Simulation of Evolution of Enzyme Under Constraints
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Documentation for package ‘SimEvolEnzCons’ version 2.0.0
Help Pages
| SimEvolEnzCons-package | SimEvolEnzCons: Simulation of Enzyme Evolution Under Constraints |
| activities | Activity computation |
| alpha_ij | Redistribution coefficient computation |
| apparent.activities.Aq | Apparent activity computation |
| class_group | Classify enzymes in regulation groups |
| coef_rep | Response coefficient computation |
| coef_sel.continue | Selection coefficient computation |
| coef_sel.discrete | Selection coefficient computation |
| compute.B.from.beta | Global co-regulation coefficient computation |
| compute.beta.from.B | Co-regulation coefficient computation |
| compute.delta | Computation of mutation actual effect |
| data_sim | Simulation results for each constraint |
| data_sim_Comp | Simulation results for each constraint |
| data_sim_CRNeg | Simulation results for each constraint |
| data_sim_CRNeg_1grpNeg1sgl | Simulation results for each constraint |
| data_sim_CRPos | Simulation results for each constraint |
| data_sim_RegNeg | Simulation results for each constraint |
| data_sim_RegNeg_1grpNeg1grpPos | Simulation results for each constraint |
| data_sim_RegPos | Simulation results for each constraint |
| data_sim_SC | Simulation results for each constraint |
| droites | Line of relative enzyme concentrations (co-regulations cases) |
| droite_e | Line of relative enzyme concentrations (co-regulations cases) |
| droite_E.CR | Line of relative enzyme concentrations (co-regulations cases) |
| droite_E.Reg | Line of relative enzyme concentrations (co-regulations cases) |
| droite_tau | Line of relative enzyme concentrations (co-regulations cases) |
| extract.tabEtot | Table of concentrations |
| flux | Flux computation |
| flux.dome.graph3D | Plot of the flux dome |
| flux.dome.graphics | Plot of the flux dome |
| flux.dome.projections | Plot of the flux dome |
| flux.shape.for.all.points | Flux shape computing for all points |
| flux.shape.from.one.point | Flux shape computing from one point |
| flux.shape.from.one.point.graphics | Plots of flux shape computing from one point |
| graph.simul.by.time.by.enz | Graphic methods for simulations of enzyme evolution |
| graph.simul.by.time.by.sim | Graphic methods for simulations of enzyme evolution |
| graph.simul.by.time.RNV | Graphic methods for simulations of enzyme evolution |
| graph.simul.conc.end | Graphics of simulation ends |
| graph.simul.group | Graphic methods for simulations of enzyme evolution |
| graph.simul.others.by.sim | Graphic methods for simulations of enzyme evolution |
| graph.simul.triangle.diagram.e | Triangular diagram of relative concentrations for simulations of enzyme evolution |
| group_types | Which types are the different regulation groups? |
| is.B.accurate | Verification of B accuracy |
| is.beta.accurate | Verification of beta matrix accuracy |
| is.correl.authorized | Verification of constraint name |
| mut.E.direct | Direct mutation of enzyme concentrations |
| mut.E.indirect | Indirect mutation of enzyme concentrations |
| mut.E.old | Old method for mutation of enzyme concentrations |
| mut.kin | Mutation of kinetic parameters |
| name.correl | Help to name parameter 'correl' |
| odd.discrete.sel.coef | Equation of null coefficient selection |
| predict_eff | Prediction of effective equilibrium |
| predict_eff_allE0 | Prediction of effective equilibrium for all possible initial relative concentrations |
| predict_grp | Prediction of equilibrium with regulation groups |
| predict_th | Prediction of theoretical equilibrium |
| range_delta | Bounds of _delta_i_ |
| range_tau | Bounds of _tau_ |
| RNV.compute.elements | Compute RNV and associated elements for all enzymes _(Deprecated)_ |
| RNV.delta.all.enz | Delta at RNV for all enzymes |
| RNV.for.simul | Compute RNV for simulation |
| RNV.graph.double.at.eq | Graph of e and RNV in relation to A at equilibrium |
| RNV.mean.simul | Mean of RNV size in simulation |
| RNV.mean.suitability | Compare RNV mean in simulation with predicted RNV at equilibrium |
| RNV.ranking.order.factor | Name and value of RNV-ranking-order factor |
| RNV.size.at.equilibr | Plot and linear model of RNV size at equilibrium |
| search_group | Search the regulation group for an enzyme |
| SimEvolEnzCons | SimEvolEnzCons: Simulation of Enzyme Evolution Under Constraints |
| simul.evol.enz.multiple | Multiple simulations of enzyme evolution |
| simul.evol.enz.one | Simulation of enzyme evolution |
| simul.evol.graph.methods | Graphic methods for simulations of enzyme evolution |
| simul.next.resident | Time step simulation (next resident values) |
| solv.2dg.polynom | Real solutions of quadratic equation |
| sol_eqeff | Expression of null response coefficient |
| sumbis | Sum of vector elements |