8.1.1.1.1.3. skimpy.analysis.modal¶

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Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

8.1.1.1.1.3.1. Submodules¶

8.1.1.1.1.3.1.1. skimpy.analysis.modal.modal_matrix

8.1.1.1.1.3.2. Classes¶

`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`FluxFunction`

8.1.1.1.1.3.3. Functions¶

modal_matrix(kmodel, concentration_dict, parameters[, ...])

This function computes the transformation matrix W as described in Chapter 4 of

8.1.1.1.1.3.4. Package Contents¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

class skimpy.FluxFunction(variables, expr, parameters, pool=None)¶

variables¶

expr¶

parameters¶

function¶

__call__(concentrations, parameters)¶

skimpy.modal_matrix(kmodel, concentration_dict, parameters, flux_modes=False, tolerance=1e-12)¶

This function computes the transformation matrix W as described in Chapter 4 of Heinrich, Reinhart, and Stefan Schuster. The regulation of cellular systems. Springer Science & Business Media, 2012.

The matrix W describes the composition of each pool variable X[i] whos dynamics are given by the eigenvalue lam[i] as a linear combination of the model variables S, which are concentrations.

Parameters:

kmodel – A skimpy.core.KineticModel with compiled mca functions
concentration_dict – A dict {‘variable_name’: value, }
parameters – A dict {‘param_name’: value, }

Returns: