recipe
recipe
Contains the Reaction Recipe, RecipeStep and RecipeCollection.
Classes
| Name | Description |
|---|---|
| Bind | Change topology to form a bond |
| BondOperation | Handle a bond operation on the recipe step. |
| Break | Change topology to break a bond |
| CustomTopMod | A custom recipe step that can be used to define a custom topology modification. |
| Place | Change topology and/or coordinates to place an atom. |
| Recipe | A reaction path defined by one series of RecipeSteps. |
| RecipeCollection | A RecipeCollection encompasses a number of reaction paths. |
| RecipeStep | Base class for all RecipeSteps. |
| Relax | Start a relaxation MD. |
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 | The index of the first atom. zero-based, by default None | None |
atom_ix_2 |
int | The index of the second atom. zero-based, by default None | None |
atom_id_1 |
str | The ID of the first atom. one-based, by default None | None |
atom_id_2 |
str | The ID of the second atom. one-based, by default None | None |
BondOperation
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.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
atom_ix_1 |
int | The index of the first atom. zero-based, by default None | None |
atom_ix_2 |
int | The index of the second atom. zero-based, by default None | None |
atom_id_1 |
str | The ID of the first atom. one-based, by default None | None |
atom_id_2 |
str | The ID of the second atom. one-based, by default None | None |
Raises
| Type | Description |
|---|---|
| ValueError | If neither an index nor an ID is provided for any of the atoms. |
Notes
Internally, this class stores the atom indices and converts IDs to indices as needed.
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 | The index of the first atom. zero-based, by default None | None |
atom_ix_2 |
int | The index of the second atom. zero-based, by default None | None |
atom_id_1 |
str | The ID of the first atom. one-based, by default None | None |
atom_id_2 |
str | The ID of the second atom. one-based, by default None | None |
CustomTopMod
recipe.CustomTopMod(self, f)
A custom recipe step that can be used to define a custom topology modification.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
f |
Callable[[Topology], Topology] | A function that takes a Topology object and modifies it in place. | required |
Place
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[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 | Index of atom to place. 0-based. | None |
id_to_place |
str | Index of atom to place. 1-based | None |
Recipe
recipe.Recipe(self, recipe_steps, rates, timespans)
A reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
recipe_steps |
list[RecipeStep] | Single sequence of RecipeSteps to build product | required |
rates |
list[float] | Reaction rates corresponding 1:1 to timespans. | required |
timespans |
list[list[float, float]] | List of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame. | required |
Methods
| Name | Description |
|---|---|
| check_consistency | Run consistency checks for correct size of variables |
| combine_with | Combines this Recipe with another with the same RecipeSteps. |
check_consistency
recipe.Recipe.check_consistency()
Run consistency checks for correct size of variables
combine_with
recipe.Recipe.combine_with(other)
Combines this Recipe with another with the same RecipeSteps.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
other |
Recipe | required |
RecipeCollection
recipe.RecipeCollection(self, recipes)
A RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.
Returns
| Type | Description |
|---|---|
unique_recipes_ixs |
List of lists binning the old recipe indices and maps to the new recipes list. |
Methods
| Name | Description |
|---|---|
| aggregate_reactions | Combines reactions having the same sequence of RecipeSteps. |
| calc_cumprob | Calculate cumulative probability of all contained recipe steps. |
| calc_ratesum | Calculate the sum of rates over all timesteps |
| from_csv | Create a RecipeCollection object from a CSV file |
| plot | Plot reaction rates over time |
| to_csv | Write a ReactionResult as defined in the reaction module to a csv file |
aggregate_reactions
recipe.RecipeCollection.aggregate_reactions()
Combines reactions having the same sequence of RecipeSteps.
calc_cumprob
recipe.RecipeCollection.calc_cumprob()
Calculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.
calc_ratesum
recipe.RecipeCollection.calc_ratesum()
Calculate the sum of rates over all timesteps
Returns
| Type | Description |
|---|---|
boarders |
flat list containing times of rate changes marking the boarders of the windows |
rate_windows |
flat list containing all rates in between the boarders. Each window is orderd as in recipe_windows |
recipe_windows |
flat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows |
from_csv
recipe.RecipeCollection.from_csv(path)
Create a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None
plot
recipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)
Plot reaction rates over time
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
outfile |
Path | Where to save the plot, must have compatible suffix. | required |
highlight_r |
Recipe | Recipe to highlight, by default None | None |
highlight_t |
float | Time at which the reactions starts | None |
to_csv
recipe.RecipeCollection.to_csv(path, picked_recipe=None)
Write a ReactionResult as defined in the reaction module to a csv file
RecipeStep
recipe.RecipeStep()
Base class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str
Relax
recipe.Relax(self)
Start a relaxation MD.
The molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium.