skimpy.analysis.oracle ====================== .. py:module:: skimpy.analysis.oracle .. autoapi-nested-parse:: .. module:: skimpy :platform: Unix, Windows :synopsis: Simple Kinetic Models in Python .. moduleauthor:: SKiMPy team [---------] Copyright 2018 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/oracle/add_min_displacement/index /autoapi/skimpy/analysis/oracle/dummy_free_energies/index /autoapi/skimpy/analysis/oracle/fix_directionality/index /autoapi/skimpy/analysis/oracle/flux_concentration_ratios/index /autoapi/skimpy/analysis/oracle/load_pytfa_solution/index /autoapi/skimpy/analysis/oracle/minimum_fluxes/index Attributes ---------- .. autoapisummary:: skimpy.analysis.oracle.BIGM skimpy.analysis.oracle.BIGM_THERMO skimpy.analysis.oracle.BIGM_DG skimpy.analysis.oracle.BIGM_P skimpy.analysis.oracle.EPSILON skimpy.analysis.oracle.MAX_STOICH skimpy.analysis.oracle.BIGM skimpy.analysis.oracle.BIGM_THERMO skimpy.analysis.oracle.BIGM_DG skimpy.analysis.oracle.BIGM_P skimpy.analysis.oracle.EPSILON skimpy.analysis.oracle.MIN_C skimpy.analysis.oracle.MAX_C skimpy.analysis.oracle.BIGM skimpy.analysis.oracle.EPSILON skimpy.analysis.oracle.LOG skimpy.analysis.oracle.LIN Classes ------- .. autoapisummary:: skimpy.analysis.oracle.MinFLuxVariable skimpy.analysis.oracle.MinFLux skimpy.analysis.oracle.ParameterValues skimpy.analysis.oracle.BinUseVariable skimpy.analysis.oracle.BinVariable skimpy.analysis.oracle.FluxRatioCons Functions --------- .. autoapisummary:: skimpy.analysis.oracle.add_min_log_displacement skimpy.analysis.oracle.add_undefined_delta_g skimpy.analysis.oracle.add_dummy_delta_g skimpy.analysis.oracle.add_min_flux_requirements skimpy.analysis.oracle.relax_min_flux skimpy.analysis.oracle.fix_directionality skimpy.analysis.oracle.sanitize_cobra_vars skimpy.analysis.oracle.deltag0_to_keq skimpy.analysis.oracle.load_fluxes skimpy.analysis.oracle.load_concentrations skimpy.analysis.oracle.load_equilibrium_constants skimpy.analysis.oracle.impose_turnover_concentation_ratios skimpy.analysis.oracle.add_ratio_constraints Package Contents ---------------- .. py:function:: add_min_log_displacement(tmodel, min_log_displacement, tva_fluxes=None, inplace=True) .. py:data:: BIGM .. py:data:: BIGM_THERMO .. py:data:: BIGM_DG .. py:data:: BIGM_P .. py:data:: EPSILON .. py:data:: MAX_STOICH :value: 10 .. py:function:: add_undefined_delta_g(_tmodel, solution, delta_g_std=-10, delta_g_std_err=2, add_displacement=True, inplace=True, exclude_reactions=[]) .. py:function:: add_dummy_delta_g(tmodel, rxn, delta_g_std=-100, delta_g_std_err=2, add_displacement=True) .. py:data:: BIGM .. py:data:: BIGM_THERMO .. py:data:: BIGM_DG .. py:data:: BIGM_P .. py:data:: EPSILON .. py:class:: MinFLuxVariable(reaction, **kwargs) Bases: :py:obj:`pytfa.optim.variables.ReactionVariable` Class to represent a negative slack variable for relaxation problems .. py:attribute:: prefix :value: 'MinFluxVar_' .. py:class:: MinFLux(reaction, expr, **kwargs) Bases: :py:obj:`pytfa.optim.constraints.ReactionConstraint` Class to represent thermodynamics constraints. G: Flux_FW + Fluw_BW > min_flux .. py:attribute:: prefix :value: 'MF_' .. py:function:: add_min_flux_requirements(tmodel, flux, inplace=True, exclude=[]) .. py:function:: relax_min_flux(tmodel, reactions_to_ignore=(), solver=None, in_place=False) :param t_tmodel: :type t_tmodel: pytfa.thermo.ThermoModel: :param reactions_to_ignore: Iterable of reactions that should not be relaxed :param solver: solver to use (e.g. 'optlang-glpk', 'optlang-cplex', 'optlang-gurobi' :return: a cobra_model with relaxed bounds on standard Gibbs free energy .. py:function:: fix_directionality(tmodel, solution, inplace=True) Takes a flux solution and transfers its reaction directionality as constraints for the cobra_model :param inplace: :param tmodel: :param solution: :return: .. py:function:: sanitize_cobra_vars(met_name) .. py:function:: deltag0_to_keq(deltag0, temp, unit=KCAL, gas_constant=None) .. py:class:: ParameterValues(parameter_values, kmodel=None) Bases: :py:obj:`object` Parameters set for kinetic models wich can be indexed with symbols or .. py:attribute:: _parameter_values .. py:attribute:: _sym_to_str .. py:method:: __getitem__(item) .. py:method:: __setitem__(item, value) .. py:method:: items() .. py:method:: keys() .. py:method:: values() .. py:function:: load_fluxes(solution_raw, tmodel, kmodel, density=None, ratio_gdw_gww=None, concentration_scaling=None, time_scaling=None, xmol_in_flux=0.001) .. py:function:: load_concentrations(solution_raw, tmodel, kmodel, concentration_scaling=None) .. py:function:: load_equilibrium_constants(solution_raw, tmodel, kmodel, concentration_scaling=None, in_place=False) .. py:data:: MIN_C :value: 1e-10 .. py:data:: MAX_C :value: 0.1 .. py:data:: BIGM .. py:data:: EPSILON .. py:data:: LOG :value: 'log' .. py:data:: LIN :value: 'lin' .. py:class:: BinUseVariable(model, id_, **kwargs) Bases: :py:obj:`pytfa.optim.variables.ModelVariable`, :py:obj:`pytfa.optim.variables.BinaryVariable` .. py:attribute:: prefix :value: 'BinUseVariable_' .. py:class:: BinVariable(model, id_, **kwargs) Bases: :py:obj:`pytfa.optim.variables.ModelVariable` .. py:attribute:: prefix :value: 'BinVariable_' .. py:class:: FluxRatioCons(model, expr, id_, **kwargs) Bases: :py:obj:`pytfa.optim.constraints.ModelConstraint` Class to represent thermodynamics constraints. G: Flux_FW + Fluw_BW > min_flux .. py:attribute:: prefix :value: 'FluxRatioCons_' .. py:function:: impose_turnover_concentation_ratios(tmodel, metabolites, tva, ratio, in_place=False, discretization=LOG, N=11) .. py:function:: add_ratio_constraints(model, lc, fwd, bwd, ratio, concentration_range=(MIN_C, MAX_C), discretization=LOG, N=11)