Index

_

__add__() (straindesign.strainDesignSolutions.SDSolutions method)

__exit__() (straindesign.pool.SDPool method) __iadd__() (straindesign.strainDesignSolutions.SDSolutions method)

A

add_eq_constraints() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) add_exclusion_constraints() (straindesign.strainDesignMILP.SDMILP method) add_exclusion_constraints_ineq() (straindesign.strainDesignMILP.SDMILP method) add_ineq_constraints() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method)

add_scaled_column() (straindesign.compression.RationalMatrix method) addExclusionConstraintIneq() (straindesign.scip_interface.SCIP_MILP method) addExclusionConstraintsIneq() (straindesign.glpk_interface.GLPK_MILP_LP method) addModule() (straindesign.strainDesignProblem.SDProblem method)

B

basic_columns() (in module straindesign.compression) basic_columns_from_numpy() (in module straindesign.compression) basic_columns_rat() (in module straindesign.efmtool_cmp_interface) basic_columns_rat_java() (in module straindesign.efmtool_cmp_interface)

begin_batch_edit() (straindesign.compression.RationalMatrix method) bound_blocked_or_irrevers_fva() (in module straindesign.networktools) build_primal_from_cbm() (in module straindesign.strainDesignProblem) build_sd_solution() (straindesign.strainDesignMILP.SDMILP method)

C

ceil_dec() (in module straindesign.lptools) clear_objective() (straindesign.solver_interface.MILP_LP method) clone() (straindesign.compression.RationalMatrix method) close() (straindesign.pool.SDPool method) compress() (straindesign.compression.StoichMatrixCompressor method) compress_cobra_model() (in module straindesign.compression) compress_ki_ko_cost() (in module straindesign.networktools) compress_model() (in module straindesign.compression) compress_model_coupled() (in module straindesign.compression) compress_model_java() (in module straindesign.efmtool_cmp_interface) compress_model_parallel() (in module straindesign.compression) compress_modules() (in module straindesign.networktools)

CompressionConverter (class in straindesign.compression) CompressionMethod (class in straindesign.compression) CompressionRecord (class in straindesign.compression) CompressionResult (class in straindesign.compression) CompressionStatistics (class in straindesign.compression) compute() (straindesign.strainDesignMILP.SDMILP method) compute_optimal() (straindesign.strainDesignMILP.SDMILP method) compute_strain_designs() (in module straindesign.compute_strain_designs) compute_strain_designs_from_preprocessed() (in module straindesign.compute_strain_designs) ContMILP (class in straindesign.strainDesignProblem) copy() (straindesign.strainDesignModule.SDModule method) Cplex_MILP_LP (class in straindesign.cplex_interface)

D

detect_max_precision() (in module straindesign.compression)

DisableLogger (class in straindesign)

E

end_batch_edit() (straindesign.compression.RationalMatrix method) enumerate() (straindesign.strainDesignMILP.SDMILP method) estimate_expansion_size() (in module straindesign.networktools) evaluate_gpr_ast() (in module straindesign.networktools) expand_all() (straindesign.strainDesignSolutions.SDSolutions method)

expand_expression() (straindesign.compression.CompressionConverter method) expand_group() (straindesign.strainDesignSolutions.SDSolutions method) expand_sd() (in module straindesign.networktools) extend_model_gpr() (in module straindesign.networktools) extend_model_regulatory() (in module straindesign.networktools)

F

farkas_dualize() (in module straindesign.strainDesignProblem) fba() (in module straindesign.lptools) filter_sd_maxcost() (in module straindesign.networktools) fixObjective() (straindesign.strainDesignMILP.SDMILP method) float_to_rational() (in module straindesign.compression) floor_dec() (in module straindesign.lptools) from_cobra_model() (straindesign.compression.RationalMatrix class method)

from_numpy() (straindesign.compression.RationalMatrix class method) fva() (in module straindesign.lptools) fva_legacy() (in module straindesign.lptools) fva_worker_compute() (in module straindesign.lptools) fva_worker_compute_glpk() (in module straindesign.lptools) fva_worker_init() (in module straindesign.lptools) fva_worker_init_glpk() (in module straindesign.lptools)

G

gene_kos_to_constraints() (in module straindesign.networktools) get_basis() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) get_gene_reac_sd_assoc() (straindesign.strainDesignSolutions.SDSolutions method) get_gene_reac_sd_assoc_mark_no_ki() (straindesign.strainDesignSolutions.SDSolutions method) get_gene_sd() (straindesign.strainDesignSolutions.SDSolutions method) get_gene_sd_mark_no_ki() (straindesign.strainDesignSolutions.SDSolutions method) get_group() (straindesign.strainDesignSolutions.SDSolutions method) get_lp_method() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method)

get_num_groups() (straindesign.strainDesignSolutions.SDSolutions method) get_num_materialized() (straindesign.strainDesignSolutions.SDSolutions method) get_num_sols() (straindesign.strainDesignSolutions.SDSolutions method) get_reaction_sd() (straindesign.strainDesignSolutions.SDSolutions method) get_reaction_sd_bnds() (straindesign.strainDesignSolutions.SDSolutions method) get_reaction_sd_mark_no_ki() (straindesign.strainDesignSolutions.SDSolutions method) get_representative_sd() (straindesign.strainDesignSolutions.SDSolutions method) get_rids() (in module straindesign.parse_constr) get_signum() (straindesign.compression.RationalMatrix method) get_strain_design_costs() (straindesign.strainDesignSolutions.SDSolutions method) get_strain_designs() (straindesign.strainDesignSolutions.SDSolutions method) get_subset() (in module straindesign.strainDesignSolutions) getSolution() (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_MILP method) getSolutions() (straindesign.gurobi_interface.Gurobi_MILP_LP method) GLPK_MILP_LP (class in straindesign.glpk_interface) gpr_eval() (in module straindesign.strainDesignSolutions) Gurobi_MILP_LP (class in straindesign.gurobi_interface)

I

identity() (straindesign.compression.RationalMatrix class method) idx2c() (in module straindesign.lptools)

IndicatorConstraints (class in straindesign.indicatorConstraints) is_lazy (straindesign.strainDesignSolutions.SDSolutions property) iter_column_fractions() (straindesign.compression.RationalMatrix method)

J

jBigFraction2sympyRat() (in module straindesign.efmtool_cmp_interface)

jBigIntegerPair2sympyRat() (in module straindesign.efmtool_cmp_interface) jpypeArrayOfArrays2numpy_mat() (in module straindesign.efmtool_cmp_interface)

L

lineq2list() (in module straindesign.parse_constr) lineq2mat() (in module straindesign.parse_constr) lineqlist2mat() (in module straindesign.parse_constr) lineqlist2str() (in module straindesign.parse_constr) linexpr2dict() (in module straindesign.parse_constr)

linexpr2mat() (in module straindesign.parse_constr) linexprdict2mat() (in module straindesign.parse_constr) linexprdict2str() (in module straindesign.parse_constr) link_z() (straindesign.strainDesignProblem.SDProblem method) load() (straindesign.strainDesignSolutions.SDSolutions class method) LP_dualize() (in module straindesign.strainDesignProblem)

M

MILP_LP (class in straindesign.solver_interface) module straindesign straindesign.compression straindesign.compute_strain_designs straindesign.cplex_interface straindesign.efmtool_cmp_interface straindesign.glpk_interface straindesign.gurobi_interface straindesign.indicatorConstraints straindesign.lptools straindesign.names straindesign.networktools straindesign.parse_constr straindesign.pool straindesign.scip_interface straindesign.solver_interface straindesign.speedy_fva straindesign.strainDesignMILP straindesign.strainDesignModule straindesign.strainDesignProblem straindesign.strainDesignSolutions

modules_coeff2float() (in module straindesign.networktools) modules_coeff2rational() (in module straindesign.networktools)

N

nullspace() (in module straindesign.compression)

numpy_mat2jpypeArrayOfArrays() (in module straindesign.efmtool_cmp_interface)

