fix: squiggly lines begone (#399)

address inconsistencies in types and make sure all code paths are covered

fix: discover correct gromacs data dir for gmx compiled from source

refactor: sort imports

refactor(recipe): make BondOperation and Place regular classes instead
of dataclasses

_reference/analysis.qmd

@@ -17,23 +17,25 @@ For command line usage, run `kimmdy-analysis -h`.
 | [plot_energy](#kimmdy.analysis.plot_energy) | Plot GROMACS energy for a KIMMDY run. |
 | [plot_rates](#kimmdy.analysis.plot_rates) | Plot rates of all possible reactions for each 'decide_recipe' step. |
 | [plot_runtime](#kimmdy.analysis.plot_runtime) | Plot runtime of all tasks. |
+| [radical_migration](#kimmdy.analysis.radical_migration) | Plot population of radicals for a KIMMDY run. |
 | [radical_population](#kimmdy.analysis.radical_population) | Plot population of radicals for a KIMMDY run. |
 | [reaction_participation](#kimmdy.analysis.reaction_participation) | Plot runtime of all tasks. |
 
 ### concat_traj { #kimmdy.analysis.concat_traj }
 
-`analysis.concat_traj(dir, filetype, steps, open_vmd=False)`
+`analysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)`
 
 Find and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.
 The concatenated trajectory is centered and pbc corrected.
 
 #### Parameters
 
-| Name       | Type                                                                    | Description                                                                                      | Default    |
-|------------|-------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|------------|
-| `dir`      | [str](`str`)                                                            | Directory to search for subdirectories                                                           | _required_ |
-| `steps`    | [Union](`typing.Union`)\[[list](`list`)\[[str](`str`)\], [str](`str`)\] | List of steps e.g. ["equilibrium", "production"]. Or a string "all" to return all subdirectories | _required_ |
-| `open_vmd` | [bool](`bool`)                                                          | Open concatenated trajectory in VMD                                                              | `False`    |
+| Name           | Type                                                                    | Description                                                                                      | Default    |
+|----------------|-------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------|------------|
+| `dir`          | [str](`str`)                                                            | Directory to search for subdirectories                                                           | _required_ |
+| `steps`        | [Union](`typing.Union`)\[[list](`list`)\[[str](`str`)\], [str](`str`)\] | List of steps e.g. ["equilibrium", "production"]. Or a string "all" to return all subdirectories | _required_ |
+| `open_vmd`     | [bool](`bool`)                                                          | Open concatenated trajectory in VMD                                                              | `False`    |
+| `output_group` | [Optional](`typing.Optional`)\[[str](`str`)\]                           | index group for output. Default is "Protein" for xtc and "System" for trr.                       | `None`     |
 
 ### entry_point_analysis { #kimmdy.analysis.entry_point_analysis }
 
@@ -129,6 +131,20 @@ Plot runtime of all tasks.
 | `datefmt`   | [str](`str`)   | Date format in the KIMMDY logfile   | _required_ |
 | `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False`    |
 
+### radical_migration { #kimmdy.analysis.radical_migration }
+
+`analysis.radical_migration(dirs, type='qualitative', cutoff=1)`
+
+Plot population of radicals for a KIMMDY run.
+
+#### Parameters
+
+| Name     | Type                           | Description                                                                                | Default         |
+|----------|--------------------------------|--------------------------------------------------------------------------------------------|-----------------|
+| `dirs`   | [list](`list`)\[[str](`str`)\] | KIMMDY run directories to be analysed.                                                     | _required_      |
+| `type`   | [str](`str`)                   | How to analyse radical migration. Available are 'qualitative','occurence' and 'min_rate'", | `'qualitative'` |
+| `cutoff` | [int](`int`)                   | Ignore migration between two atoms if it happened less often than the specified value.     | `1`             |
+
 ### radical_population { #kimmdy.analysis.radical_population }
 
 `analysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)`

_reference/coordinates.qmd

@@ -58,13 +58,13 @@ Merge one to two Dihedrals or -Types into a Dihedral in free-energy syntax
 
 ### merge_top_moleculetypes_slow_growth { #kimmdy.coordinates.merge_top_moleculetypes_slow_growth }
 
-`coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff, focus_nr=None)`
+`coordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)`
 
 Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation
 
 ### merge_top_slow_growth { #kimmdy.coordinates.merge_top_slow_growth }
 
-`coordinates.merge_top_slow_growth(topA, topB, focus_nr=None)`
+`coordinates.merge_top_slow_growth(topA, topB)`
 
 Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation.
 

