KMatrix¶

class glotaran.builtin.models.kinetic_image.k_matrix.KMatrix[source]¶

Bases: object

A K-Matrix represents a first order differental system.

Attributes Summary

`label`
`matrix`

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.
`combine`	Creates a combined matrix.
`eigen`	Returns the eigenvalues and eigenvectors of the k matrix.
`empty`	Creates an empty K-Matrix.
`fill`	Returns a copy of the {cls._name} instance with all members which are Parameters are replaced by the value of the corresponding parameter in the parameter group.
`from_dict`
`from_list`
`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.
`matrix_as_markdown`	Returns the KMatrix as markdown formatted table.
`mprint`
`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.models.kinetic_image.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.models.kinetic_image.initial_concentration.InitialConcentration) → str [source]¶

Returns the A Matrix as markdown formatted table.

Parameters: initial_concentration – The initial concentration.

a_matrix_non_unibranch(initial_concentration: glotaran.builtin.models.kinetic_image.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.models.kinetic_image.initial_concentration.InitialConcentration) → numpy.array[source]¶

The resulting A matrix of the KMatrix for an unibranched model.

Parameters: initial_concentration – The initial concentration.

combine(k_matrix: glotaran.builtin.models.kinetic_image.k_matrix.KMatrix) → glotaran.builtin.models.kinetic_image.k_matrix.KMatrix [source]¶

Creates a combined matrix.

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¶

Returns a copy of the {cls._name} instance with all members which are Parameters are replaced by the value of the corresponding parameter in the parameter group.

Parameters

model – A glotaran model.
parameter (ParameterGroup) – The parameter group to fill from.

classmethod from_dict(values: dict) → cls¶

classmethod from_list(values: list) → 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.models.kinetic_image.initial_concentration.InitialConcentration) → bool [source]¶

Returns true in the KMatrix represents an unibranched model.

Parameters: initial_concentration – The initial concentration.

property label¶

property matrix¶

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

mprint(parameters: ParameterGroup = None, initial_parameters: ParameterGroup = None) → str ¶

rates(initial_concentration: glotaran.builtin.models.kinetic_image.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=None) → list[str]¶