pySTDLM.StandardReactions Namespace Reference

Functions
def	addMembraneTransporter
	Adds a membrane transport system to an RDME system. More...
def	addPassiveTransport
	Adds a passive transport system to an RDME system. More...
def	addMichaelisMenten
	Adds a Michaelis Menten Reaction. More...
def	addReversibleMichaelisMenten
	Add a Reversible Michaelis Menten Reaction. More...
def	createExpressionModel
	Create a set of gene/mRNA/protein reactions based on a genebank file and a set of rates assuming constitutive expression. More...

Variables
	hasBio = True

Function Documentation

def 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.

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

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

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

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

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

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

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

def 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.

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

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

Variable Documentation

pySTDLM.StandardReactions.hasBio = True