_reference/recipe.qmd

@@ -20,35 +20,35 @@ Contains the Reaction Recipe, RecipeStep and RecipeCollection.
 
 ### Bind { #kimmdy.recipe.Bind }
 
-`recipe.Bind()`
+`recipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)`
 
 Change topology to form a bond
 
 #### Parameters
 
-| Name        | Type         | Description                                               | Default    |
-|-------------|--------------|-----------------------------------------------------------|------------|
-| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None  | _required_ |
-| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | _required_ |
-| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None      | _required_ |
-| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None     | _required_ |
+| Name        | Type         | Description                                               | Default   |
+|-------------|--------------|-----------------------------------------------------------|-----------|
+| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None  | `None`    |
+| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | `None`    |
+| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None      | `None`    |
+| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None     | `None`    |
 
 ### BondOperation { #kimmdy.recipe.BondOperation }
 
-`recipe.BondOperation(_atom_ix_1=field(init=False, repr=False, default=None), _atom_ix_2=field(init=False, repr=False, default=None))`
+`recipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)`
 
 Handle a bond operation on the recipe step.
 
-This class takes in either zero-based indices or one-base IDs for two atoms
+This class takes in either zero-based indices or one-base IDs for two atoms.
 
 #### Parameters
 
-| Name        | Type         | Description                                               | Default    |
-|-------------|--------------|-----------------------------------------------------------|------------|
-| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None  | _required_ |
-| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | _required_ |
-| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None      | _required_ |
-| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None     | _required_ |
+| Name        | Type         | Description                                               | Default   |
+|-------------|--------------|-----------------------------------------------------------|-----------|
+| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None  | `None`    |
+| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | `None`    |
+| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None      | `None`    |
+| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None     | `None`    |
 
 #### Raises
 
@@ -62,18 +62,18 @@ Internally, this class stores the atom indices and converts IDs to indices as ne
 
 ### Break { #kimmdy.recipe.Break }
 
-`recipe.Break()`
+`recipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)`
 
 Change topology to break a bond
 
 #### Parameters
 
-| Name        | Type         | Description                                               | Default    |
-|-------------|--------------|-----------------------------------------------------------|------------|
-| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None  | _required_ |
-| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | _required_ |
-| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None      | _required_ |
-| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None     | _required_ |
+| Name        | Type         | Description                                               | Default   |
+|-------------|--------------|-----------------------------------------------------------|-----------|
+| `atom_ix_1` | [int](`int`) | The index of the first atom. zero-based, by default None  | `None`    |
+| `atom_ix_2` | [int](`int`) | The index of the second atom. zero-based, by default None | `None`    |
+| `atom_id_1` | [str](`str`) | The ID of the first atom. one-based, by default None      | `None`    |
+| `atom_id_2` | [str](`str`) | The ID of the second atom. one-based, by default None     | `None`    |
 
 ### CustomTopMod { #kimmdy.recipe.CustomTopMod }
 
@@ -89,17 +89,19 @@ A custom recipe step that can be used to define a custom topology modification.
 
 ### Place { #kimmdy.recipe.Place }
 
-`recipe.Place(new_coords, _ix_to_place=field(init=False, repr=False, default=None))`
+`recipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)`
 
 Change topology and/or coordinates to place an atom.
 
+Either provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.
+
 #### Parameters
 
 | Name          | Type                                                                     | Description                                                                               | Default    |
 |---------------|--------------------------------------------------------------------------|-------------------------------------------------------------------------------------------|------------|
 | `new_coords`  | [tuple](`tuple`)\[[float](`float`), [float](`float`), [float](`float`)\] | New xyz coordinates for atom to place to. Valid for the end point of the recipe timespan. | _required_ |
-| `ix_to_place` | [int](`int`)                                                             | Index of atom to place. 0-based.                                                          | _required_ |
-| `id_to_place` | [str](`str`)                                                             | Index of atom to place. 1-based                                                           | _required_ |
+| `ix_to_place` | [int](`int`)                                                             | Index of atom to place. 0-based.                                                          | `None`     |
+| `id_to_place` | [str](`str`)                                                             | Index of atom to place. 1-based                                                           | `None`     |
 
 ### Recipe { #kimmdy.recipe.Recipe }
 
@@ -121,22 +123,9 @@ product state from the educt state.
 
 | Name | Description |
 | --- | --- |
-| [calc_averages](#kimmdy.recipe.Recipe.calc_averages) | Calulate average rates over some window size |
 | [check_consistency](#kimmdy.recipe.Recipe.check_consistency) | Run consistency checks for correct size of variables |
 | [combine_with](#kimmdy.recipe.Recipe.combine_with) | Combines this Recipe with another with the same RecipeSteps. |
 
-##### calc_averages { #kimmdy.recipe.Recipe.calc_averages }
-
-`recipe.Recipe.calc_averages(window_size)`
-
-Calulate average rates over some window size
-
-###### Parameters
-
-| Name          | Type         | Description                                                                   | Default    |
-|---------------|--------------|-------------------------------------------------------------------------------|------------|
-| `window_size` | [int](`int`) | Size of the window to average over, -1 to average over whole available range. | _required_ |
-
 ##### check_consistency { #kimmdy.recipe.Recipe.check_consistency }
 
 `recipe.Recipe.check_consistency()`

_reference/runmanager.qmd

@@ -82,6 +82,6 @@ one of IDLE, MD, REACTION, SETUP, DONE.
 
 ### get_existing_files { #kimmdy.runmanager.get_existing_files }
 
-`runmanager.get_existing_files(config, section='root')`
+`runmanager.get_existing_files(config)`
 
