Index

_

__add__() (biocrnpyler.core.parameter.ParameterKey method) __class_getitem__() (biocrnpyler.core.parameter.ParameterKey method) __contains__() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.parameter.ParameterDatabase method) (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.reaction.Reaction method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.Reaction method) __eq__() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.compartment.Compartment method) (biocrnpyler.core.parameter.ModelParameter method) (biocrnpyler.core.parameter.Parameter method) (biocrnpyler.core.parameter.ParameterEntry method) (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.propensities.GeneralPropensity method) (biocrnpyler.core.propensities.Hill method) (biocrnpyler.core.propensities.HillNegative method) (biocrnpyler.core.propensities.HillPositive method) (biocrnpyler.core.propensities.MassAction method) (biocrnpyler.core.propensities.Propensity method) (biocrnpyler.core.propensities.ProportionalHillNegative method) (biocrnpyler.core.propensities.ProportionalHillPositive method) (biocrnpyler.core.reaction.Reaction method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.core.species.WeightedSpecies method) (biocrnpyler.Parameter method) (biocrnpyler.Reaction method) (biocrnpyler.Species method) __ge__() (biocrnpyler.core.parameter.ParameterKey method) __getattribute__() (biocrnpyler.core.parameter.ParameterKey method) __getitem__() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.parameter.ParameterDatabase method) (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) __getnewargs__() (biocrnpyler.core.parameter.ParameterKey method) __gt__() (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) __hash__() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.parameter.ModelParameter method) (biocrnpyler.core.parameter.Parameter method) (biocrnpyler.core.parameter.ParameterEntry method) (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.core.species.WeightedSpecies method) (biocrnpyler.Parameter method) (biocrnpyler.Species method)

__init__() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.Complex method) (biocrnpyler.Parameter method) (biocrnpyler.Reaction method) (biocrnpyler.Species method) __iter__() (biocrnpyler.core.parameter.ParameterDatabase method) (biocrnpyler.core.parameter.ParameterKey method) __le__() (biocrnpyler.core.parameter.ParameterKey method) __len__() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.parameter.ParameterDatabase method) (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) __lt__() (biocrnpyler.core.parameter.ParameterKey method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) __mul__() (biocrnpyler.core.parameter.ParameterKey method) __ne__() (biocrnpyler.core.parameter.ParameterKey method) __new__() (biocrnpyler.Complex static method) (biocrnpyler.core.parameter.ParameterKey static method) (biocrnpyler.core.species.Complex static method) __next__() (biocrnpyler.core.parameter.ParameterDatabase method) __replace__() (biocrnpyler.core.parameter.ParameterKey method) __rmul__() (biocrnpyler.core.parameter.ParameterKey method) __setitem__() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.parameter.ParameterDatabase method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) __swig_destroy__() (biocrnpyler.utils.sbmlutil.SetIdFromNames method)

A

ActivatablePromoter (class in biocrnpyler.components.dna.promoter) add_all_compartments() (in module biocrnpyler.utils.sbmlutil) add_all_reactions() (in module biocrnpyler.utils.sbmlutil) add_all_species() (in module biocrnpyler.utils.sbmlutil) add_attribute() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) add_compartment() (in module biocrnpyler.utils.sbmlutil) add_component() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) add_components() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) add_global_mechanism() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) add_mechanism() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method)

add_mechanisms() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) add_parameter() (biocrnpyler.core.parameter.ParameterDatabase method) add_reaction() (in module biocrnpyler.utils.sbmlutil) add_reactions() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) add_species() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) (in module biocrnpyler.utils.sbmlutil) add_species_to_crn() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) AntiDilutionConstitutiveCreation (class in biocrnpyler.mechanisms.global_mechanisms) append() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) apply_filter() (biocrnpyler.mechanisms.global_mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.global_mechanisms.Dilution method) (biocrnpyler.mechanisms.global_mechanisms.GlobalMechanism method) apply_global_mechanisms() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method)

B

BasicCatalysis (class in biocrnpyler.mechanisms.enzyme) BasicIntegration (class in biocrnpyler.mechanisms.integrase) BasicProduction (class in biocrnpyler.mechanisms.enzyme) BasicPURE (class in biocrnpyler.mixtures.pure) binds_to() (biocrnpyler.components.integrase_enumerator.IntegraseRule method) biocrnpyler module biocrnpyler.components module, [1] biocrnpyler.components.basic module biocrnpyler.components.combinatorial_complex module biocrnpyler.components.combinatorial_conformation module biocrnpyler.components.component_enumerator module biocrnpyler.components.construct_explorer module biocrnpyler.components.dna module biocrnpyler.components.dna.assembly module biocrnpyler.components.dna.cds module biocrnpyler.components.dna.construct module biocrnpyler.components.dna.misc module biocrnpyler.components.dna.promoter module biocrnpyler.components.dna.rbs module biocrnpyler.components.dna.terminator module biocrnpyler.components.integrase_enumerator module biocrnpyler.components.membrane module biocrnpyler.core module biocrnpyler.core.chemical_reaction_network module biocrnpyler.core.compartment module biocrnpyler.core.component module biocrnpyler.core.mechanism module biocrnpyler.core.mixture module

biocrnpyler.core.parameter module biocrnpyler.core.polymer module biocrnpyler.core.propensities module biocrnpyler.core.reaction module biocrnpyler.core.species module biocrnpyler.mechanisms module, [1] biocrnpyler.mechanisms.binding module biocrnpyler.mechanisms.conformation module biocrnpyler.mechanisms.enzyme module biocrnpyler.mechanisms.global_mechanisms module biocrnpyler.mechanisms.integrase module biocrnpyler.mechanisms.metabolite module biocrnpyler.mechanisms.signaling module biocrnpyler.mechanisms.transport module biocrnpyler.mechanisms.txtl module biocrnpyler.mixtures module, [1] biocrnpyler.mixtures.cell module biocrnpyler.mixtures.extract module biocrnpyler.mixtures.pure module biocrnpyler.utils module biocrnpyler.utils.fileutil module biocrnpyler.utils.general module biocrnpyler.utils.plotting module biocrnpyler.utils.sbmlutil module biocrnpyler.utils.units module

