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Clean modify top api (#378)
* fix: modify_top: sync python and cmd api --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
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‎_reference/analysis.qmd

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| [plot_rates](#kimmdy.analysis.plot_rates) | Plot rates of all possible reactions for each 'decide_recipe' step. |
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| [plot_runtime](#kimmdy.analysis.plot_runtime) | Plot runtime of all tasks. |
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| [radical_population](#kimmdy.analysis.radical_population) | Plot population of radicals for a KIMMDY run. |
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| [reaction_participation](#kimmdy.analysis.reaction_participation) | Plot runtime of all tasks. |
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### concat_traj { #kimmdy.analysis.concat_traj }
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| `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. Default is "all". | `'all'` |
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| `select_atoms` | [str](`str`) | Atoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax) | `'protein'` |
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| `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False` |
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| `open_vmd` | [bool](`bool`) | Open a pdb in VMD with the radical occupation as B-factors. | `False` |
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| `open_vmd` | [bool](`bool`) | Open a pdb in VMD with the radical occupation as B-factors. | `False` |
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### reaction_participation { #kimmdy.analysis.reaction_participation }
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`analysis.reaction_participation(dir, open_plot=False)`
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Plot runtime of all tasks.
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#### Parameters
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| Name | Type | Description | Default |
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|-------------|----------------|-------------------------------------|------------|
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| `dir` | [str](`str`) | Directory of KIMMDY run | _required_ |
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| `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False` |

‎_reference/tools.qmd

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### modify_top { #kimmdy.tools.modify_top }
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`tools.modify_top(topology, out, parameterize, removeH, gro, residuetypes, radicals)`
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`tools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)`
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Modify topology in various ways.
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#### Parameters
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| Name | Type | Description | Default |
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|----------------|-----------------------------------------------------------------|--------------------------------------------------------------------------------------------|------------|
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| `topology` | [str](`str`) | Path to GROMACS top file | _required_ |
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| `out` | [str](`str`) | Output topology file path, stem also used for gro. Can be relative to cwd. | _required_ |
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| `parameterize` | [bool](`bool`) | Parameterize topology with grappa after removing hydrogen | _required_ |
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| `removeH` | [Optional](`typing.Optional`)\[[list](`list`)\[[int](`int`)\]\] | Remove one or more hydrogens by atom nrs in the top file. One based. | _required_ |
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| `gro` | [Optional](`typing.Optional`)\[[str](`str`)\] | GROMACS gro input file. Updates structure when deleting H. Output named like top output. | _required_ |
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| `residuetypes` | [Optional](`typing.Optional`)\[[str](`str`)\] | GROMACS style residuetypes file. Necessary for parameterization with non-amber atom types. | _required_ |
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| `radicals` | [str](`str`) | Radicals in the system PRIOR to removing hydrogens with the removeH option. | _required_ |
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| Name | Type | Description | Default |
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|--------------------|-----------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
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| `topology` | [str](`str`) | Path to GROMACS top file | _required_ |
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| `out` | [str](`str`) | Output topology file path, stem also used for gro. Can be relative to cwd. | _required_ |
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| `parameterize` | [bool](`bool`) | Parameterize topology with grappa after removing hydrogen | `False` |
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| `removeH` | [Optional](`typing.Optional`)\[[list](`list`)\[[int](`int`)\]\] | Remove one or more hydrogens by atom nrs in the top file. One based. | `None` |
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| `gro` | [Optional](`typing.Optional`)\[[str](`str`)\] | GROMACS gro input file. Updates structure when deleting H. Output named like top output. | `None` |
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| `residuetypes` | [Optional](`typing.Optional`)\[[str](`str`)\] | GROMACS style residuetypes file. Necessary for parameterization with non-amber atom types. | `None` |
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| `radicals` | [Optional](`typing.Optional`)\[[list](`list`)\[[int](`int`)\]\] | Radicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies. | `None` |
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| `search_amber_rad` | [bool](`bool`) | Automatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary. | `True` |
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### top_to_graph { #kimmdy.tools.top_to_graph }
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‎docs/_reference/analysis.html

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<span class="menu-text">Reaction only</span></a>
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<ul class="collapse">
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<li><a href="#parameters-6" id="toc-parameters-6" class="nav-link" data-scroll-target="#parameters-6">Parameters</a></li>
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</ul></li>
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<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>
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<ul class="collapse">
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<li><a href="#parameters-7" id="toc-parameters-7" class="nav-link" data-scroll-target="#parameters-7">Parameters</a></li>
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</ul></li>
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<td><a href="#kimmdy.analysis.radical_population">radical_population</a></td>
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<td>Plot population of radicals for a KIMMDY run.</td>
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</tr>
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<tr class="even">
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<td><a href="#kimmdy.analysis.reaction_participation">reaction_participation</a></td>
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<td>Plot runtime of all tasks.</td>
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</tr>
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<section id="kimmdy.analysis.concat_traj" class="level3">
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</section>
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<section id="kimmdy.analysis.reaction_participation" class="level3">
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<h3 class="anchored" data-anchor-id="kimmdy.analysis.reaction_participation">reaction_participation</h3>
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<p><code>analysis.reaction_participation(dir, open_plot=False)</code></p>
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<p>Plot runtime of all tasks.</p>
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<section id="parameters-7" class="level4">
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<h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
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<table class="table">
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<thead>
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<th>Name</th>
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<th>Type</th>
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<th>Description</th>
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<td><code>dir</code></td>
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<td><a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a></td>
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<td>Directory of KIMMDY run</td>
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<td><em>required</em></td>
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<td><code>open_plot</code></td>
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<td><a href="https://docs.python.org/3.10/library/functions.html#bool">bool</a></td>
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<td>Open plot in default system viewer.</td>
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<td><code>False</code></td>
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