skimpy.analysis.ode =================== .. py:module:: skimpy.analysis.ode .. autoapi-nested-parse:: .. module:: skimpy :platform: Unix, Windows :synopsis: Simple Kinetic Models in Python .. moduleauthor:: SKiMPy team [---------] Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB), Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland 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. Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/skimpy/analysis/ode/flux_fun/index /autoapi/skimpy/analysis/ode/gamma_fun/index /autoapi/skimpy/analysis/ode/ode_fun/index /autoapi/skimpy/analysis/ode/sample_concentrations/index /autoapi/skimpy/analysis/ode/symbolic_jacobian_fun/index /autoapi/skimpy/analysis/ode/utils/index Attributes ---------- .. autoapisummary:: skimpy.analysis.ode.QSSA skimpy.analysis.ode.TQSSA skimpy.analysis.ode.MCA skimpy.analysis.ode.ODE skimpy.analysis.ode.ELEMENTARY skimpy.analysis.ode.NUMERICAL skimpy.analysis.ode.SYMBOLIC skimpy.analysis.ode.NET skimpy.analysis.ode.SPLIT skimpy.analysis.ode.PARAMETER skimpy.analysis.ode.VARIABLE skimpy.analysis.ode.KCAL skimpy.analysis.ode.KJ skimpy.analysis.ode.JOULE skimpy.analysis.ode.WATER_FORMULA skimpy.analysis.ode.EPSILON Classes ------- .. autoapisummary:: skimpy.analysis.ode.ODEFunction skimpy.analysis.ode.FluxFunction skimpy.analysis.ode.GammaFunction skimpy.analysis.ode.TabDict skimpy.analysis.ode.FluxFunction skimpy.analysis.ode.TabDict skimpy.analysis.ode.ODEFunction Functions --------- .. autoapisummary:: skimpy.analysis.ode.iterable_to_tabdict skimpy.analysis.ode.join_dicts skimpy.analysis.ode.make_ode_fun skimpy.analysis.ode.make_flux_fun skimpy.analysis.ode.make_gamma_fun skimpy.analysis.ode.make_expressions skimpy.analysis.ode.make_expresson_single_var skimpy.analysis.ode.get_expressions_from_model skimpy.analysis.ode.make_cython_function skimpy.analysis.ode.make_cython_function skimpy.analysis.ode.robust_index skimpy.analysis.ode.sample_initial_concentrations skimpy.analysis.ode.create_linear_model Package Contents ---------------- .. py:class:: ODEFunction(model, variables, expressions, parameters, pool=None, with_time=False, custom_ode_update=None) .. py:attribute:: variables .. py:attribute:: expressions .. py:attribute:: model .. py:attribute:: with_time :value: False .. py:attribute:: custom_ode_update :value: None .. py:attribute:: _parameters .. py:attribute:: function .. py:property:: parameters .. py:method:: get_params() .. py:method:: __call__(t, y, ydot) .. py:class:: FluxFunction(variables, expr, parameters, pool=None) .. py:attribute:: variables .. py:attribute:: expr .. py:attribute:: parameters .. py:attribute:: function .. py:method:: __call__(concentrations, parameters) .. py:class:: GammaFunction(variables, expr, parameters, pool=None) Bases: :py:obj:`skimpy.analysis.ode.flux_fun.FluxFunction` .. py:function:: 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 :param iterable: :return: .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: join_dicts(dicts) .. py:function:: make_ode_fun(kinetic_model, sim_type, pool=None, custom_ode_update=None) :param kinetic_model: :param sim_type: :return: .. py:function:: make_flux_fun(kinetic_model, sim_type) :param kinetic_model: :param sim_type: :return: .. py:function:: make_gamma_fun(kinetic_model) Return a function that calculates the thermodynamic displacement for all the reactions in a model :param kinetic_model: :return: .. py:function:: make_expressions(variables, all_flux_expr, volume_ratios=None, pool=None) .. py:function:: make_expresson_single_var(input) .. py:function:: get_expressions_from_model(kinetic_model, sim_type, medium_symbols=None, biomass_symbol=None) .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:function:: make_cython_function(symbols, expressions, quiet=True, simplify=True, optimize=False, pool=None) .. py:class:: FluxFunction(variables, expr, parameters, pool=None) .. py:attribute:: variables .. py:attribute:: expr .. py:attribute:: parameters .. py:attribute:: function .. py:method:: __call__(concentrations, parameters) .. py:function:: make_cython_function(symbols, expressions, quiet=True, simplify=True, optimize=False, pool=None) .. py:function:: robust_index(in_var) Indexing can be done with symbols or strings representing the symbol, so we harmonize it by returning the name of the symbol if the input is of type symbol :param in_var: :type in_var: str or sympy.Symbol :return: .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:class:: ODEFunction(model, variables, expressions, parameters, pool=None, with_time=False, custom_ode_update=None) .. py:attribute:: variables .. py:attribute:: expressions .. py:attribute:: model .. py:attribute:: with_time :value: False .. py:attribute:: custom_ode_update :value: None .. py:attribute:: _parameters .. py:attribute:: function .. py:property:: parameters .. py:method:: get_params() .. py:method:: __call__(t, y, ydot) .. py:data:: EPSILON :value: 1e-07 .. py:function:: sample_initial_concentrations(kmodel, reference_concentrations, lower_bound=0.8, upper_bound=1.2, n_samples=10, absolute_bounds=False) .. py:function:: create_linear_model(A, rhs, variables, lower_bound=None, upper_bound=None)