8.1.1.1.1.4. `skimpy.analysis.ode`¶

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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.

8.1.1.1.1.4.1. Submodules¶

8.1.1.1.1.4.2. Package Contents¶

8.1.1.1.1.4.2.1. 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`

8.1.1.1.1.4.2.2. Functions¶

`iterable_to_tabdict`(iterable, use_name=True)	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=None, custom_ode_update=None)	param kinetic_model
`make_flux_fun`(kinetic_model, sim_type)	param kinetic_model
`make_gamma_fun`(kinetic_model)	Return a function that calculates the thermodynamic displacement for
`make_expressions`(variables, all_flux_expr, volume_ratios=None, pool=None)
`make_expresson_single_var`(input)
`get_expressions_from_model`(kinetic_model, sim_type, medium_symbols=None, biomass_symbol=None)
`make_cython_function`(symbols, expressions, quiet=True, simplify=True, optimize=False, pool=None)
`make_cython_function`(symbols, expressions, quiet=True, simplify=True, optimize=False, pool=None)
`robust_index`(in_var)	Indexing can be done with symbols or strings representing the symbol,
`sample_initial_concentrations`(kmodel, reference_concentrations, lower_bound=0.8, upper_bound=1.2, n_samples=10, absolute_bounds=False)
`create_linear_model`(A, rhs, variables, lower_bound=None, upper_bound=None)

8.1.1.1.1.4.2.3. 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`

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

property parameters(self)¶

get_params(self)¶

__call__(self, t, y, ydot)¶

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

__call__(self, 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__(self)¶: __dir__() -> list default dir() implementation

__getattr__(self, attr)¶

iloc(self, 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)¶