pySTDLM.StandardReactions Namespace Reference

Functions
	addMembraneTransporter (sim, transporter, number, name1, name2, dRate, kf, kr, region1='cytoplasm', region2='default', intoRegion='membrane')
	addPassiveTransport (sim, specie, dRate, region1='cytoplasm', region2='default', region3='membrane')
	addMichaelisMenten (sim, reactant, enzyme, product, k1f, k1b, k2, region='cytoplasm')
	addReversibleMichaelisMenten (sim, reactant, enzyme, product, k1f, k1b, k2f, k2b, k3f, k3b, region='cytoplasm')
	createExpressionModel (sim, gb, kt, kd, kr, kdil=None, regions=None)

Variables
bool	hasBio = True

Function Documentation

addMembraneTransporter()

pySTDLM.StandardReactions.addMembraneTransporter	(		sim,
			transporter,
			number,
			name1,
			name2,
			dRate,
			kf,
			kr,
			region1 = 'cytoplasm',
			region2 = 'default',
			intoRegion = 'membrane' )

Adds a membrane transport system to an RDME system

Args:
    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

addMichaelisMenten()

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

Adds a Michaelis Menten Reaction

Args:
    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

addPassiveTransport()

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

Adds a passive transport system to an RDME system

Args:
    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

addReversibleMichaelisMenten()

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

Add a Reversible Michaelis Menten Reaction

Args:
    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

createExpressionModel()

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

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

Args:
    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:
    SeqIO representation of the Genbank file with qualifiers added: qualifiers["dna_id"->(str,int),"rna_id"->(str,int), "protein_id"->(str,int)]

Variable Documentation

hasBio

bool pySTDLM.StandardReactions.hasBio = True