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 resulting A matrix of the KMatrix.
`a_matrix_as_markdown`	Returns the A Matrix as markdown formatted table.
`a_matrix_non_unibranch`	The resulting A matrix of the KMatrix for a non-unibranched model.
`a_matrix_unibranch`	The resulting A matrix of the KMatrix for an unibranched 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.
`involved_compartments`	A list of all compartments in the Matrix.
`is_unibranched`	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(initial_concentration: glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration) → numpy.ndarray[source]

The resulting A matrix of the KMatrix.

Parameters: initial_concentration – The initial concentration.

a_matrix_as_markdown(initial_concentration: glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration) → glotaran.utils.ipython.MarkdownStr[source]

Returns the A Matrix as markdown formatted table.

Parameters: initial_concentration – The initial concentration.

a_matrix_non_unibranch(initial_concentration: glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration) → numpy.ndarray[source]

The resulting A matrix of the KMatrix for a non-unibranched model.

Parameters: initial_concentration – The initial concentration.

a_matrix_unibranch(initial_concentration: glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration) → numpy.ndarray[source]

The resulting A matrix of the KMatrix for an unibranched 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.

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

is_unibranched(initial_concentration: glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration) → 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(initial_concentration: glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration) → numpy.ndarray[source]

The resulting rates of the matrix.

Parameters: initial_concentration – 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]