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chore(main): release 6.0.1 #357

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chore(main): release 6.0.1
github-actions[bot] Jan 3, 2024
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chore(docs): render docs
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7 changes: 7 additions & 0 deletions CHANGELOG.md
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# Changelog

## [6.0.1](https://github.com/hits-mbm-dev/kimmdy/compare/v6.0.0...v6.0.1) (2024-01-03)


### Documentation

* minor improvement ([111112e](https://github.com/hits-mbm-dev/kimmdy/commit/111112ebcbd3ef79e5a3fea7026c1df9b64402ce))

## [6.0.0](https://github.com/hits-mbm-dev/kimmdy/compare/v5.3.2...v6.0.0) (2024-01-03)


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12 changes: 7 additions & 5 deletions _reference/topology.topology.qmd
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Expand Up @@ -85,7 +85,7 @@ Assumptions:
| [break_bond](#kimmdy.topology.topology.Topology.break_bond) | Break bonds in topology homolytically. |
| [del_atom](#kimmdy.topology.topology.Topology.del_atom) | Deletes atom |
| [reindex_atomnrs](#kimmdy.topology.topology.Topology.reindex_atomnrs) | Reindex atom numbers in topology. |
| [update_partial_charges](#kimmdy.topology.topology.Topology.update_partial_charges) | Update the topology atom partial charges based on recipe_steps. |
| [update_partial_charges](#kimmdy.topology.topology.Topology.update_partial_charges) | Update the topology atom partial charges. |
| [validate_bond](#kimmdy.topology.topology.Topology.validate_bond) | Validates bond consistency between both atoms and top |

##### bind_bond { #kimmdy.topology.topology.Topology.bind_bond }
Expand Down Expand Up @@ -157,11 +157,13 @@ Returns a dict of all moleculetypes to their update maps (old -> new).

`topology.topology.Topology.update_partial_charges(recipe_steps)`

Update the topology atom partial charges based on recipe_steps.
Update the topology atom partial charges.

Update rules follow a simple assignment scheme that works well with grappa.
If fragments are created, their partial charges are kept integers. If previously
broken bonds are formed again, the original partial charges are restored
This function must be called after the recipe_steps are applied.
Changes are based on the recipe_steps. Update rules follow a simple
assignment scheme that works well with grappa. If fragments are created,
their partial charges are kept integers. If previously broken bonds are
formed again, the original partial charges are restored.

##### validate_bond { #kimmdy.topology.topology.Topology.validate_bond }

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23 changes: 23 additions & 0 deletions _reference/topology.utils.qmd
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Expand Up @@ -13,6 +13,7 @@
| [get_moleculetype_header](#kimmdy.topology.utils.get_moleculetype_header) | Get content of the header of a moleculetype from a topology dict. |
| [get_protein_section](#kimmdy.topology.utils.get_protein_section) | Get content of a section in the first moleculetype (protein) from a topology dict. |
| [get_reactive_section](#kimmdy.topology.utils.get_reactive_section) | Get content of a section in the Reactive moleculetype from a topology dict. |
| [get_residue_fragments](#kimmdy.topology.utils.get_residue_fragments) | Splits a residue into fragments after a bond has been broken. |
| [get_top_section](#kimmdy.topology.utils.get_top_section) | Get content of a section from a topology dict. |
| [is_not_solvent_or_ion](#kimmdy.topology.utils.is_not_solvent_or_ion) | Returns whether a moleculetype name is not solvent or ion. |
| [set_moleculetype_atomics](#kimmdy.topology.utils.set_moleculetype_atomics) | Set content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict. |
Expand Down Expand Up @@ -56,6 +57,28 @@ Get content of a section in the first moleculetype (protein) from a topology dic

Get content of a section in the Reactive moleculetype from a topology dict.

### get_residue_fragments { #kimmdy.topology.utils.get_residue_fragments }

`topology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)`

Splits a residue into fragments after a bond has been broken.

#### Parameters

| Name | Type | Description | Default |
|--------------|---------------------------------------------------------|------------------------------------------------------------------------------------------------------------------|------------|
| `top` | [Topology](`kimmdy.topology.topology.Topology`) | Topology | _required_ |
| `residue` | [list](`list`)\[[Atom](`kimmdy.topology.atomic.Atom`)\] | All atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond. | _required_ |
| `start1` | [Atom](`kimmdy.topology.atomic.Atom`) | First atom with broken bond | _required_ |
| `start2` | [Atom](`kimmdy.topology.atomic.Atom`) | Second atom with broken bond | _required_ |
| `iterations` | [int](`int`) | Max number of bonds from start atoms to be included when building fragmets, by default 20 | `20` |

#### Returns

| Type | Description |
|----------------------------------------------------------|----------------------------------|
| Two fragments, or one fragment and empty set in case the | residue did not change its size. |

### get_top_section { #kimmdy.topology.utils.get_top_section }

`topology.utils.get_top_section(top, name, moleculetype=None)`
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6 changes: 3 additions & 3 deletions docs/_reference/topology.topology.html
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Expand Up @@ -657,7 +657,7 @@ <h4 class="anchored" data-anchor-id="methods-1">Methods</h4>
</tr>
<tr class="odd">
<td><a href="#kimmdy.topology.topology.Topology.update_partial_charges">update_partial_charges</a></td>
<td>Update the topology atom partial charges based on recipe_steps.</td>
<td>Update the topology atom partial charges.</td>
</tr>
<tr class="even">
<td><a href="#kimmdy.topology.topology.Topology.validate_bond">validate_bond</a></td>
Expand Down Expand Up @@ -782,8 +782,8 @@ <h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.reindex_a
<section id="kimmdy.topology.topology.Topology.update_partial_charges" class="level5">
<h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.update_partial_charges">update_partial_charges</h5>
<p><code>topology.topology.Topology.update_partial_charges(recipe_steps)</code></p>
<p>Update the topology atom partial charges based on recipe_steps.</p>
<p>Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored</p>
<p>Update the topology atom partial charges.</p>
<p>This function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.</p>
</section>
<section id="kimmdy.topology.topology.Topology.validate_bond" class="level5">
<h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.validate_bond">validate_bond</h5>
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90 changes: 85 additions & 5 deletions docs/_reference/topology.utils.html
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Expand Up @@ -452,6 +452,11 @@ <h2 id="toc-title">On this page</h2>
<li><a href="#kimmdy.topology.utils.get_moleculetype_header" id="toc-kimmdy.topology.utils.get_moleculetype_header" class="nav-link" data-scroll-target="#kimmdy.topology.utils.get_moleculetype_header">get_moleculetype_header</a></li>
<li><a href="#kimmdy.topology.utils.get_protein_section" id="toc-kimmdy.topology.utils.get_protein_section" class="nav-link" data-scroll-target="#kimmdy.topology.utils.get_protein_section">get_protein_section</a></li>
<li><a href="#kimmdy.topology.utils.get_reactive_section" id="toc-kimmdy.topology.utils.get_reactive_section" class="nav-link" data-scroll-target="#kimmdy.topology.utils.get_reactive_section">get_reactive_section</a></li>
<li><a href="#kimmdy.topology.utils.get_residue_fragments" id="toc-kimmdy.topology.utils.get_residue_fragments" class="nav-link" data-scroll-target="#kimmdy.topology.utils.get_residue_fragments">get_residue_fragments</a>
<ul class="collapse">
<li><a href="#parameters" id="toc-parameters" class="nav-link" data-scroll-target="#parameters">Parameters</a></li>
<li><a href="#returns" id="toc-returns" class="nav-link" data-scroll-target="#returns">Returns</a></li>
</ul></li>
<li><a href="#kimmdy.topology.utils.get_top_section" id="toc-kimmdy.topology.utils.get_top_section" class="nav-link" data-scroll-target="#kimmdy.topology.utils.get_top_section">get_top_section</a></li>
<li><a href="#kimmdy.topology.utils.is_not_solvent_or_ion" id="toc-kimmdy.topology.utils.is_not_solvent_or_ion" class="nav-link" data-scroll-target="#kimmdy.topology.utils.is_not_solvent_or_ion">is_not_solvent_or_ion</a></li>
<li><a href="#kimmdy.topology.utils.set_moleculetype_atomics" id="toc-kimmdy.topology.utils.set_moleculetype_atomics" class="nav-link" data-scroll-target="#kimmdy.topology.utils.set_moleculetype_atomics">set_moleculetype_atomics</a></li>
Expand Down Expand Up @@ -502,26 +507,30 @@ <h2 class="anchored" data-anchor-id="functions">Functions</h2>
<td>Get content of a section in the Reactive moleculetype from a topology dict.</td>
</tr>
<tr class="even">
<td><a href="#kimmdy.topology.utils.get_residue_fragments">get_residue_fragments</a></td>
<td>Splits a residue into fragments after a bond has been broken.</td>
</tr>
<tr class="odd">
<td><a href="#kimmdy.topology.utils.get_top_section">get_top_section</a></td>
<td>Get content of a section from a topology dict.</td>
</tr>
<tr class="odd">
<tr class="even">
<td><a href="#kimmdy.topology.utils.is_not_solvent_or_ion">is_not_solvent_or_ion</a></td>
<td>Returns whether a moleculetype name is not solvent or ion.</td>
</tr>
<tr class="even">
<tr class="odd">
<td><a href="#kimmdy.topology.utils.set_moleculetype_atomics">set_moleculetype_atomics</a></td>
<td>Set content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.</td>
</tr>
<tr class="odd">
<tr class="even">
<td><a href="#kimmdy.topology.utils.set_protein_section">set_protein_section</a></td>
<td>Set content of a section in the first moleculetype (protein) from a topology dict.</td>
</tr>
<tr class="even">
<tr class="odd">
<td><a href="#kimmdy.topology.utils.set_reactive_section">set_reactive_section</a></td>
<td>Set content of a section in the first moleculetype (protein) from a topology dict.</td>
</tr>
<tr class="odd">
<tr class="even">
<td><a href="#kimmdy.topology.utils.set_top_section">set_top_section</a></td>
<td>Set content of a section from a topology dict.</td>
</tr>
Expand Down Expand Up @@ -554,6 +563,77 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.utils.get_reactive_section"
<p><code>topology.utils.get_reactive_section(top, name)</code></p>
<p>Get content of a section in the Reactive moleculetype from a topology dict.</p>
</section>
<section id="kimmdy.topology.utils.get_residue_fragments" class="level3">
<h3 class="anchored" data-anchor-id="kimmdy.topology.utils.get_residue_fragments">get_residue_fragments</h3>
<p><code>topology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)</code></p>
<p>Splits a residue into fragments after a bond has been broken.</p>
<section id="parameters" class="level4">
<h4 class="anchored" data-anchor-id="parameters">Parameters</h4>
<table class="table">
<thead>
<tr class="header">
<th>Name</th>
<th>Type</th>
<th>Description</th>
<th>Default</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>top</code></td>
<td><a href="../_reference/topology.topology.html#kimmdy.topology.topology.Topology">Topology</a></td>
<td>Topology</td>
<td><em>required</em></td>
</tr>
<tr class="even">
<td><code>residue</code></td>
<td><a href="https://docs.python.org/3.10/library/stdtypes.html#list">list</a>[<a href="../_reference/topology.atomic.html#kimmdy.topology.atomic.Atom">Atom</a>]</td>
<td>All atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.</td>
<td><em>required</em></td>
</tr>
<tr class="odd">
<td><code>start1</code></td>
<td><a href="../_reference/topology.atomic.html#kimmdy.topology.atomic.Atom">Atom</a></td>
<td>First atom with broken bond</td>
<td><em>required</em></td>
</tr>
<tr class="even">
<td><code>start2</code></td>
<td><a href="../_reference/topology.atomic.html#kimmdy.topology.atomic.Atom">Atom</a></td>
<td>Second atom with broken bond</td>
<td><em>required</em></td>
</tr>
<tr class="odd">
<td><code>iterations</code></td>
