KMatrix

class glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix[source]

Bases: object

A K-Matrix represents a first order differental system.

Attributes Summary

`label`	ModelProperty is an extension of the property decorator.
`matrix`	ModelProperty is an extension of the property decorator.

Methods Summary

`a_matrix`	The A matrix of the KMatrix.
`a_matrix_as_markdown`	Returns the A Matrix as markdown formatted table.
`a_matrix_general`	The A matrix of the KMatrix for a general model.
`a_matrix_sequential`	The A matrix of the KMatrix for a sequential model.
`as_dict`
`combine`	Creates a combined matrix.
`eigen`	Returns the eigenvalues and eigenvectors of the k matrix.
`empty`	Creates an empty K-Matrix.
`fill`
`from_dict`
`full`	The full representation of the KMatrix as numpy array.
`get_parameter_labels`
`involved_compartments`	A list of all compartments in the Matrix.
`is_sequential`	Returns true in the KMatrix represents an unibranched model.
`markdown`
`matrix_as_markdown`	Returns the KMatrix as markdown formatted table.
`rates`	The resulting rates of the matrix.
`reduced`	The reduced representation of the KMatrix as numpy array.
`validate`

Methods Documentation

a_matrix(compartments: list[str], initial_concentration: np.ndarray) → np.ndarray[source]

The A matrix of the KMatrix.

Parameters: initial_concentration – The initial concentration.

a_matrix_as_markdown(compartments: list[str], initial_concentration: np.ndarray) → MarkdownStr[source]

Returns the A Matrix as markdown formatted table.

Parameters: initial_concentration – The initial concentration.

a_matrix_general(compartments: list[str], initial_concentration: np.ndarray) → np.ndarray[source]

The A matrix of the KMatrix for a general model.

Parameters: initial_concentration – The initial concentration.

a_matrix_sequential(compartments: list[str]) → np.ndarray[source]

The A matrix of the KMatrix for a sequential model.

Parameters: initial_concentration – The initial concentration.

as_dict() → dict

combine(k_matrix: glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix) → glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix[source]

Creates a combined matrix.

When combining k-matrices km1 and km2 (km1.combine(km2)), entries in km1 will be overwritten by corresponding entries in km2.

Parameters: k_matrix – KMatrix to combine with.
Returns: The combined KMatrix.
Return type: combined

eigen(compartments: list[str]) → tuple[np.ndarray, np.ndarray][source]

Returns the eigenvalues and eigenvectors of the k matrix.

Parameters: compartments – The compartment order.

classmethod empty(label: str, compartments: list[str]) → KMatrix[source]

Creates an empty K-Matrix. Useful for combining.

Parameters

label – Label of the K-Matrix
compartments – A list of all compartments in the model.

fill(model: Model, parameters: ParameterGroup) → cls

classmethod from_dict(values: dict) → cls

full(compartments: list[str]) → np.ndarray[source]

The full representation of the KMatrix as numpy array.

Parameters: compartments – The compartment order.

get_parameter_labels() → list[str]

involved_compartments() → list[str][source]: A list of all compartments in the Matrix.

is_sequential(compartments: list[str], initial_concentration: np.ndarray) → bool[source]

Returns true in the KMatrix represents an unibranched model.

Parameters: initial_concentration – The initial concentration.

property label: model_property.glotaran_property_type

ModelProperty is an extension of the property decorator.

It adds convenience functions for meta programming model items.

markdown(all_parameters: ParameterGroup = None, initial_parameters: ParameterGroup = None) → MarkdownStr

property matrix: model_property.glotaran_property_type

ModelProperty is an extension of the property decorator.

It adds convenience functions for meta programming model items.

matrix_as_markdown(compartments: list[str] = None, fill_parameters: bool = False) → MarkdownStr[source]

Returns the KMatrix as markdown formatted table.

Parameters

compartments – (default = None) An optional list defining the desired order of compartments.
fill_parameters (bool) – (default = False) If true, the entries will be filled with the actual parameter values instead of labels.

rates(compartments: list[str], initial_concentration: np.ndarray) → np.ndarray[source]

The resulting rates of the matrix.

By definition, the eigenvalues of the compartmental model are negative and the rates are the negatives of the eigenvalues, thus the eigenvalues need to be multiplied with -1 to get rates with the correct sign.

Parameters

compartments (list[str]) – Names of compartment used to order the matrix.
initial_concentration (np.ndarray) – The initial concentration.

reduced(compartments: list[str]) → np.ndarray[source]

The reduced representation of the KMatrix as numpy array.

Parameters: compartments – The compartment order.

validate(model: Model, parameters: ParameterGroup | None = None) → list[str]