8.1.1.1.1.4. skimpy.analysis.ode¶

[———]

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.

8.1.1.1.1.4.1. Submodules¶

8.1.1.1.1.4.2. Attributes¶

`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`EPSILON`

8.1.1.1.1.4.3. Classes¶

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

8.1.1.1.1.4.4. Functions¶

`iterable_to_tabdict`(iterable[, use_name])	Takes the items from an iterable and puts them in a TabDict, indexed by the
`join_dicts`(dicts)
`make_ode_fun`(kinetic_model, sim_type[, pool, ...])
`make_flux_fun`(kinetic_model, sim_type)
`make_gamma_fun`(kinetic_model)	Return a function that calculates the thermodynamic displacement for
`make_expressions`(variables, all_flux_expr[, ...])
`make_expresson_single_var`(input)
`get_expressions_from_model`(kinetic_model, sim_type[, ...])
`make_cython_function`(symbols, expressions[, quiet, ...])
`make_cython_function`(symbols, expressions[, quiet, ...])
`robust_index`(in_var)	Indexing can be done with symbols or strings representing the symbol,
`sample_initial_concentrations`(kmodel, ...[, ...])
`create_linear_model`(A, rhs, variables[, lower_bound, ...])

8.1.1.1.1.4.5. Package Contents¶

class skimpy.ODEFunction(model, variables, expressions, parameters, pool=None, with_time=False, custom_ode_update=None)¶

variables¶

expressions¶

model¶

with_time = False¶

custom_ode_update = None¶

_parameters¶

function¶

property parameters¶

get_params()¶

__call__(t, y, ydot)¶

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

variables¶

expr¶

parameters¶

function¶

__call__(concentrations, parameters)¶

class skimpy.GammaFunction(variables, expr, parameters, pool=None)¶: Bases: skimpy.analysis.ode.flux_fun.FluxFunction

skimpy.iterable_to_tabdict(iterable, use_name=True)¶

Takes the items from an iterable and puts them in a TabDict, indexed by the elements’ .name property

Parameters:: iterable
Returns:

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)¶

skimpy.join_dicts(dicts)¶

skimpy.make_ode_fun(kinetic_model, sim_type, pool=None, custom_ode_update=None)¶

Parameters:

kinetic_model
sim_type

Returns:

skimpy.make_flux_fun(kinetic_model, sim_type)¶