<td><a href="https://docs.python.org/3.10/library/functions.html#int">int</a></td>
<td>Max number of bonds from start atoms to be included when building fragmets, by default 20</td>
<td><code>20</code></td>
</tr>
</tbody>
</table>
</section>
<section id="returns" class="level4">
<h4 class="anchored" data-anchor-id="returns">Returns</h4>
<table class="table">
<colgroup>
<col style="width: 63%">
<col style="width: 36%">
</colgroup>
<thead>
<tr class="header">
<th>Type</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>Two fragments, or one fragment and empty set in case the</td>
<td>residue did not change its size.</td>
</tr>
</tbody>
</table>
</section>
</section>
<section id="kimmdy.topology.utils.get_top_section" class="level3">
<h3 class="anchored" data-anchor-id="kimmdy.topology.utils.get_top_section">get_top_section</h3>
<p><code>topology.utils.get_top_section(top, name, moleculetype=None)</code></p>
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2 changes: 1 addition & 1 deletion docs/guide/explanation/index.html
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Expand Up @@ -531,7 +531,7 @@ <h1 class="title">Explanations</h1>
</tr>
</thead>
<tbody class="list">
<tr data-index="0" data-listing-file-modified-sort="1703005998016" 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="1704279185249" 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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8 changes: 4 additions & 4 deletions docs/guide/how-to/index.html
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Expand Up @@ -531,31 +531,31 @@ <h1 class="title">How-To</h1>
</tr>
</thead>
<tbody class="list">
<tr data-index="0" data-listing-file-modified-sort="1703005998016" 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="1704279185249" 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="1703005998016" 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="1704279185249" 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="1703005998016" 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="1704279185249" 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="1703005998016" 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="1704279185249" 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>
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15 changes: 14 additions & 1 deletion docs/guide/tutorials/getting-started.html
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Expand Up @@ -534,6 +534,19 @@ <h3 class="anchored" data-anchor-id="prerequisites">Prerequisites</h3>
<ul>
<li><code>plumed</code>-patched version of <code>gromacs</code> (for the homolysis reaction).</li>
</ul>
<div class="callout callout-style-simple callout-tip callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">

</div>
</div>
<div class="callout-body-container callout-body">
<p>If you plan to use our machine-learning plugins, take a look at the <a href="../../guide/how-to/install-ml-plugins.html">full installation instruction</a></p>
</div>
</div>
<p>Let’s first create a directory and a virtual environment for <code>kimmdy</code>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> kimmdy-tutorial</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> kimmdy-tutorial</span>
Expand Down Expand Up @@ -584,7 +597,7 @@ <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", {"layoutShowLog":false,"layoutShowRemoteState":false,"layoutShowLeftPanel":true,"viewportShowExpand":true,"viewportShowAnimation":true,"emdbProvider":"rcsb","layoutShowSequence":false,"layoutIsExpanded":false,"pdbProvider":"rcsb","viewportShowSelectionMode":false,"layoutShowControls":false}).then(viewer => {
molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutIsExpanded":false,"viewportShowExpand":true,"emdbProvider":"rcsb","layoutShowRemoteState":false,"layoutShowLeftPanel":true,"pdbProvider":"rcsb","layoutShowSequence":false,"viewportShowAnimation":true,"layoutShowLog":false,"layoutShowControls":false,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj"); });
</script>

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