graeter-group · KRiedmiller · Mar 22, 2024 · Mar 21, 2024 · Mar 22, 2024 · Mar 22, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,23 @@
 # Changelog
 
+## [6.4.1](https://github.com/hits-mbm-dev/kimmdy/compare/v6.4.0...v6.4.1) (2024-03-21)
+
+
+### Bug Fixes
+
+* allow reactions with no chosen recipe ([171c7e1](https://github.com/hits-mbm-dev/kimmdy/commit/171c7e1df818b8da71198a99e9dbcb0738b7f800))
+* colormap normalization ([#415](https://github.com/hits-mbm-dev/kimmdy/issues/415)) ([1238397](https://github.com/hits-mbm-dev/kimmdy/commit/12383974b1930af38a89ccdcd7b9d1f5c74ed60a))
+* energy labels sorted correctly ([855272f](https://github.com/hits-mbm-dev/kimmdy/commit/855272f44f965d9240abd2cb529449597badd8da))
+* expose arrhenius equation in morse function and fix wrong default value ([#417](https://github.com/hits-mbm-dev/kimmdy/issues/417)) ([58c47b3](https://github.com/hits-mbm-dev/kimmdy/commit/58c47b31dda698f6005e52e5fc8cf4e7736a5774))
+* plot_energy now handles numbers in terms correctly. ([c16888b](https://github.com/hits-mbm-dev/kimmdy/commit/c16888bf6fc08715c0819638a2869fd435831d90))
+* remove pd warning ([abc4afe](https://github.com/hits-mbm-dev/kimmdy/commit/abc4afe11fa0ddb5e35bfdd7889afe1114c0a576))
+* runmanager now handles empty kmcresults correctly. ([c94bd2a](https://github.com/hits-mbm-dev/kimmdy/commit/c94bd2a2a92765a4e2d88496ea377725fd11d3b5))
+
+
+### Documentation
+
+* fix docstring ([9572791](https://github.com/hits-mbm-dev/kimmdy/commit/9572791ef4e3375bcb82def24c9cf1af2d7c4678))
+
 ## [6.4.0](https://github.com/hits-mbm-dev/kimmdy/compare/v6.3.0...v6.4.0) (2024-03-07)
 
 

diff --git a/_reference/utils.qmd b/_reference/utils.qmd
@@ -95,7 +95,7 @@ Run command in shell and capture stdout.
 
 ### morse_transition_rate { #kimmdy.utils.morse_transition_rate }
 
-`utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)`
+`utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)`
 
 Calculates reaction rate constant for a bond breaking event.
 
@@ -108,14 +108,14 @@ The calculation should be according to the derivation in the original KIMMDY pap
 
 #### Parameters
 
-| Name           | Type                               | Description                                                                                                                                                               | Default    |
-|----------------|------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `r_curr`       | [list](`list`)\[[float](`float`)\] | Bond distances for a single bond, typically from a time series.                                                                                                           | _required_ |
-| `r_0`          | [float](`float`)                   | Equilibrium bond length of the bond.                                                                                                                                      | _required_ |
-| `dissociation` |                                    | Dissociation energy of the bond.                                                                                                                                          | _required_ |
-| `k_f`          | [float](`float`)                   | Spring constant of the bond.                                                                                                                                              | _required_ |
-| `k_0`          | [float](`float`)                   | Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m). | `0.288`    |
-| `kT`           | [float](`float`)                   | Constant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.                                                                                         | `2.479`    |
+| Name               | Type                               | Description                                                                                                                                                               | Default    |
+|--------------------|------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
+| `r_curr`           | [list](`list`)\[[float](`float`)\] | Bond distances for a single bond, typically from a time series.                                                                                                           | _required_ |
+| `r_0`              | [float](`float`)                   | Equilibrium bond length of the bond.                                                                                                                                      | _required_ |
+| `dissociation`     |                                    | Dissociation energy of the bond.                                                                                                                                          | _required_ |
+| `k_f`              | [float](`float`)                   | Spring constant of the bond.                                                                                                                                              | _required_ |
+| `frequency_factor` | [float](`float`)                   | Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m). | `0.288`    |
+| `temperature`      | [float](`float`)                   | Temperature for the Arrhenius equation in GROMACS units.                                                                                                                  | `300`      |
 
 ### run_gmx { #kimmdy.utils.run_gmx }
 

diff --git a/docs/_reference/utils.html b/docs/_reference/utils.html
@@ -692,7 +692,7 @@ <h3 class="anchored" data-anchor-id="kimmdy.utils.get_shell_stdout">get_shell_st
 </section>
 <section id="kimmdy.utils.morse_transition_rate" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.utils.morse_transition_rate">morse_transition_rate</h3>
-<p><code>utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, k_0=0.288, kT=2.479)</code></p>
+<p><code>utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)</code></p>
 <p>Calculates reaction rate constant for a bond breaking event.</p>
 <p>Uses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.</p>
 <p>The calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786</p>
@@ -733,16 +733,16 @@ <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
 <td><em>required</em></td>
 </tr>
 <tr class="odd">
-<td><code>k_0</code></td>
+<td><code>frequency_factor</code></td>
 <td><a href="https://docs.python.org/3.10/library/functions.html#float">float</a></td>
 <td>Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).</td>
 <td><code>0.288</code></td>
 </tr>
 <tr class="even">
-<td><code>kT</code></td>
+<td><code>temperature</code></td>
 <td><a href="https://docs.python.org/3.10/library/functions.html#float">float</a></td>
-<td>Constant in the Arrhenius equation in GROMACS units [kJ mol-1], default for 310K.</td>
-<td><code>2.479</code></td>
+<td>Temperature for the Arrhenius equation in GROMACS units.</td>
+<td><code>300</code></td>
 </tr>
 </tbody>
 </table>

diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html
@@ -537,7 +537,7 @@ <h1 class="title">Explanations</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1710844940646" 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="1711113090438" 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>

diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html
@@ -537,39 +537,39 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1710844940646" 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="1711113090438" 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="1710844940646" 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="1711113090438" 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="1710844940646" 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="1711113090438" 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="1710844940646" 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="1711113090438" 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="1710844940646" 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="1711113090438" 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>

diff --git a/docs/guide/tutorials/getting-started.html b/docs/guide/tutorials/getting-started.html
@@ -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", {"viewportShowExpand":true,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowLeftPanel":true,"viewportShowSelectionMode":false,"layoutIsExpanded":false,"layoutShowRemoteState":false,"layoutShowLog":false,"layoutShowSequence":false}).then(viewer => {
+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutShowLog":false,"layoutShowSequence":false,"emdbProvider":"rcsb","layoutIsExpanded":false,"layoutShowRemoteState":false,"layoutShowControls":false,"viewportShowSelectionMode":false,"viewportShowAnimation":true,"viewportShowExpand":true,"layoutShowLeftPanel":true,"pdbProvider":"rcsb"}).then(viewer => {
     viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj");    });
     </script>
 

diff --git a/docs/guide/tutorials/index.html b/docs/guide/tutorials/index.html
@@ -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="1710844940650" data-listing-reading-time-sort="3">
+<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1711113090442" 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>
@@ -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="1710844940650" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1711113090438" 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>
@@ -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="1710844940654" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1711113090446" 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>