C

CDS (class in biocrnpyler.components.dna.cds) changed() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) check_crn_validity() (biocrnpyler.ChemicalReactionNetwork static method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork static method) check_loop() (biocrnpyler.components.construct_explorer.ConstructExplorer method) (biocrnpyler.components.construct_explorer.TlExplorer method) (biocrnpyler.components.construct_explorer.TxExplorer method) ChemicalComplex (class in biocrnpyler.components.basic) ChemicalReactionNetwork (class in biocrnpyler) (class in biocrnpyler.core.chemical_reaction_network) clone() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) Combinatorial_Cooperative_Binding (class in biocrnpyler.mechanisms.binding) combinatorial_enumeration() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) CombinatorialComplex (class in biocrnpyler.components.combinatorial_complex) CombinatorialConformation (class in biocrnpyler.components.combinatorial_conformation) CombinatorialConformationPromoter (class in biocrnpyler.components.combinatorial_conformation) CombinatorialPromoter (class in biocrnpyler.components.dna.promoter) combine_dictionaries() (in module biocrnpyler.utils.general) compartment (biocrnpyler.components.basic.ChemicalComplex property) (biocrnpyler.components.basic.DNA property) (biocrnpyler.components.basic.Enzyme property) (biocrnpyler.components.basic.Metabolite property) (biocrnpyler.components.basic.Protein property) (biocrnpyler.components.basic.RNA property) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) (biocrnpyler.components.dna.assembly.DNAassembly property) (biocrnpyler.components.dna.cds.CDS property) (biocrnpyler.components.dna.construct.Construct property) (biocrnpyler.components.dna.construct.DNA_construct property) (biocrnpyler.components.dna.construct.DNA_part property) (biocrnpyler.components.dna.construct.RNA_construct property) (biocrnpyler.components.dna.misc.DNABindingSite property) (biocrnpyler.components.dna.misc.IntegraseSite property) (biocrnpyler.components.dna.misc.Operator property) (biocrnpyler.components.dna.misc.Origin property) (biocrnpyler.components.dna.misc.UserDefined property) (biocrnpyler.components.dna.promoter.ActivatablePromoter property) (biocrnpyler.components.dna.promoter.CombinatorialPromoter property) (biocrnpyler.components.dna.promoter.Promoter property) (biocrnpyler.components.dna.promoter.RegulatedPromoter property) (biocrnpyler.components.dna.promoter.RepressiblePromoter property) (biocrnpyler.components.dna.rbs.RBS property) (biocrnpyler.components.dna.terminator.Terminator property) (biocrnpyler.components.membrane.DiffusibleMolecule property) (biocrnpyler.components.membrane.IntegralMembraneProtein property) (biocrnpyler.components.membrane.MembraneChannel property) (biocrnpyler.components.membrane.MembranePump property) (biocrnpyler.components.membrane.MembraneSensor property) (biocrnpyler.core.component.Component property)

Compartment (class in biocrnpyler.core.compartment) compile_crn() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) Complex (class in biocrnpyler) (class in biocrnpyler.core.species) ComplexSpecies (class in biocrnpyler.core.species) Component (class in biocrnpyler.core.component) component_enumeration() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) ComponentEnumerator (class in biocrnpyler.components.component_enumerator) compute_species_changes() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) compute_species_to_add() (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) Construct (class in biocrnpyler.components.dna.construct) ConstructExplorer (class in biocrnpyler.components.construct_explorer) contains_species_monomer() (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) copy_remove_complexes() (biocrnpyler.core.species.PolymerConformation method) count() (biocrnpyler.core.parameter.ParameterKey method) create_hashless_reverse() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method) create_kinetic_law() (biocrnpyler.core.propensities.GeneralPropensity method) (biocrnpyler.core.propensities.Hill method) (biocrnpyler.core.propensities.HillNegative method) (biocrnpyler.core.propensities.HillPositive method) (biocrnpyler.core.propensities.MassAction method) (biocrnpyler.core.propensities.Propensity method) (biocrnpyler.core.propensities.ProportionalHillNegative method) (biocrnpyler.core.propensities.ProportionalHillPositive method) create_new_unit_definition() (in module biocrnpyler.utils.units) create_parameter_key() (biocrnpyler.core.parameter.ModelParameter static method) (biocrnpyler.core.parameter.ParameterEntry static method) create_polymer() (biocrnpyler.components.integrase_enumerator.Polymer_transformation method) create_sbml_model() (in module biocrnpyler.utils.sbmlutil)

D

d (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property) Deg_Tagged_Degradation (class in biocrnpyler.mechanisms.global_mechanisms) Degradation_mRNA_MM (class in biocrnpyler.mechanisms.global_mechanisms) delpart() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) DiffusibleMolecule (class in biocrnpyler.components.membrane) Dilution (class in biocrnpyler.mechanisms.global_mechanisms) direction_invert() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) direction_rotation_free_hash() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method) DNA (class in biocrnpyler.components.basic)

DNA_construct (class in biocrnpyler.components.dna.construct) DNA_part (class in biocrnpyler.components.dna.construct) dna_species (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) (biocrnpyler.components.dna.cds.CDS property) (biocrnpyler.components.dna.construct.DNA_part property) (biocrnpyler.components.dna.misc.DNABindingSite property) (biocrnpyler.components.dna.misc.IntegraseSite property) (biocrnpyler.components.dna.misc.Operator property) (biocrnpyler.components.dna.misc.Origin property) (biocrnpyler.components.dna.misc.UserDefined property) (biocrnpyler.components.dna.promoter.ActivatablePromoter property) (biocrnpyler.components.dna.promoter.CombinatorialPromoter property) (biocrnpyler.components.dna.promoter.Promoter property) (biocrnpyler.components.dna.promoter.RegulatedPromoter property) (biocrnpyler.components.dna.promoter.RepressiblePromoter property) (biocrnpyler.components.dna.rbs.RBS property) (biocrnpyler.components.dna.terminator.Terminator property) dna_to_bind (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) (biocrnpyler.components.dna.promoter.ActivatablePromoter property) (biocrnpyler.components.dna.promoter.CombinatorialPromoter property) (biocrnpyler.components.dna.promoter.Promoter property) (biocrnpyler.components.dna.promoter.RegulatedPromoter property) (biocrnpyler.components.dna.promoter.RepressiblePromoter property) DNAassembly (class in biocrnpyler.components.dna.assembly) DNABindingSite (class in biocrnpyler.components.dna.misc) dummify() (biocrnpyler.components.integrase_enumerator.Polymer_transformation class method)

E

EmptyMechanism (class in biocrnpyler.core.mechanism) Energy_Transcription_MM (class in biocrnpyler.mechanisms.txtl) Energy_Translation_MM (class in biocrnpyler.mechanisms.txtl) EnergyTxTlExtract (class in biocrnpyler.mixtures.extract) enumerate_components() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.component_enumerator.ComponentEnumerator method) (biocrnpyler.components.component_enumerator.GlobalComponentEnumerator method) (biocrnpyler.components.component_enumerator.LocalComponentEnumerator method) (biocrnpyler.components.construct_explorer.ConstructExplorer method) (biocrnpyler.components.construct_explorer.TlExplorer method) (biocrnpyler.components.construct_explorer.TxExplorer method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.integrase_enumerator.Integrase_Enumerator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method)

enumerate_constructs() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) Enzyme (class in biocrnpyler.components.basic) EnzymeIntegration (class in biocrnpyler.mechanisms.integrase) excluded_states (biocrnpyler.components.combinatorial_complex.CombinatorialComplex property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) ExpressionDilutionMixture (class in biocrnpyler.mixtures.cell) ExpressionExtract (class in biocrnpyler.mixtures.extract)

F

Facilitated_Transport_MM (class in biocrnpyler.mechanisms.transport) final_states (biocrnpyler.components.combinatorial_complex.CombinatorialComplex property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) find_dna_construct() (biocrnpyler.components.integrase_enumerator.Integrase_Enumerator class method) find_file_in_bcp_path() (in module biocrnpyler.utils.fileutil) find_parameter() (biocrnpyler.core.parameter.ParameterDatabase method) find_polymer_component() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method)

flatten_list() (biocrnpyler.core.species.ComplexSpecies static method) (biocrnpyler.core.species.OrderedComplexSpecies static method) (biocrnpyler.core.species.OrderedPolymerSpecies static method) (biocrnpyler.core.species.PolymerConformation static method) (biocrnpyler.core.species.Species static method) (biocrnpyler.Species static method) found_key (biocrnpyler.core.parameter.ModelParameter property) from_dict() (biocrnpyler.core.propensities.GeneralPropensity class method) (biocrnpyler.core.propensities.Hill class method) (biocrnpyler.core.propensities.HillNegative class method) (biocrnpyler.core.propensities.HillPositive class method) (biocrnpyler.core.propensities.MassAction class method) (biocrnpyler.core.propensities.Propensity class method) (biocrnpyler.core.propensities.ProportionalHillNegative class method) (biocrnpyler.core.propensities.ProportionalHillPositive class method) from_massaction() (biocrnpyler.core.reaction.Reaction class method) (biocrnpyler.Reaction class method) from_polymer_conformation() (biocrnpyler.core.species.PolymerConformation class method) from_polymer_replacement() (biocrnpyler.core.species.PolymerConformation class method) from_polymer_species() (biocrnpyler.core.species.OrderedPolymerSpecies class method) from_promoter() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter class method) (biocrnpyler.components.dna.promoter.ActivatablePromoter class method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter class method) (biocrnpyler.components.dna.promoter.Promoter class method) (biocrnpyler.components.dna.promoter.RegulatedPromoter class method) (biocrnpyler.components.dna.promoter.RepressiblePromoter class method) from_rbs() (biocrnpyler.components.dna.rbs.RBS class method)

G

GeneralPropensity (class in biocrnpyler.core.propensities) generate_networkx_graph() (in module biocrnpyler.utils.plotting) generate_products() (biocrnpyler.components.integrase_enumerator.IntegraseRule method) generate_sbml_model() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) get_all_species_containing() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) get_available_propensities() (biocrnpyler.core.propensities.GeneralPropensity static method) (biocrnpyler.core.propensities.Hill static method) (biocrnpyler.core.propensities.HillNegative static method) (biocrnpyler.core.propensities.HillPositive static method) (biocrnpyler.core.propensities.MassAction static method) (biocrnpyler.core.propensities.Propensity static method) (biocrnpyler.core.propensities.ProportionalHillNegative static method) (biocrnpyler.core.propensities.ProportionalHillPositive static method) get_circularly_permuted() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) get_combinations_between() (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) get_compartment_by_name() (in module biocrnpyler.utils.sbmlutil) get_complexed_species() (biocrnpyler.components.dna.misc.IntegraseSite method) get_component() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) get_initial_concentration() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) get_mechanism() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) get_orphan() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) get_parameter() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mechanisms.global_mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.global_mechanisms.Dilution method) (biocrnpyler.mechanisms.global_mechanisms.GlobalMechanism method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method)

get_part() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) get_partlist_hash() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method) get_partstring() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method) get_protein_for_expression() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) get_removed() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) get_renumbered() (biocrnpyler.components.integrase_enumerator.Polymer_transformation method) get_reversed() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) get_sbml_id() (biocrnpyler.core.parameter.ModelParameter method) (biocrnpyler.core.parameter.ParameterEntry method) get_species() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) getSpeciesByName() (in module biocrnpyler.utils.sbmlutil) global_component_enumeration() (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) global_mechanisms (biocrnpyler.core.mixture.Mixture property) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture property) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture property) (biocrnpyler.mixtures.cell.TxTlDilutionMixture property) (biocrnpyler.mixtures.extract.EnergyTxTlExtract property) (biocrnpyler.mixtures.extract.ExpressionExtract property) (biocrnpyler.mixtures.extract.SimpleTxTlExtract property) (biocrnpyler.mixtures.extract.TxTlExtract property) (biocrnpyler.mixtures.pure.BasicPURE property) GlobalComponentEnumerator (class in biocrnpyler.components.component_enumerator) GlobalMechanism (class in biocrnpyler.mechanisms.global_mechanisms) graphPlot() (in module biocrnpyler.utils.plotting)

H

Hill (class in biocrnpyler.core.propensities)

HillNegative (class in biocrnpyler.core.propensities) HillPositive (class in biocrnpyler.core.propensities)

I

index() (biocrnpyler.core.parameter.ParameterKey method) initial_concentration_dict (biocrnpyler.ChemicalReactionNetwork property) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork property) initial_condition_vector() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) initial_states (biocrnpyler.components.combinatorial_complex.CombinatorialComplex property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) inputs (biocrnpyler.core.reaction.Reaction property) (biocrnpyler.Reaction property) insert() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) IntegralMembraneProtein (class in biocrnpyler.components.membrane) Integrase_Enumerator (class in biocrnpyler.components.integrase_enumerator) IntegraseRule (class in biocrnpyler.components.integrase_enumerator) IntegraseSite (class in biocrnpyler.components.dna.misc) integrate() (biocrnpyler.components.integrase_enumerator.IntegraseRule method) intermediate_states (biocrnpyler.components.combinatorial_complex.CombinatorialComplex property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation property) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property)

is_reversible (biocrnpyler.core.propensities.GeneralPropensity property) (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.MassAction property) (biocrnpyler.core.propensities.Propensity property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property) (biocrnpyler.core.reaction.Reaction property) (biocrnpyler.Reaction property) is_valid_propensity() (biocrnpyler.core.propensities.GeneralPropensity static method) (biocrnpyler.core.propensities.Hill static method) (biocrnpyler.core.propensities.HillNegative static method) (biocrnpyler.core.propensities.HillPositive static method) (biocrnpyler.core.propensities.MassAction static method) (biocrnpyler.core.propensities.Propensity static method) (biocrnpyler.core.propensities.ProportionalHillNegative static method) (biocrnpyler.core.propensities.ProportionalHillPositive static method) iterate_part() (biocrnpyler.components.construct_explorer.TlExplorer method) (biocrnpyler.components.construct_explorer.TxExplorer method)

K

K (biocrnpyler.core.propensities.Hill property) k (biocrnpyler.core.propensities.Hill property) K (biocrnpyler.core.propensities.HillNegative property) k (biocrnpyler.core.propensities.HillNegative property) K (biocrnpyler.core.propensities.HillPositive property) k (biocrnpyler.core.propensities.HillPositive property) K (biocrnpyler.core.propensities.ProportionalHillNegative property) k (biocrnpyler.core.propensities.ProportionalHillNegative property) K (biocrnpyler.core.propensities.ProportionalHillPositive property) k (biocrnpyler.core.propensities.ProportionalHillPositive property) k_forward (biocrnpyler.core.propensities.GeneralPropensity property) (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.MassAction property) (biocrnpyler.core.propensities.Propensity property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property)

k_reverse (biocrnpyler.core.propensities.GeneralPropensity property) (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.MassAction property) (biocrnpyler.core.propensities.Propensity property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property)

L

linear_direction_free_hash() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method) list_integrase() (biocrnpyler.components.integrase_enumerator.Integrase_Enumerator method) load_parameters_from_database() (biocrnpyler.core.parameter.ParameterDatabase method)

load_parameters_from_dictionary() (biocrnpyler.core.parameter.ParameterDatabase method) load_parameters_from_file() (biocrnpyler.core.parameter.ParameterDatabase method) LocalComponentEnumerator (class in biocrnpyler.components.component_enumerator) located_allcomb() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method)

M

make_cooperative_complex() (biocrnpyler.mechanisms.binding.Combinatorial_Cooperative_Binding method) make_name() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) make_polymers() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) makeArrows2() (in module biocrnpyler.utils.plotting) MassAction (class in biocrnpyler.core.propensities) mechanism (biocrnpyler.core.parameter.ParameterKey attribute) Mechanism (class in biocrnpyler.core.mechanism) mechanisms (biocrnpyler.core.mixture.Mixture property) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture property) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture property) (biocrnpyler.mixtures.cell.TxTlDilutionMixture property) (biocrnpyler.mixtures.extract.EnergyTxTlExtract property) (biocrnpyler.mixtures.extract.ExpressionExtract property) (biocrnpyler.mixtures.extract.SimpleTxTlExtract property) (biocrnpyler.mixtures.extract.TxTlExtract property) (biocrnpyler.mixtures.pure.BasicPURE property) member_dictionary_search() (in module biocrnpyler.utils.general) Membrane_Protein_Integration (class in biocrnpyler.mechanisms.transport) Membrane_Signaling_Pathway_MM (class in biocrnpyler.mechanisms.signaling) MembraneChannel (class in biocrnpyler.components.membrane) MembranePump (class in biocrnpyler.components.membrane) MembraneSensor (class in biocrnpyler.components.membrane) Metabolite (class in biocrnpyler.components.basic) MichaelisMenten (class in biocrnpyler.mechanisms.enzyme) MichaelisMentenCopy (class in biocrnpyler.mechanisms.enzyme) MichaelisMentenReversible (class in biocrnpyler.mechanisms.enzyme) Mixture (class in biocrnpyler.core.mixture) ModelParameter (class in biocrnpyler.core.parameter) module biocrnpyler biocrnpyler.components, [1] biocrnpyler.components.basic biocrnpyler.components.combinatorial_complex biocrnpyler.components.combinatorial_conformation biocrnpyler.components.component_enumerator biocrnpyler.components.construct_explorer biocrnpyler.components.dna biocrnpyler.components.dna.assembly biocrnpyler.components.dna.cds biocrnpyler.components.dna.construct biocrnpyler.components.dna.misc biocrnpyler.components.dna.promoter biocrnpyler.components.dna.rbs biocrnpyler.components.dna.terminator biocrnpyler.components.integrase_enumerator biocrnpyler.components.membrane biocrnpyler.core biocrnpyler.core.chemical_reaction_network biocrnpyler.core.compartment biocrnpyler.core.component biocrnpyler.core.mechanism biocrnpyler.core.mixture biocrnpyler.core.parameter biocrnpyler.core.polymer biocrnpyler.core.propensities biocrnpyler.core.reaction biocrnpyler.core.species biocrnpyler.mechanisms, [1] biocrnpyler.mechanisms.binding biocrnpyler.mechanisms.conformation biocrnpyler.mechanisms.enzyme biocrnpyler.mechanisms.global_mechanisms biocrnpyler.mechanisms.integrase biocrnpyler.mechanisms.metabolite biocrnpyler.mechanisms.signaling biocrnpyler.mechanisms.transport biocrnpyler.mechanisms.txtl biocrnpyler.mixtures, [1] biocrnpyler.mixtures.cell biocrnpyler.mixtures.extract biocrnpyler.mixtures.pure biocrnpyler.utils biocrnpyler.utils.fileutil biocrnpyler.utils.general biocrnpyler.utils.plotting biocrnpyler.utils.sbmlutil biocrnpyler.utils.units

monomer_count() (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) monomer_eq() (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) monomer_insert() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) MonomerCollection (class in biocrnpyler.core.polymer) multi_tl (class in biocrnpyler.mechanisms.txtl) multi_tx (class in biocrnpyler.mechanisms.txtl)

N

n (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property)

name (biocrnpyler.core.compartment.Compartment property) (biocrnpyler.core.parameter.ParameterKey attribute) NamedPolymer (class in biocrnpyler.core.polymer) NegativeHillTranscription (class in biocrnpyler.mechanisms.txtl)

O

omnihash() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method) One_Step_Binding (class in biocrnpyler.mechanisms.binding) One_Step_Cooperative_Binding (class in biocrnpyler.mechanisms.binding) One_Step_Reversible_Conformation_Change (class in biocrnpyler.mechanisms.conformation) OneStepGeneExpression (class in biocrnpyler.mechanisms.txtl) OneStepPathway (class in biocrnpyler.mechanisms.metabolite)

Operator (class in biocrnpyler.components.dna.misc) OrderedComplexSpecies (class in biocrnpyler.core.species) OrderedMonomer (class in biocrnpyler.core.polymer) OrderedPolymer (class in biocrnpyler.core.polymer) OrderedPolymerSpecies (class in biocrnpyler.core.species) Origin (class in biocrnpyler.components.dna.misc) outputs (biocrnpyler.core.reaction.Reaction property) (biocrnpyler.Reaction property)

P

Parameter (class in biocrnpyler) (class in biocrnpyler.core.parameter) parameter_info (biocrnpyler.core.parameter.ModelParameter property) (biocrnpyler.core.parameter.ParameterEntry property) parameter_key (biocrnpyler.core.parameter.ModelParameter property) (biocrnpyler.core.parameter.ParameterEntry property) parameter_name (biocrnpyler.core.parameter.ModelParameter property) (biocrnpyler.core.parameter.Parameter property) (biocrnpyler.core.parameter.ParameterEntry property) (biocrnpyler.Parameter property) ParameterDatabase (class in biocrnpyler.core.parameter) ParameterEntry (class in biocrnpyler.core.parameter) ParameterKey (class in biocrnpyler.core.parameter) part_id (biocrnpyler.core.parameter.ParameterKey attribute) Polymer_transformation (class in biocrnpyler.components.integrase_enumerator) PolymerConformation (class in biocrnpyler.core.species) PositiveHillTranscription (class in biocrnpyler.mechanisms.txtl) pretty_print() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) (biocrnpyler.core.propensities.GeneralPropensity method) (biocrnpyler.core.propensities.Hill method) (biocrnpyler.core.propensities.HillNegative method) (biocrnpyler.core.propensities.HillPositive method) (biocrnpyler.core.propensities.MassAction method) (biocrnpyler.core.propensities.Propensity method) (biocrnpyler.core.propensities.ProportionalHillNegative method) (biocrnpyler.core.propensities.ProportionalHillPositive method) (biocrnpyler.core.reaction.Reaction method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Reaction method) (biocrnpyler.Species method)

pretty_print_parameters() (biocrnpyler.core.propensities.GeneralPropensity method) (biocrnpyler.core.propensities.Hill method) (biocrnpyler.core.propensities.HillNegative method) (biocrnpyler.core.propensities.HillPositive method) (biocrnpyler.core.propensities.MassAction method) (biocrnpyler.core.propensities.Propensity method) (biocrnpyler.core.propensities.ProportionalHillNegative method) (biocrnpyler.core.propensities.ProportionalHillPositive method) pretty_print_rate() (biocrnpyler.core.propensities.GeneralPropensity method) (biocrnpyler.core.propensities.Hill method) (biocrnpyler.core.propensities.HillNegative method) (biocrnpyler.core.propensities.HillPositive method) (biocrnpyler.core.propensities.MassAction method) (biocrnpyler.core.propensities.Propensity method) (biocrnpyler.core.propensities.ProportionalHillNegative method) (biocrnpyler.core.propensities.ProportionalHillPositive method) Primary_Active_Transport_MM (class in biocrnpyler.mechanisms.transport) products (biocrnpyler.components.basic.Enzyme property) Promoter (class in biocrnpyler.components.dna.promoter) promoter_states (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter property) Propensity (class in biocrnpyler.core.propensities) propensity_type (biocrnpyler.core.reaction.Reaction property) (biocrnpyler.Reaction property) ProportionalHillNegative (class in biocrnpyler.core.propensities) ProportionalHillPositive (class in biocrnpyler.core.propensities) Protein (class in biocrnpyler.components.basic)

R

RBS (class in biocrnpyler.components.dna.rbs) Reaction (class in biocrnpyler) (class in biocrnpyler.core.reaction) reaction_allowed() (biocrnpyler.components.integrase_enumerator.IntegraseRule method) reactions (biocrnpyler.ChemicalReactionNetwork property) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork property) reactive_sites() (biocrnpyler.components.integrase_enumerator.IntegraseRule method) RegulatedPromoter (class in biocrnpyler.components.dna.promoter) remove() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) remove_attribute() (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) remove_bindloc() (in module biocrnpyler.utils.general) render_constructs() (in module biocrnpyler.utils.plotting) renumber_output() (biocrnpyler.components.integrase_enumerator.Polymer_transformation method) replace() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method)

replace_species() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) (biocrnpyler.core.reaction.Reaction method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Reaction method) (biocrnpyler.Species method) RepressiblePromoter (class in biocrnpyler.components.dna.promoter) reset() (biocrnpyler.components.integrase_enumerator.Integrase_Enumerator method) reset_enumerator() (biocrnpyler.components.construct_explorer.ConstructExplorer method) (biocrnpyler.components.construct_explorer.TlExplorer method) (biocrnpyler.components.construct_explorer.TxExplorer method) reset_stored_data() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) reverse() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.NamedPolymer method) (biocrnpyler.core.polymer.OrderedPolymer method) (biocrnpyler.core.species.OrderedPolymerSpecies method) reversed() (biocrnpyler.components.integrase_enumerator.Polymer_transformation method) RNA (class in biocrnpyler.components.basic) RNA_construct (class in biocrnpyler.components.dna.construct) rotation_free_hash() (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.RNA_construct class method)

S

s1 (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property) search_key (biocrnpyler.core.parameter.ModelParameter property) set_attributes() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) set_dir() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) set_mixture() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method)

set_species() (biocrnpyler.components.basic.ChemicalComplex class method) (biocrnpyler.components.basic.DNA class method) (biocrnpyler.components.basic.Enzyme class method) (biocrnpyler.components.basic.Metabolite class method) (biocrnpyler.components.basic.Protein class method) (biocrnpyler.components.basic.RNA class method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex class method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation class method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter class method) (biocrnpyler.components.dna.assembly.DNAassembly class method) (biocrnpyler.components.dna.cds.CDS class method) (biocrnpyler.components.dna.construct.Construct class method) (biocrnpyler.components.dna.construct.DNA_construct class method) (biocrnpyler.components.dna.construct.DNA_part class method) (biocrnpyler.components.dna.construct.RNA_construct class method) (biocrnpyler.components.dna.misc.DNABindingSite class method) (biocrnpyler.components.dna.misc.IntegraseSite class method) (biocrnpyler.components.dna.misc.Operator class method) (biocrnpyler.components.dna.misc.Origin class method) (biocrnpyler.components.dna.misc.UserDefined class method) (biocrnpyler.components.dna.promoter.ActivatablePromoter class method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter class method) (biocrnpyler.components.dna.promoter.Promoter class method) (biocrnpyler.components.dna.promoter.RegulatedPromoter class method) (biocrnpyler.components.dna.promoter.RepressiblePromoter class method) (biocrnpyler.components.dna.rbs.RBS class method) (biocrnpyler.components.dna.terminator.Terminator class method) (biocrnpyler.components.membrane.DiffusibleMolecule class method) (biocrnpyler.components.membrane.IntegralMembraneProtein class method) (biocrnpyler.components.membrane.MembraneChannel class method) (biocrnpyler.components.membrane.MembranePump class method) (biocrnpyler.components.membrane.MembraneSensor class method) (biocrnpyler.core.component.Component class method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) SetIdFromNames (class in biocrnpyler.utils.sbmlutil) Simple_Diffusion (class in biocrnpyler.mechanisms.transport) Simple_Transport (class in biocrnpyler.mechanisms.transport) SimpleTranscription (class in biocrnpyler.mechanisms.txtl) SimpleTranslation (class in biocrnpyler.mechanisms.txtl) SimpleTxTlDilutionMixture (class in biocrnpyler.mixtures.cell) SimpleTxTlExtract (class in biocrnpyler.mixtures.extract) simulate_with_bioscrape() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) simulate_with_bioscrape_via_sbml() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) simulate_with_roadrunner() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method) size (biocrnpyler.core.compartment.Compartment property) spatial_dimensions (biocrnpyler.core.compartment.Compartment property) species (biocrnpyler.ChemicalReactionNetwork property) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork property) (biocrnpyler.core.propensities.GeneralPropensity property) (biocrnpyler.core.propensities.Hill property) (biocrnpyler.core.propensities.HillNegative property) (biocrnpyler.core.propensities.HillPositive property) (biocrnpyler.core.propensities.MassAction property) (biocrnpyler.core.propensities.Propensity property) (biocrnpyler.core.propensities.ProportionalHillNegative property) (biocrnpyler.core.propensities.ProportionalHillPositive property) (biocrnpyler.core.reaction.Reaction property) (biocrnpyler.Reaction property) Species (class in biocrnpyler) (class in biocrnpyler.core.species) subhash() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.core.polymer.OrderedMonomer method) (biocrnpyler.core.species.ComplexSpecies method) (biocrnpyler.core.species.OrderedComplexSpecies method) (biocrnpyler.core.species.OrderedPolymerSpecies method) (biocrnpyler.core.species.PolymerConformation method) (biocrnpyler.core.species.Species method) (biocrnpyler.Species method) substrates (biocrnpyler.components.basic.Enzyme property)

T

Terminator (class in biocrnpyler.components.dna.terminator) thisown (biocrnpyler.utils.sbmlutil.SetIdFromNames property) TlExplorer (class in biocrnpyler.components.construct_explorer) Transcription_MM (class in biocrnpyler.mechanisms.txtl) transform() (biocrnpyler.utils.sbmlutil.SetIdFromNames method)

Translation_MM (class in biocrnpyler.mechanisms.txtl) Two_Step_Cooperative_Binding (class in biocrnpyler.mechanisms.binding) TxExplorer (class in biocrnpyler.components.construct_explorer) TxTlDilutionMixture (class in biocrnpyler.mixtures.cell) TxTlExtract (class in biocrnpyler.mixtures.extract)

U

unclone() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) unit (biocrnpyler.core.compartment.Compartment property) (biocrnpyler.core.parameter.ModelParameter property) (biocrnpyler.core.parameter.Parameter property) (biocrnpyler.core.parameter.ParameterEntry property) (biocrnpyler.Parameter property) update_base_species() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) update_combinatorial_complexes() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) update_component() (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) update_dna() (biocrnpyler.components.dna.assembly.DNAassembly method) update_integrase() (biocrnpyler.components.dna.misc.IntegraseSite method) update_parameters() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mixture.Mixture method) (biocrnpyler.mixtures.cell.ExpressionDilutionMixture method) (biocrnpyler.mixtures.cell.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.cell.TxTlDilutionMixture method) (biocrnpyler.mixtures.extract.EnergyTxTlExtract method) (biocrnpyler.mixtures.extract.ExpressionExtract method) (biocrnpyler.mixtures.extract.SimpleTxTlExtract method) (biocrnpyler.mixtures.extract.TxTlExtract method) (biocrnpyler.mixtures.pure.BasicPURE method) update_permutation_hash() (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.RNA_construct method) update_promoter() (biocrnpyler.components.dna.assembly.DNAassembly method) update_protein() (biocrnpyler.components.dna.assembly.DNAassembly method) update_rbs() (biocrnpyler.components.dna.assembly.DNAassembly method) update_reactions() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mechanism.EmptyMechanism method) (biocrnpyler.core.mechanism.Mechanism method) (biocrnpyler.mechanisms.binding.Combinatorial_Cooperative_Binding method) (biocrnpyler.mechanisms.binding.One_Step_Binding method) (biocrnpyler.mechanisms.binding.One_Step_Cooperative_Binding method) (biocrnpyler.mechanisms.binding.Two_Step_Cooperative_Binding method) (biocrnpyler.mechanisms.conformation.One_Step_Reversible_Conformation_Change method) (biocrnpyler.mechanisms.enzyme.BasicCatalysis method) (biocrnpyler.mechanisms.enzyme.BasicProduction method) (biocrnpyler.mechanisms.enzyme.MichaelisMenten method) (biocrnpyler.mechanisms.enzyme.MichaelisMentenCopy method) (biocrnpyler.mechanisms.enzyme.MichaelisMentenReversible method) (biocrnpyler.mechanisms.global_mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.global_mechanisms.Dilution method) (biocrnpyler.mechanisms.global_mechanisms.GlobalMechanism method) (biocrnpyler.mechanisms.integrase.BasicIntegration method) (biocrnpyler.mechanisms.integrase.EnzymeIntegration method) (biocrnpyler.mechanisms.metabolite.OneStepPathway method) (biocrnpyler.mechanisms.signaling.Membrane_Signaling_Pathway_MM method) (biocrnpyler.mechanisms.transport.Facilitated_Transport_MM method) (biocrnpyler.mechanisms.transport.Membrane_Protein_Integration method) (biocrnpyler.mechanisms.transport.Primary_Active_Transport_MM method) (biocrnpyler.mechanisms.transport.Simple_Diffusion method) (biocrnpyler.mechanisms.transport.Simple_Transport method) (biocrnpyler.mechanisms.txtl.Energy_Transcription_MM method) (biocrnpyler.mechanisms.txtl.Energy_Translation_MM method) (biocrnpyler.mechanisms.txtl.multi_tl method) (biocrnpyler.mechanisms.txtl.multi_tx method) (biocrnpyler.mechanisms.txtl.NegativeHillTranscription method) (biocrnpyler.mechanisms.txtl.OneStepGeneExpression method) (biocrnpyler.mechanisms.txtl.PositiveHillTranscription method) (biocrnpyler.mechanisms.txtl.SimpleTranscription method) (biocrnpyler.mechanisms.txtl.SimpleTranslation method) (biocrnpyler.mechanisms.txtl.Transcription_MM method) (biocrnpyler.mechanisms.txtl.Translation_MM method)

update_reactions_global() (biocrnpyler.mechanisms.global_mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.global_mechanisms.Dilution method) (biocrnpyler.mechanisms.global_mechanisms.GlobalMechanism method) update_species() (biocrnpyler.components.basic.ChemicalComplex method) (biocrnpyler.components.basic.DNA method) (biocrnpyler.components.basic.Enzyme method) (biocrnpyler.components.basic.Metabolite method) (biocrnpyler.components.basic.Protein method) (biocrnpyler.components.basic.RNA method) (biocrnpyler.components.combinatorial_complex.CombinatorialComplex method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformation method) (biocrnpyler.components.combinatorial_conformation.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.assembly.DNAassembly method) (biocrnpyler.components.dna.cds.CDS method) (biocrnpyler.components.dna.construct.Construct method) (biocrnpyler.components.dna.construct.DNA_construct method) (biocrnpyler.components.dna.construct.DNA_part method) (biocrnpyler.components.dna.construct.RNA_construct method) (biocrnpyler.components.dna.misc.DNABindingSite method) (biocrnpyler.components.dna.misc.IntegraseSite method) (biocrnpyler.components.dna.misc.Operator method) (biocrnpyler.components.dna.misc.Origin method) (biocrnpyler.components.dna.misc.UserDefined method) (biocrnpyler.components.dna.promoter.ActivatablePromoter method) (biocrnpyler.components.dna.promoter.CombinatorialPromoter method) (biocrnpyler.components.dna.promoter.Promoter method) (biocrnpyler.components.dna.promoter.RegulatedPromoter method) (biocrnpyler.components.dna.promoter.RepressiblePromoter method) (biocrnpyler.components.dna.rbs.RBS method) (biocrnpyler.components.dna.terminator.Terminator method) (biocrnpyler.components.membrane.DiffusibleMolecule method) (biocrnpyler.components.membrane.IntegralMembraneProtein method) (biocrnpyler.components.membrane.MembraneChannel method) (biocrnpyler.components.membrane.MembranePump method) (biocrnpyler.components.membrane.MembraneSensor method) (biocrnpyler.core.component.Component method) (biocrnpyler.core.mechanism.EmptyMechanism method) (biocrnpyler.core.mechanism.Mechanism method) (biocrnpyler.mechanisms.binding.Combinatorial_Cooperative_Binding method) (biocrnpyler.mechanisms.binding.One_Step_Binding method) (biocrnpyler.mechanisms.binding.One_Step_Cooperative_Binding method) (biocrnpyler.mechanisms.binding.Two_Step_Cooperative_Binding method) (biocrnpyler.mechanisms.conformation.One_Step_Reversible_Conformation_Change method) (biocrnpyler.mechanisms.enzyme.BasicCatalysis method) (biocrnpyler.mechanisms.enzyme.BasicProduction method) (biocrnpyler.mechanisms.enzyme.MichaelisMenten method) (biocrnpyler.mechanisms.enzyme.MichaelisMentenCopy method) (biocrnpyler.mechanisms.enzyme.MichaelisMentenReversible method) (biocrnpyler.mechanisms.global_mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.global_mechanisms.Dilution method) (biocrnpyler.mechanisms.global_mechanisms.GlobalMechanism method) (biocrnpyler.mechanisms.integrase.BasicIntegration method) (biocrnpyler.mechanisms.integrase.EnzymeIntegration method) (biocrnpyler.mechanisms.metabolite.OneStepPathway method) (biocrnpyler.mechanisms.signaling.Membrane_Signaling_Pathway_MM method) (biocrnpyler.mechanisms.transport.Facilitated_Transport_MM method) (biocrnpyler.mechanisms.transport.Membrane_Protein_Integration method) (biocrnpyler.mechanisms.transport.Primary_Active_Transport_MM method) (biocrnpyler.mechanisms.transport.Simple_Diffusion method) (biocrnpyler.mechanisms.transport.Simple_Transport method) (biocrnpyler.mechanisms.txtl.Energy_Transcription_MM method) (biocrnpyler.mechanisms.txtl.Energy_Translation_MM method) (biocrnpyler.mechanisms.txtl.multi_tl method) (biocrnpyler.mechanisms.txtl.multi_tx method) (biocrnpyler.mechanisms.txtl.NegativeHillTranscription method) (biocrnpyler.mechanisms.txtl.OneStepGeneExpression method) (biocrnpyler.mechanisms.txtl.PositiveHillTranscription method) (biocrnpyler.mechanisms.txtl.SimpleTranscription method) (biocrnpyler.mechanisms.txtl.SimpleTranslation method) (biocrnpyler.mechanisms.txtl.Transcription_MM method) (biocrnpyler.mechanisms.txtl.Translation_MM method) update_species_global() (biocrnpyler.mechanisms.global_mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.global_mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.global_mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.global_mechanisms.Dilution method) (biocrnpyler.mechanisms.global_mechanisms.GlobalMechanism method) update_transcript() (biocrnpyler.components.dna.assembly.DNAassembly method) UserDefined (class in biocrnpyler.components.dna.misc)

V

validate() (biocrnpyler.utils.sbmlutil.validateSBML method) validate_sbml() (in module biocrnpyler.utils.sbmlutil) validateSBML (class in biocrnpyler.utils.sbmlutil)

value (biocrnpyler.core.parameter.ModelParameter property) (biocrnpyler.core.parameter.Parameter property) (biocrnpyler.core.parameter.ParameterEntry property) (biocrnpyler.Parameter property)

W

WeightedSpecies (class in biocrnpyler.core.species)

write_sbml_file() (biocrnpyler.ChemicalReactionNetwork method) (biocrnpyler.core.chemical_reaction_network.ChemicalReactionNetwork method)