 Initialize latest_files with every existing file defined in config

docs/_reference/analysis.html

@@ -483,14 +483,18 @@ <h2 id="toc-title">On this page</h2>
   <ul class="collapse">
   <li><a href="#parameters-5" id="toc-parameters-5" class="nav-link" data-scroll-target="#parameters-5">Parameters</a></li>
   </ul></li>
-  <li><a href="#kimmdy.analysis.radical_population" id="toc-kimmdy.analysis.radical_population" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_population">radical_population</a>
+  <li><a href="#kimmdy.analysis.radical_migration" id="toc-kimmdy.analysis.radical_migration" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_migration">radical_migration</a>
   <ul class="collapse">
   <li><a href="#parameters-6" id="toc-parameters-6" class="nav-link" data-scroll-target="#parameters-6">Parameters</a></li>
   </ul></li>
-  <li><a href="#kimmdy.analysis.reaction_participation" id="toc-kimmdy.analysis.reaction_participation" class="nav-link" data-scroll-target="#kimmdy.analysis.reaction_participation">reaction_participation</a>
+  <li><a href="#kimmdy.analysis.radical_population" id="toc-kimmdy.analysis.radical_population" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_population">radical_population</a>
   <ul class="collapse">
   <li><a href="#parameters-7" id="toc-parameters-7" class="nav-link" data-scroll-target="#parameters-7">Parameters</a></li>
   </ul></li>
+  <li><a href="#kimmdy.analysis.reaction_participation" id="toc-kimmdy.analysis.reaction_participation" class="nav-link" data-scroll-target="#kimmdy.analysis.reaction_participation">reaction_participation</a>
+  <ul class="collapse">
+  <li><a href="#parameters-8" id="toc-parameters-8" class="nav-link" data-scroll-target="#parameters-8">Parameters</a></li>
+  </ul></li>
   </ul></li>
   </ul></li>
   </ul>
@@ -548,18 +552,22 @@ <h2 class="anchored" data-anchor-id="functions">Functions</h2>
 <td>Plot runtime of all tasks.</td>
 </tr>
 <tr class="odd">
-<td><a href="#kimmdy.analysis.radical_population">radical_population</a></td>
+<td><a href="#kimmdy.analysis.radical_migration">radical_migration</a></td>
 <td>Plot population of radicals for a KIMMDY run.</td>
 </tr>
 <tr class="even">
+<td><a href="#kimmdy.analysis.radical_population">radical_population</a></td>
+<td>Plot population of radicals for a KIMMDY run.</td>
+</tr>
+<tr class="odd">
 <td><a href="#kimmdy.analysis.reaction_participation">reaction_participation</a></td>
 <td>Plot runtime of all tasks.</td>
 </tr>
 </tbody>
 </table>
 <section id="kimmdy.analysis.concat_traj" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.analysis.concat_traj">concat_traj</h3>
-<p><code>analysis.concat_traj(dir, filetype, steps, open_vmd=False)</code></p>
+<p><code>analysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)</code></p>
 <p>Find and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.</p>
 <section id="parameters" class="level4">
 <h4 class="anchored" data-anchor-id="parameters">Parameters</h4>
@@ -591,6 +599,12 @@ <h4 class="anchored" data-anchor-id="parameters">Parameters</h4>
 <td>Open concatenated trajectory in VMD</td>
 <td><code>False</code></td>
 </tr>
+<tr class="even">
+<td><code>output_group</code></td>
+<td><a href="https://docs.python.org/3.10/library/typing.html#typing.Optional">Optional</a>[<a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a>]</td>
+<td>index group for output. Default is “Protein” for xtc and “System” for trr.</td>
+<td><code>None</code></td>
+</tr>
 </tbody>
 </table>
 </section>
@@ -812,12 +826,50 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
 </table>
 </section>
 </section>
+<section id="kimmdy.analysis.radical_migration" class="level3">
+<h3 class="anchored" data-anchor-id="kimmdy.analysis.radical_migration">radical_migration</h3>
+<p><code>analysis.radical_migration(dirs, type='qualitative', cutoff=1)</code></p>
+<p>Plot population of radicals for a KIMMDY run.</p>
+<section id="parameters-6" class="level4">
+<h4 class="anchored" data-anchor-id="parameters-6">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>dirs</code></td>
+<td><a href="https://docs.python.org/3.10/library/stdtypes.html#list">list</a>[<a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a>]</td>
+<td>KIMMDY run directories to be analysed.</td>
+<td><em>required</em></td>
+</tr>
+<tr class="even">
+<td><code>type</code></td>
+<td><a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a></td>
+<td>How to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,</td>
+<td><code>'qualitative'</code></td>
+</tr>
+<tr class="odd">
+<td><code>cutoff</code></td>
+<td><a href="https://docs.python.org/3.10/library/functions.html#int">int</a></td>
+<td>Ignore migration between two atoms if it happened less often than the specified value.</td>
+<td><code>1</code></td>
+</tr>
+</tbody>
+</table>
+</section>
+</section>
 <section id="kimmdy.analysis.radical_population" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.analysis.radical_population">radical_population</h3>
 <p><code>analysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)</code></p>
 <p>Plot population of radicals for a KIMMDY run.</p>
-<section id="parameters-6" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
+<section id="parameters-7" class="level4">
+<h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
 <table class="table">
 <thead>
 <tr class="header">
@@ -872,8 +924,8 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
 <h3 class="anchored" data-anchor-id="kimmdy.analysis.reaction_participation">reaction_participation</h3>
 <p><code>analysis.reaction_participation(dir, open_plot=False)</code></p>
 <p>Plot runtime of all tasks.</p>
-<section id="parameters-7" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
+<section id="parameters-8" class="level4">
+<h4 class="anchored" data-anchor-id="parameters-8">Parameters</h4>
 <table class="table">
 <thead>
 <tr class="header">