plugins
plugins
Plugin base classes and basic instances thereof.
Also discovers and loads KIMMDY plugins.
Classes
| Name | Description |
|---|---|
| BasicParameterizer | reconstruct base force field state |
| ReactionPlugin | Reaction base class |
BasicParameterizer
plugins.BasicParameterizer(self, **kwargs)
reconstruct base force field state
Methods
| Name | Description |
|---|---|
| parameterize_topology | Do nothing, |
parameterize_topology
plugins.BasicParameterizer.parameterize_topology(current_topology, focus_nrs=None)
Do nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology
ReactionPlugin
plugins.ReactionPlugin(self, name, runmng)
Reaction base class
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
name |
str | Name of the reaction. | required |
runmng |
RunManager | RunManager instance. | required |
config |
Subconfig of the reaction (i.e. self.runmng.config.reactions.__getattribute__(self.name). Use this to access and pass settings to the reaction. |
required |
Methods
| Name | Description |
|---|---|
| get_recipe_collection | Get a RecipeCollection as a result of the reaction. |
get_recipe_collection
plugins.ReactionPlugin.get_recipe_collection(files)
Get a RecipeCollection as a result of the reaction.
This is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
files |
TaskFiles | TaskFiles instance | required |