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pyLM
v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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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 | |
def pySTDLM.StandardReactions.addMembraneTransporter | ( | sim, | |
transporter, | |||
number, | |||
name1, | |||
name2, | |||
dRate, | |||
kf, | |||
kr, | |||
region1 = 'cytoplasm' , |
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region2 = 'default' , |
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intoRegion = 'membrane' |
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) |
Adds a membrane transport system to an RDME system.
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 |
def pySTDLM.StandardReactions.addMichaelisMenten | ( | sim, | |
reactant, | |||
enzyme, | |||
product, | |||
k1f, | |||
k1b, | |||
k2, | |||
region = 'cytoplasm' |
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) |
Adds a Michaelis Menten Reaction.
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) |
def pySTDLM.StandardReactions.addPassiveTransport | ( | sim, | |
specie, | |||
dRate, | |||
region1 = 'cytoplasm' , |
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region2 = 'default' , |
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region3 = 'membrane' |
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) |
Adds a passive transport system to an RDME system.
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 |
def pySTDLM.StandardReactions.addReversibleMichaelisMenten | ( | sim, | |
reactant, | |||
enzyme, | |||
product, | |||
k1f, | |||
k1b, | |||
k2f, | |||
k2b, | |||
k3f, | |||
k3b, | |||
region = 'cytoplasm' |
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) |
Add a Reversible Michaelis Menten Reaction.
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) |
def pySTDLM.StandardReactions.createExpressionModel | ( | sim, | |
gb, | |||
kt, | |||
kd, | |||
kr, | |||
kdil = None , |
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regions = None |
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) |
Create a set of gene/mRNA/protein reactions based on a genebank file and a set of rates assuming constitutive expression.
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) |
pySTDLM.StandardReactions.hasBio = True |