title">High Performance Computing</a>
</td>
<td>
<span class="listing-author">&nbsp;</span>
</td>
</tr>
<tr data-index="3" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
<tr data-index="3" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
<td>
<a href="../../guide/how-to/install-ml-plugins.html" class="title listing-title">Install Machine Learning Plugins</a>
</td>
<td>
<span class="listing-author">&nbsp;</span>
</td>
</tr>
<tr data-index="4" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
<tr data-index="4" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
<td>
<a href="../../guide/how-to/reaction_only.html" class="title listing-title">Reaction only</a>
</td>
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2 changes: 1 addition & 1 deletion docs/guide/tutorials/getting-started.html
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Expand Up @@ -603,7 +603,7 @@ <h2 class="anchored" data-anchor-id="setup-the-simulation">Setup the Simulation<
<p>Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin <code>hat_reaction</code> to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.</p>
<div id="app-./getting-started-files/vis-ala.molj" class="molstar-app"></div>
<script type="text/javascript">
molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutIsExpanded":false,"layoutShowLog":false,"emdbProvider":"rcsb","viewportShowAnimation":true,"viewportShowExpand":true,"layoutShowRemoteState":false,"pdbProvider":"rcsb","layoutShowControls":false,"viewportShowSelectionMode":false,"layoutShowSequence":false,"layoutShowLeftPanel":true}).then(viewer => {
molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutShowRemoteState":false,"layoutShowSequence":false,"layoutShowLog":false,"viewportShowAnimation":true,"viewportShowExpand":true,"layoutIsExpanded":false,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","layoutShowLeftPanel":true,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj"); });
</script>

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6 changes: 3 additions & 3 deletions docs/guide/tutorials/index.html
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Expand Up @@ -507,7 +507,7 @@ <h1 class="title">Tutorials</h1>

<div class="quarto-listing quarto-listing-container-default" id="listing-listing">
<div class="list quarto-listing-default">
<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="3">
<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1709047597701" data-listing-reading-time-sort="3">
<div class="thumbnail">
<p><a href="../../guide/tutorials/getting-started.html"> <img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"> </a></p>
</div>
Expand Down Expand Up @@ -539,7 +539,7 @@ <h3 class="no-anchor listing-title">
</a>
</div>
</div>
<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1708949801653" data-listing-reading-time-sort="6">
<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709047597697" data-listing-reading-time-sort="6">
<div class="thumbnail">
<p><a href="../../guide/tutorials/colbuilder.html"> <img src="../../guide/tutorials/img/colbuilder.png" class="thumbnail-image"> </a></p>
</div>
Expand Down Expand Up @@ -571,7 +571,7 @@ <h3 class="no-anchor listing-title">
</a>
</div>
</div>
<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1708949801657" data-listing-reading-time-sort="6">
<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709047597705" data-listing-reading-time-sort="6">
<div class="thumbnail">
<p><a href="../../guide/tutorials/write-plugin.html"> <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div> </a></p>
</div>
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