pySTDLM.StandardReactions#

Functions

addMembraneTransporter(sim, transporter, ...)

Adds a membrane transport system to an RDME system

addMichaelisMenten(sim, reactant, enzyme, ...)

Adds a Michaelis Menten Reaction

addPassiveTransport(sim, specie, dRate[, ...])

Adds a passive transport system to an RDME system

addReversibleMichaelisMenten(sim, reactant, ...)

Add a Reversible Michaelis Menten Reaction

createExpressionModel(sim, gb, kt, kd, kr[, ...])

Create a set of gene/mRNA/protein reactions based on a genebank file and a set of rates assuming constitutive expression
pySTDLM.StandardReactions.addMembraneTransporter(sim, transporter, number, name1, name2, dRate, kf, kr, region1='cytoplasm', region2='default', intoRegion='membrane')[source]#

Adds a membrane transport system to an RDME system

Parameters:

  • sim – An RDMESimulation to add the transporter system to

  • transporter – Name of the transporter particle

  • number – The number of transporter molecules

  • name1 – Name of the transported particle in region1

  • name2 – Name of the transported particle in region2

  • dRate – The rate of diffusion from region1<->intoRegion and region2<->intoRegion

  • kf – The forward reaction rate

  • kr – The reverse reaction rate

  • region1 – The region on the first side of the membrane

  • region2 – The region on the second side of the membrane

  • intoRegion – The region representing the membrane

Returns:

The simulation object so this can be a chained call

pySTDLM.StandardReactions.addMichaelisMenten(sim, reactant, enzyme, product, k1f, k1b, k2, region='cytoplasm')[source]#

Adds a Michaelis Menten Reaction

Parameters:

  • sim – The RDME or CME reaction

  • reactant – The reactant that reacts with the enzyme

  • enzyme – The enzyme catalyzing the reaction

  • product – The product of the reaction

  • k1f – The forward reaction rate

  • k1b – The backward reaction rate

  • k2 – The second forward rate

  • region – The region in which the reaction should occur (RDME only)

Returns:

The simulation object so this can be a chained call

pySTDLM.StandardReactions.addPassiveTransport(sim, specie, dRate, region1='cytoplasm', region2='default', region3='membrane')[source]#

Adds a passive transport system to an RDME system

Parameters:

  • sim – An RDMESimulation to add the passive transport to

  • specie – The species that can diffuse across the membrane

  • dRate – The rate of diffusion across the membrane

  • region1 – The region on the first side of the membrane

  • region2 – The region on the second side of the membrane

  • region3 – The region representing the membrane

Returns:

The simulation object so this can be a chained call

pySTDLM.StandardReactions.addReversibleMichaelisMenten(sim, reactant, enzyme, product, k1f, k1b, k2f, k2b, k3f, k3b, region='cytoplasm')[source]#

Add a Reversible Michaelis Menten Reaction

Parameters:

  • sim – The RDME or CME reaction

  • reactant – The reactant that reacts with the enzyme

  • enzyme – The enzyme catalyzing the reaction

  • product – The product of the reaction

  • k1f – The forward reaction rate

  • k1b – The backward reaction rate

  • k2f – The second forward rate

  • k2b – the second backward rate

  • k3f – The third forward rate

  • k3b – the third backward rate

  • region – the region in which the reaction should occur (RDME only)

Returns:

The simulation object so this can be a chained call

pySTDLM.StandardReactions.createExpressionModel(sim, gb, kt, kd, kr, kdil=None, regions=None)[source]#

Create a set of gene/mRNA/protein reactions based on a genebank file and a set of rates assuming constitutive expression

Parameters:

  • sim – The RDME or CME simulation

  • gb – The genbank filename. File should be readable by BioPython.

  • kt – mRNA transcription rate dictionary { locusTag -> rate }

  • kd – mRNA degradation rate dictionary { locusTag -> rate }

  • kr – Protein transcription rate dictionary {locusTag -> rate }

  • kdil – Protein dillution/degradation rate dictionary {locusTag -> rate} (Optional; Default “None”, meaning no dillution reaction will be specified)

  • regions – Regions for the reactions to occur. Degradation is allowed in both regions. {locusTag -> (transcriptionRegion, translationRegion)} (required for RDMESimulations)

Returns:

qualifiers[“dna_id”->(str,int),”rna_id”->(str,int), “protein_id”->(str,int)]

Return type:

SeqIO representation of the Genbank file with qualifiers added