P

parse_constraints() (in module straindesign.parse_constr) parse_linexpr() (in module straindesign.parse_constr) plot_flux_space() (in module straindesign.lptools) populate() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.solver_interface.MILP_LP method)

populateZ() (straindesign.strainDesignMILP.SDMILP method) postprocess_reg_sd() (in module straindesign.compute_strain_designs) prevent_boundary_knockouts() (in module straindesign.strainDesignProblem)

R

RationalMatrix (class in straindesign.compression) reassign_lb_ub_from_ineq() (in module straindesign.strainDesignProblem) reduce_gpr() (in module straindesign.networktools) remove_blocked_reactions() (in module straindesign.compression) remove_columns() (straindesign.compression.RationalMatrix method) remove_conservation_relations() (in module straindesign.compression)

remove_dummy_bounds() (in module straindesign.compression) remove_ext_mets() (in module straindesign.compression) remove_redundant_bounds() (in module straindesign.lptools) remove_rows() (straindesign.compression.RationalMatrix method) resetObjective() (straindesign.strainDesignMILP.SDMILP method) resetTargetableZ() (straindesign.strainDesignMILP.SDMILP method) resolve_gene_constraints() (in module straindesign.networktools)

S

save() (straindesign.strainDesignSolutions.SDSolutions method) SCIP_LP (class in straindesign.scip_interface) SCIP_MILP (class in straindesign.scip_interface) sd2dict() (straindesign.strainDesignMILP.SDMILP method) SDMILP (class in straindesign.strainDesignMILP) SDModule (class in straindesign.strainDesignModule) SDPool (class in straindesign.pool) SDProblem (class in straindesign.strainDesignProblem) SDSolutions (class in straindesign.strainDesignSolutions) select_solver() (in module straindesign.lptools) set_basis() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) set_ineq_constraint() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) set_lp_method() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) set_objective() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) set_objective_idx() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) set_time_limit() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) set_ub() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) setMinIntvCostObjective() (straindesign.strainDesignMILP.SDMILP method) setTargetableZ() (straindesign.strainDesignMILP.SDMILP method) slim_solve() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method)

solve() (straindesign.cplex_interface.Cplex_MILP_LP method) (straindesign.glpk_interface.GLPK_MILP_LP method) (straindesign.gurobi_interface.Gurobi_MILP_LP method) (straindesign.scip_interface.SCIP_LP method) (straindesign.scip_interface.SCIP_MILP method) (straindesign.solver_interface.MILP_LP method) solve_MILP_LP() (straindesign.glpk_interface.GLPK_MILP_LP method) solveZ() (straindesign.strainDesignMILP.SDMILP method) speedy_fva() (in module straindesign.speedy_fva) standard() (straindesign.compression.CompressionMethod class method) stoichmat_coeff2float() (in module straindesign.compression) stoichmat_coeff2rational() (in module straindesign.compression) StoichMatrixCompressor (class in straindesign.compression) straindesign module straindesign.compression module straindesign.compute_strain_designs module straindesign.cplex_interface module straindesign.efmtool_cmp_interface module straindesign.glpk_interface module straindesign.gurobi_interface module straindesign.indicatorConstraints module straindesign.lptools module straindesign.names module straindesign.networktools module straindesign.parse_constr module straindesign.pool module straindesign.scip_interface module straindesign.solver_interface module straindesign.speedy_fva module straindesign.strainDesignMILP module straindesign.strainDesignModule module straindesign.strainDesignProblem module straindesign.strainDesignSolutions module strip_non_ki() (in module straindesign.strainDesignSolutions) submatrix() (straindesign.compression.RationalMatrix method) suppress_lp_context() (in module straindesign.networktools) sympyRat2jBigIntegerPair() (in module straindesign.efmtool_cmp_interface)

T

to_numpy() (straindesign.compression.RationalMatrix method)

to_sparse_csr() (straindesign.compression.RationalMatrix method) to_sparse_pattern() (straindesign.compression.RationalMatrix method)

V

verify_sd() (straindesign.strainDesignMILP.SDMILP method)

W

with_suppressed_lp() (in module straindesign.networktools)

worker_compute() (in module straindesign.strainDesignProblem) worker_init() (in module straindesign.strainDesignProblem)

Y

yopt() (in module straindesign.lptools)