Index

_

__contains__() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.ParameterDatabase method) (biocrnpyler.core.Reaction method) __eq__() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.Compartment method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.GeneralPropensity method) (biocrnpyler.core.Hill method) (biocrnpyler.core.HillNegative method) (biocrnpyler.core.HillPositive method) (biocrnpyler.core.MassAction method) (biocrnpyler.core.ModelParameter method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.Parameter method) (biocrnpyler.core.ParameterEntry method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Propensity method) (biocrnpyler.core.ProportionalHillNegative method) (biocrnpyler.core.ProportionalHillPositive method) (biocrnpyler.core.Reaction method) (biocrnpyler.core.Species method) (biocrnpyler.core.WeightedSpecies method)

__getitem__() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.ParameterDatabase method) __gt__() (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) __iter__() (biocrnpyler.core.ParameterDatabase method) __len__() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.ParameterDatabase method) __lt__() (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) __new__() (biocrnpyler.core.Complex static method) __next__() (biocrnpyler.core.ParameterDatabase method) __setitem__() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.ParameterDatabase method)

A

ActivatablePromoter (class in biocrnpyler.components.dna) add_attribute() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.Component method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) add_component() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) add_components() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) add_global_mechanism() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) add_mechanism() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method)

add_mechanisms() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) add_parameter() (biocrnpyler.core.ParameterDatabase method) add_reactions() (biocrnpyler.core.ChemicalReactionNetwork method) add_species() (biocrnpyler.core.ChemicalReactionNetwork method) (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) add_species_to_crn() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) AntiDilutionConstitutiveCreation (class in biocrnpyler.mechanisms) append() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) apply_filter() (biocrnpyler.mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.Dilution method) (biocrnpyler.mechanisms.GlobalMechanism method) apply_global_mechanisms() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method)

B

BasicCatalysis (class in biocrnpyler.mechanisms) BasicIntegration (class in biocrnpyler.mechanisms) BasicProduction (class in biocrnpyler.mechanisms) BasicPURE (class in biocrnpyler.mixtures) binds_to() (biocrnpyler.components.IntegraseRule method) biocrnpyler module

biocrnpyler.components module biocrnpyler.core module biocrnpyler.mechanisms module biocrnpyler.mixtures module

C

CDS (class in biocrnpyler.components.dna) changed() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) check_crn_validity() (biocrnpyler.core.ChemicalReactionNetwork static method) check_loop() (biocrnpyler.components.ConstructExplorer method) (biocrnpyler.components.TlExplorer method) (biocrnpyler.components.TxExplorer method) ChemicalComplex (class in biocrnpyler.components) ChemicalReactionNetwork (class in biocrnpyler.core) clone() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) Combinatorial_Cooperative_Binding (class in biocrnpyler.mechanisms) combinatorial_enumeration() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) CombinatorialComplex (class in biocrnpyler.components) CombinatorialConformation (class in biocrnpyler.components) CombinatorialConformationPromoter (class in biocrnpyler.components) CombinatorialPromoter (class in biocrnpyler.components.dna) compartment (biocrnpyler.components.ChemicalComplex property) (biocrnpyler.components.CombinatorialComplex property) (biocrnpyler.components.CombinatorialConformation property) (biocrnpyler.components.CombinatorialConformationPromoter property) (biocrnpyler.components.DiffusibleMolecule property) (biocrnpyler.components.DNA property) (biocrnpyler.components.dna.ActivatablePromoter property) (biocrnpyler.components.dna.CDS property) (biocrnpyler.components.dna.CombinatorialPromoter property) (biocrnpyler.components.dna.Construct property) (biocrnpyler.components.dna.DNA_construct property) (biocrnpyler.components.dna.DNA_part property) (biocrnpyler.components.dna.DNAassembly property) (biocrnpyler.components.dna.DNABindingSite property) (biocrnpyler.components.dna.IntegraseSite property) (biocrnpyler.components.dna.Operator property) (biocrnpyler.components.dna.Origin property) (biocrnpyler.components.dna.Promoter property) (biocrnpyler.components.dna.RBS property) (biocrnpyler.components.dna.RegulatedPromoter property) (biocrnpyler.components.dna.RepressiblePromoter property) (biocrnpyler.components.dna.RNA_construct property) (biocrnpyler.components.dna.Terminator property) (biocrnpyler.components.dna.UserDefined property) (biocrnpyler.components.Enzyme property) (biocrnpyler.components.IntegralMembraneProtein property) (biocrnpyler.components.MembraneChannel property) (biocrnpyler.components.MembranePump property) (biocrnpyler.components.MembraneSensor property) (biocrnpyler.components.Metabolite property) (biocrnpyler.components.Protein property) (biocrnpyler.components.RNA property) (biocrnpyler.core.Component property)

Compartment (class in biocrnpyler.core) compile_crn() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) Complex (class in biocrnpyler.core) ComplexSpecies (class in biocrnpyler.core) Component (class in biocrnpyler.core) component_enumeration() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) ComponentEnumerator (class in biocrnpyler.components) compute_species_changes() (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) compute_species_to_add() (biocrnpyler.components.CombinatorialComplex method) Construct (class in biocrnpyler.components.dna) ConstructExplorer (class in biocrnpyler.components) contains_species_monomer() (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) copy_remove_complexes() (biocrnpyler.core.PolymerConformation method) create_hashless_reverse() (biocrnpyler.components.dna.Construct class method) (biocrnpyler.components.dna.DNA_construct class method) (biocrnpyler.components.dna.RNA_construct class method) create_kinetic_law() (biocrnpyler.core.GeneralPropensity method) (biocrnpyler.core.Hill method) (biocrnpyler.core.HillNegative method) (biocrnpyler.core.HillPositive method) (biocrnpyler.core.MassAction method) (biocrnpyler.core.Propensity method) (biocrnpyler.core.ProportionalHillNegative method) (biocrnpyler.core.ProportionalHillPositive method) create_parameter_key() (biocrnpyler.core.ModelParameter static method) (biocrnpyler.core.ParameterEntry static method) create_polymer() (biocrnpyler.components.Polymer_transformation method)

D

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

DNA_construct (class in biocrnpyler.components.dna) DNA_part (class in biocrnpyler.components.dna) dna_species (biocrnpyler.components.CombinatorialConformationPromoter property) (biocrnpyler.components.dna.ActivatablePromoter property) (biocrnpyler.components.dna.CDS property) (biocrnpyler.components.dna.CombinatorialPromoter property) (biocrnpyler.components.dna.DNA_part property) (biocrnpyler.components.dna.DNABindingSite property) (biocrnpyler.components.dna.IntegraseSite property) (biocrnpyler.components.dna.Operator property) (biocrnpyler.components.dna.Origin property) (biocrnpyler.components.dna.Promoter property) (biocrnpyler.components.dna.RBS property) (biocrnpyler.components.dna.RegulatedPromoter property) (biocrnpyler.components.dna.RepressiblePromoter property) (biocrnpyler.components.dna.Terminator property) (biocrnpyler.components.dna.UserDefined property) dna_to_bind (biocrnpyler.components.CombinatorialConformationPromoter property) (biocrnpyler.components.dna.ActivatablePromoter property) (biocrnpyler.components.dna.CombinatorialPromoter property) (biocrnpyler.components.dna.Promoter property) (biocrnpyler.components.dna.RegulatedPromoter property) (biocrnpyler.components.dna.RepressiblePromoter property) DNAassembly (class in biocrnpyler.components.dna) DNABindingSite (class in biocrnpyler.components.dna) dummify() (biocrnpyler.components.Polymer_transformation class method)

E

Energy_Transcription_MM (class in biocrnpyler.mechanisms) Energy_Translation_MM (class in biocrnpyler.mechanisms) EnergyTxTlExtract (class in biocrnpyler.mixtures) enumerate_components() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.ComponentEnumerator method) (biocrnpyler.components.ConstructExplorer method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.GlobalComponentEnumerator method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.Integrase_Enumerator method) (biocrnpyler.components.LocalComponentEnumerator method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.components.TlExplorer method) (biocrnpyler.components.TxExplorer method) (biocrnpyler.core.Component method)

enumerate_constructs() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) Enzyme (class in biocrnpyler.components) EnzymeIntegration (class in biocrnpyler.mechanisms) excluded_states (biocrnpyler.components.CombinatorialComplex property) (biocrnpyler.components.CombinatorialConformation property) (biocrnpyler.components.CombinatorialConformationPromoter property) ExpressionDilutionMixture (class in biocrnpyler.mixtures) ExpressionExtract (class in biocrnpyler.mixtures)

F

Facilitated_Transport_MM (class in biocrnpyler.mechanisms) final_states (biocrnpyler.components.CombinatorialComplex property) (biocrnpyler.components.CombinatorialConformation property) (biocrnpyler.components.CombinatorialConformationPromoter property) find_dna_construct() (biocrnpyler.components.Integrase_Enumerator class method) find_parameter() (biocrnpyler.core.ParameterDatabase method) find_polymer_component() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method)

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

G

GeneralPropensity (class in biocrnpyler.core) generate_products() (biocrnpyler.components.IntegraseRule method) generate_sbml_model() (biocrnpyler.core.ChemicalReactionNetwork method) get_all_species_containing() (biocrnpyler.core.ChemicalReactionNetwork method) get_available_propensities() (biocrnpyler.core.GeneralPropensity static method) (biocrnpyler.core.Hill static method) (biocrnpyler.core.HillNegative static method) (biocrnpyler.core.HillPositive static method) (biocrnpyler.core.MassAction static method) (biocrnpyler.core.Propensity static method) (biocrnpyler.core.ProportionalHillNegative static method) (biocrnpyler.core.ProportionalHillPositive static method) get_circularly_permuted() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) get_combinations_between() (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) get_complexed_species() (biocrnpyler.components.dna.IntegraseSite method) get_component() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) get_initial_concentration() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) get_mechanism() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) get_orphan() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) get_parameter() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mixture method) (biocrnpyler.mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.Dilution method) (biocrnpyler.mechanisms.GlobalMechanism method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method)

get_part() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) get_partlist_hash() (biocrnpyler.components.dna.Construct class method) (biocrnpyler.components.dna.DNA_construct class method) (biocrnpyler.components.dna.RNA_construct class method) get_partstring() (biocrnpyler.components.dna.Construct class method) (biocrnpyler.components.dna.DNA_construct class method) (biocrnpyler.components.dna.RNA_construct class method) get_protein_for_expression() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) get_removed() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) get_renumbered() (biocrnpyler.components.Polymer_transformation method) get_reversed() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) get_sbml_id() (biocrnpyler.core.ModelParameter method) (biocrnpyler.core.ParameterEntry method) get_species() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.Component method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) global_component_enumeration() (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) global_mechanisms (biocrnpyler.core.Mixture property) (biocrnpyler.mixtures.BasicPURE property) (biocrnpyler.mixtures.EnergyTxTlExtract property) (biocrnpyler.mixtures.ExpressionDilutionMixture property) (biocrnpyler.mixtures.ExpressionExtract property) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture property) (biocrnpyler.mixtures.SimpleTxTlExtract property) (biocrnpyler.mixtures.TxTlDilutionMixture property) (biocrnpyler.mixtures.TxTlExtract property) GlobalComponentEnumerator (class in biocrnpyler.components) GlobalMechanism (class in biocrnpyler.mechanisms)

H

Hill (class in biocrnpyler.core)

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

I

initial_concentration_dict (biocrnpyler.core.ChemicalReactionNetwork property) initial_condition_vector() (biocrnpyler.core.ChemicalReactionNetwork method) initial_states (biocrnpyler.components.CombinatorialComplex property) (biocrnpyler.components.CombinatorialConformation property) (biocrnpyler.components.CombinatorialConformationPromoter property) inputs (biocrnpyler.core.Reaction property) insert() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) IntegralMembraneProtein (class in biocrnpyler.components) Integrase_Enumerator (class in biocrnpyler.components) IntegraseRule (class in biocrnpyler.components) IntegraseSite (class in biocrnpyler.components.dna) integrate() (biocrnpyler.components.IntegraseRule method) intermediate_states (biocrnpyler.components.CombinatorialComplex property) (biocrnpyler.components.CombinatorialConformation property) (biocrnpyler.components.CombinatorialConformationPromoter property)

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

K

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

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

L

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

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

M

make_cooperative_complex() (biocrnpyler.mechanisms.Combinatorial_Cooperative_Binding method) make_name() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) make_polymers() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) MassAction (class in biocrnpyler.core) Mechanism (class in biocrnpyler.core) mechanisms (biocrnpyler.core.Mixture property) (biocrnpyler.mixtures.BasicPURE property) (biocrnpyler.mixtures.EnergyTxTlExtract property) (biocrnpyler.mixtures.ExpressionDilutionMixture property) (biocrnpyler.mixtures.ExpressionExtract property) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture property) (biocrnpyler.mixtures.SimpleTxTlExtract property) (biocrnpyler.mixtures.TxTlDilutionMixture property) (biocrnpyler.mixtures.TxTlExtract property) Membrane_Protein_Integration (class in biocrnpyler.mechanisms) Membrane_Signaling_Pathway_MM (class in biocrnpyler.mechanisms) MembraneChannel (class in biocrnpyler.components) MembranePump (class in biocrnpyler.components) MembraneSensor (class in biocrnpyler.components) Metabolite (class in biocrnpyler.components) MichaelisMenten (class in biocrnpyler.mechanisms) MichaelisMentenCopy (class in biocrnpyler.mechanisms) MichaelisMentenReversible (class in biocrnpyler.mechanisms) Mixture (class in biocrnpyler.core) ModelParameter (class in biocrnpyler.core) module biocrnpyler biocrnpyler.components biocrnpyler.core biocrnpyler.mechanisms biocrnpyler.mixtures

monomer_count() (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) monomer_eq() (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) monomer_insert() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) MonomerCollection (class in biocrnpyler.core) multi_tl (class in biocrnpyler.mechanisms) multi_tx (class in biocrnpyler.mechanisms)

N

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

name (biocrnpyler.core.Compartment property) NamedPolymer (class in biocrnpyler.core) NegativeHillTranscription (class in biocrnpyler.mechanisms)

O

omnihash() (biocrnpyler.components.dna.Construct class method) (biocrnpyler.components.dna.DNA_construct class method) (biocrnpyler.components.dna.RNA_construct class method) One_Step_Binding (class in biocrnpyler.mechanisms) One_Step_Cooperative_Binding (class in biocrnpyler.mechanisms) One_Step_Reversible_Conformation_Change (class in biocrnpyler.mechanisms) OneStepGeneExpression (class in biocrnpyler.mechanisms)

OneStepPathway (class in biocrnpyler.mechanisms) Operator (class in biocrnpyler.components.dna) OrderedComplexSpecies (class in biocrnpyler.core) OrderedMonomer (class in biocrnpyler.core) OrderedPolymer (class in biocrnpyler.core) OrderedPolymerSpecies (class in biocrnpyler.core) Origin (class in biocrnpyler.components.dna) outputs (biocrnpyler.core.Reaction property)

P

Parameter (class in biocrnpyler.core) parameter_info (biocrnpyler.core.ModelParameter property) (biocrnpyler.core.ParameterEntry property) parameter_key (biocrnpyler.core.ModelParameter property) (biocrnpyler.core.ParameterEntry property) parameter_name (biocrnpyler.core.ModelParameter property) (biocrnpyler.core.Parameter property) (biocrnpyler.core.ParameterEntry property) ParameterDatabase (class in biocrnpyler.core) ParameterEntry (class in biocrnpyler.core) Polymer_transformation (class in biocrnpyler.components) PolymerConformation (class in biocrnpyler.core) PositiveHillTranscription (class in biocrnpyler.mechanisms) pretty_print() (biocrnpyler.core.ChemicalReactionNetwork method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.GeneralPropensity method) (biocrnpyler.core.Hill method) (biocrnpyler.core.HillNegative method) (biocrnpyler.core.HillPositive method) (biocrnpyler.core.MassAction method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Propensity method) (biocrnpyler.core.ProportionalHillNegative method) (biocrnpyler.core.ProportionalHillPositive method) (biocrnpyler.core.Reaction method) (biocrnpyler.core.Species method)

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

R

RBS (class in biocrnpyler.components.dna) Reaction (class in biocrnpyler.core) reaction_allowed() (biocrnpyler.components.IntegraseRule method) reactions (biocrnpyler.core.ChemicalReactionNetwork property) reactive_sites() (biocrnpyler.components.IntegraseRule method) RegulatedPromoter (class in biocrnpyler.components.dna) remove() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) remove_attribute() (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) renumber_output() (biocrnpyler.components.Polymer_transformation method) replace() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) replace_species() (biocrnpyler.core.ChemicalReactionNetwork method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Reaction method) (biocrnpyler.core.Species method)

RepressiblePromoter (class in biocrnpyler.components.dna) reset() (biocrnpyler.components.Integrase_Enumerator method) reset_enumerator() (biocrnpyler.components.ConstructExplorer method) (biocrnpyler.components.TlExplorer method) (biocrnpyler.components.TxExplorer method) reset_stored_data() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) reverse() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.NamedPolymer method) (biocrnpyler.core.OrderedPolymer method) (biocrnpyler.core.OrderedPolymerSpecies method) reversed() (biocrnpyler.components.Polymer_transformation method) RNA (class in biocrnpyler.components) RNA_construct (class in biocrnpyler.components.dna) rotation_free_hash() (biocrnpyler.components.dna.Construct class method) (biocrnpyler.components.dna.DNA_construct class method) (biocrnpyler.components.dna.RNA_construct class method)

S

s1 (biocrnpyler.core.Hill property) (biocrnpyler.core.HillNegative property) (biocrnpyler.core.HillPositive property) (biocrnpyler.core.ProportionalHillNegative property) (biocrnpyler.core.ProportionalHillPositive property) search_key (biocrnpyler.core.ModelParameter property) set_attributes() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) set_dir() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) set_mixture() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method)

set_species() (biocrnpyler.components.ChemicalComplex class method) (biocrnpyler.components.CombinatorialComplex class method) (biocrnpyler.components.CombinatorialConformation class method) (biocrnpyler.components.CombinatorialConformationPromoter class method) (biocrnpyler.components.DiffusibleMolecule class method) (biocrnpyler.components.DNA class method) (biocrnpyler.components.dna.ActivatablePromoter class method) (biocrnpyler.components.dna.CDS class method) (biocrnpyler.components.dna.CombinatorialPromoter class method) (biocrnpyler.components.dna.Construct class method) (biocrnpyler.components.dna.DNA_construct class method) (biocrnpyler.components.dna.DNA_part class method) (biocrnpyler.components.dna.DNAassembly class method) (biocrnpyler.components.dna.DNABindingSite class method) (biocrnpyler.components.dna.IntegraseSite class method) (biocrnpyler.components.dna.Operator class method) (biocrnpyler.components.dna.Origin class method) (biocrnpyler.components.dna.Promoter class method) (biocrnpyler.components.dna.RBS class method) (biocrnpyler.components.dna.RegulatedPromoter class method) (biocrnpyler.components.dna.RepressiblePromoter class method) (biocrnpyler.components.dna.RNA_construct class method) (biocrnpyler.components.dna.Terminator class method) (biocrnpyler.components.dna.UserDefined class method) (biocrnpyler.components.Enzyme class method) (biocrnpyler.components.IntegralMembraneProtein class method) (biocrnpyler.components.MembraneChannel class method) (biocrnpyler.components.MembranePump class method) (biocrnpyler.components.MembraneSensor class method) (biocrnpyler.components.Metabolite class method) (biocrnpyler.components.Protein class method) (biocrnpyler.components.RNA class method) (biocrnpyler.core.Component class method) (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) Simple_Diffusion (class in biocrnpyler.mechanisms) Simple_Transport (class in biocrnpyler.mechanisms) SimpleTranscription (class in biocrnpyler.mechanisms) SimpleTranslation (class in biocrnpyler.mechanisms) SimpleTxTlDilutionMixture (class in biocrnpyler.mixtures) SimpleTxTlExtract (class in biocrnpyler.mixtures) simulate_with_bioscrape() (biocrnpyler.core.ChemicalReactionNetwork method) simulate_with_bioscrape_via_sbml() (biocrnpyler.core.ChemicalReactionNetwork method) simulate_with_roadrunner() (biocrnpyler.core.ChemicalReactionNetwork method) size (biocrnpyler.core.Compartment property) spatial_dimensions (biocrnpyler.core.Compartment property) species (biocrnpyler.core.ChemicalReactionNetwork property) (biocrnpyler.core.GeneralPropensity property) (biocrnpyler.core.Hill property) (biocrnpyler.core.HillNegative property) (biocrnpyler.core.HillPositive property) (biocrnpyler.core.MassAction property) (biocrnpyler.core.Propensity property) (biocrnpyler.core.ProportionalHillNegative property) (biocrnpyler.core.ProportionalHillPositive property) (biocrnpyler.core.Reaction property) Species (class in biocrnpyler.core) subhash() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.core.ComplexSpecies method) (biocrnpyler.core.OrderedComplexSpecies method) (biocrnpyler.core.OrderedMonomer method) (biocrnpyler.core.OrderedPolymerSpecies method) (biocrnpyler.core.PolymerConformation method) (biocrnpyler.core.Species method) substrates (biocrnpyler.components.Enzyme property)

T

Terminator (class in biocrnpyler.components.dna) TlExplorer (class in biocrnpyler.components) Transcription_MM (class in biocrnpyler.mechanisms) Translation_MM (class in biocrnpyler.mechanisms)

Two_Step_Cooperative_Binding (class in biocrnpyler.mechanisms) TxExplorer (class in biocrnpyler.components) TxTlDilutionMixture (class in biocrnpyler.mixtures) TxTlExtract (class in biocrnpyler.mixtures)

U

unclone() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) unit (biocrnpyler.core.Compartment property) (biocrnpyler.core.ModelParameter property) (biocrnpyler.core.Parameter property) (biocrnpyler.core.ParameterEntry property) update_base_species() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) update_combinatorial_complexes() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) update_component() (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) update_dna() (biocrnpyler.components.dna.DNAassembly method) update_integrase() (biocrnpyler.components.dna.IntegraseSite method) update_parameters() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mixture method) (biocrnpyler.mixtures.BasicPURE method) (biocrnpyler.mixtures.EnergyTxTlExtract method) (biocrnpyler.mixtures.ExpressionDilutionMixture method) (biocrnpyler.mixtures.ExpressionExtract method) (biocrnpyler.mixtures.SimpleTxTlDilutionMixture method) (biocrnpyler.mixtures.SimpleTxTlExtract method) (biocrnpyler.mixtures.TxTlDilutionMixture method) (biocrnpyler.mixtures.TxTlExtract method) update_permutation_hash() (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.RNA_construct method) update_promoter() (biocrnpyler.components.dna.DNAassembly method) update_protein() (biocrnpyler.components.dna.DNAassembly method) update_rbs() (biocrnpyler.components.dna.DNAassembly method) update_reactions() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mechanism method) (biocrnpyler.mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.BasicCatalysis method) (biocrnpyler.mechanisms.BasicIntegration method) (biocrnpyler.mechanisms.BasicProduction method) (biocrnpyler.mechanisms.Combinatorial_Cooperative_Binding method) (biocrnpyler.mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.Dilution method) (biocrnpyler.mechanisms.Energy_Transcription_MM method) (biocrnpyler.mechanisms.Energy_Translation_MM method) (biocrnpyler.mechanisms.EnzymeIntegration method) (biocrnpyler.mechanisms.Facilitated_Transport_MM method) (biocrnpyler.mechanisms.GlobalMechanism method) (biocrnpyler.mechanisms.Membrane_Protein_Integration method) (biocrnpyler.mechanisms.Membrane_Signaling_Pathway_MM method) (biocrnpyler.mechanisms.MichaelisMenten method) (biocrnpyler.mechanisms.MichaelisMentenCopy method) (biocrnpyler.mechanisms.MichaelisMentenReversible method) (biocrnpyler.mechanisms.multi_tl method) (biocrnpyler.mechanisms.multi_tx method) (biocrnpyler.mechanisms.NegativeHillTranscription method) (biocrnpyler.mechanisms.One_Step_Binding method) (biocrnpyler.mechanisms.One_Step_Cooperative_Binding method) (biocrnpyler.mechanisms.One_Step_Reversible_Conformation_Change method) (biocrnpyler.mechanisms.OneStepGeneExpression method) (biocrnpyler.mechanisms.OneStepPathway method) (biocrnpyler.mechanisms.PositiveHillTranscription method) (biocrnpyler.mechanisms.Primary_Active_Transport_MM method) (biocrnpyler.mechanisms.Simple_Diffusion method) (biocrnpyler.mechanisms.Simple_Transport method) (biocrnpyler.mechanisms.SimpleTranscription method) (biocrnpyler.mechanisms.SimpleTranslation method) (biocrnpyler.mechanisms.Transcription_MM method) (biocrnpyler.mechanisms.Translation_MM method) (biocrnpyler.mechanisms.Two_Step_Cooperative_Binding method)

update_reactions_global() (biocrnpyler.mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.Dilution method) (biocrnpyler.mechanisms.GlobalMechanism method) update_species() (biocrnpyler.components.ChemicalComplex method) (biocrnpyler.components.CombinatorialComplex method) (biocrnpyler.components.CombinatorialConformation method) (biocrnpyler.components.CombinatorialConformationPromoter method) (biocrnpyler.components.DiffusibleMolecule method) (biocrnpyler.components.DNA method) (biocrnpyler.components.dna.ActivatablePromoter method) (biocrnpyler.components.dna.CDS method) (biocrnpyler.components.dna.CombinatorialPromoter method) (biocrnpyler.components.dna.Construct method) (biocrnpyler.components.dna.DNA_construct method) (biocrnpyler.components.dna.DNA_part method) (biocrnpyler.components.dna.DNAassembly method) (biocrnpyler.components.dna.DNABindingSite method) (biocrnpyler.components.dna.IntegraseSite method) (biocrnpyler.components.dna.Operator method) (biocrnpyler.components.dna.Origin method) (biocrnpyler.components.dna.Promoter method) (biocrnpyler.components.dna.RBS method) (biocrnpyler.components.dna.RegulatedPromoter method) (biocrnpyler.components.dna.RepressiblePromoter method) (biocrnpyler.components.dna.RNA_construct method) (biocrnpyler.components.dna.Terminator method) (biocrnpyler.components.dna.UserDefined method) (biocrnpyler.components.Enzyme method) (biocrnpyler.components.IntegralMembraneProtein method) (biocrnpyler.components.MembraneChannel method) (biocrnpyler.components.MembranePump method) (biocrnpyler.components.MembraneSensor method) (biocrnpyler.components.Metabolite method) (biocrnpyler.components.Protein method) (biocrnpyler.components.RNA method) (biocrnpyler.core.Component method) (biocrnpyler.core.Mechanism method) (biocrnpyler.mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.BasicCatalysis method) (biocrnpyler.mechanisms.BasicIntegration method) (biocrnpyler.mechanisms.BasicProduction method) (biocrnpyler.mechanisms.Combinatorial_Cooperative_Binding method) (biocrnpyler.mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.Dilution method) (biocrnpyler.mechanisms.Energy_Transcription_MM method) (biocrnpyler.mechanisms.Energy_Translation_MM method) (biocrnpyler.mechanisms.EnzymeIntegration method) (biocrnpyler.mechanisms.Facilitated_Transport_MM method) (biocrnpyler.mechanisms.GlobalMechanism method) (biocrnpyler.mechanisms.Membrane_Protein_Integration method) (biocrnpyler.mechanisms.Membrane_Signaling_Pathway_MM method) (biocrnpyler.mechanisms.MichaelisMenten method) (biocrnpyler.mechanisms.MichaelisMentenCopy method) (biocrnpyler.mechanisms.MichaelisMentenReversible method) (biocrnpyler.mechanisms.multi_tl method) (biocrnpyler.mechanisms.multi_tx method) (biocrnpyler.mechanisms.NegativeHillTranscription method) (biocrnpyler.mechanisms.One_Step_Binding method) (biocrnpyler.mechanisms.One_Step_Cooperative_Binding method) (biocrnpyler.mechanisms.One_Step_Reversible_Conformation_Change method) (biocrnpyler.mechanisms.OneStepGeneExpression method) (biocrnpyler.mechanisms.OneStepPathway method) (biocrnpyler.mechanisms.PositiveHillTranscription method) (biocrnpyler.mechanisms.Primary_Active_Transport_MM method) (biocrnpyler.mechanisms.Simple_Diffusion method) (biocrnpyler.mechanisms.Simple_Transport method) (biocrnpyler.mechanisms.SimpleTranscription method) (biocrnpyler.mechanisms.SimpleTranslation method) (biocrnpyler.mechanisms.Transcription_MM method) (biocrnpyler.mechanisms.Translation_MM method) (biocrnpyler.mechanisms.Two_Step_Cooperative_Binding method) update_species_global() (biocrnpyler.mechanisms.AntiDilutionConstitutiveCreation method) (biocrnpyler.mechanisms.Deg_Tagged_Degradation method) (biocrnpyler.mechanisms.Degradation_mRNA_MM method) (biocrnpyler.mechanisms.Dilution method) (biocrnpyler.mechanisms.GlobalMechanism method) update_transcript() (biocrnpyler.components.dna.DNAassembly method) UserDefined (class in biocrnpyler.components.dna)

V

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

W

WeightedSpecies (class in biocrnpyler.core)

write_sbml_file() (biocrnpyler.core.ChemicalReactionNetwork method)