Python reference¶

This is an reference for the public python pinetree interface.

Model¶

class pinetree.Model(self: pinetree.core.Model, cell_volume: float) → None¶

Define a pinetree model.

Parameters:	cell_volume (float) – The volume, in liters, of the system being simulated.

Examples

>>> import pinetree.pinetree as pt
>>> sim = pt.Model(cell_volume=8e-16) # Approximate volume of E. coli cell

add_polymerase(self: pinetree.core.Model, name: str, footprint: int, speed: float, copy_number: int) → None¶

Add a polymerase to the model. There may be multiple types of polymerases in a model.

Note

Defining a polymerase with a footprint larger than that of the promoter it binds is not currently supported.

Parameters:	name (str) – Name of the polymerase which can be referred to in `add_reaction()` and `add_promoter()`. copy_number (int) – Initial number of copies of the polymerase speed (int) – Speed, in base pairs per second, at which the polymerase transcribes footprint (int) – Footprint, in base pairs, of the polymerase on the genome

add_polymerase_with_readthrough(self: pinetree.core.Model, name: str, footprint: int, speed: float, copy_number: int) → None¶

Add a polymerase with genome end readthrough to the model. This is used to simulate transcription of a circular genome.

Note

Defining a polymerase with a footprint larger than that of the promoter it binds is not currently supported.

Parameters:	name (str) – Name of the polymerase which can be referred to in `add_reaction()` and `add_promoter()`. copy_number (int) – Initial number of copies of the polymerase speed (int) – Speed, in base pairs per second, at which the polymerase transcribes footprint (int) – Footprint, in base pairs, of the polymerase on the genome

add_reaction(self: pinetree.core.Model, rate_constant: float, reactants: List[str], products: List[str]) → None¶

Define a reaction between species, which may include free ribosomes and polymerases.

Parameters:	rate_constant (float) – Macroscopic rate constant of the reaction. This will be converted into a stochastic mesoscopic rate constant automatically. reactants (list) – List of reactants, which may be species, ribosomes, or polymerases products (list) – List of products which may be species, ribosomes, or polymerases

Note

Reaction rate constants should be given as macroscopic rate constants, the same constants used in differential equation-based models. Pinetree will automatically convert these rate constants to mesoscopic constants required for a stochastic simulation.

Example

>>> coming soon

add_ribosome(self: pinetree.core.Model, footprint: int, speed: float, copy_number: int) → None¶

Add ribosomes to the model. There may only be a single type of ribosome.

Note

Defining ribosomes with a footprint larger than that of the promoter it binds is not currently supported.

Parameters:	copy_number (int) – Initial number of copies of free ribosomes speed (int) – Mean speed, in base pairs per second, at which the ribosome translates. This speed will be scaled on a per site basis if translation weights are defined. (See Genome.AddWeights). footprint (int) – Footprint, in base pairs, of the ribosome on RNA

add_species(self: pinetree.core.Model, name: str, copy_number: int) → None¶

Defines individual chemical species not specified by either add_ribosome() or add_polymerase().

Parameters:	name (str) – Name of chemical species which can be referred to in reactions added with `add_reaction()`. copy_number (int) – Initial number of copies of the chemical species

register_genome(self: pinetree.core.Model, arg0: Genome) → None¶

Register a genome with the model.

Parameters:	genome (Genome) – a pinetree `Genome` object.

register_transcript(self: pinetree.core.Model, arg0: Transcript) → None¶

Register a genome-independent transcript with the model.

Parameters:	transcript (Transcript) – a pinetree `Transcript` object.

seed(self: pinetree.core.Model, arg0: int) → None¶

Set a seed for reproducible simulations.

Parameters:	seed (int) – a seed for the random number generator

simulate(self: pinetree.core.Model, time_limit: int, time_step: int, output: str = 'counts.tsv') → None¶

Run a gene expression simulation. Produces a tab separated file of protein and transcript counts at user-specified time intervals.

Parameters:

time_limit (int) – Simulated time, in seconds at which this simulation should stop executing reactions. Note that this simulated time and not real time. The real time that it takes for the simulation to complete depends on the number of reactions and species (genomes, transcripts, proteins, etc) in the system.
time_step (int) – Time interval, in seconds, that species counts are reported.
output (str) – Name of output file (default: counts.tsv).

Genome¶

class pinetree.Genome(self: pinetree.core.Genome, name: str, length: int, transcript_degradation_rate_ext: float = 0.0, rnase_speed: float = 0.0, rnase_footprint: int = 0, transcript_degradation_rate: float = 0.0) → None¶

Define a linear genome.

Parameters:

name (str) – Name of genome.
length (int) – Length of genome in base pairs.
transcript_degradation_rate_ext (float) – Unary binding rate constant for binding of RNases to the 5’-end of transcripts.
rnase_speed (flaot) – Mean speed at which RNase degrades transcript, in bases per second.
rnase_footprint (float) – Initial footprint of RNase on RNA.
transcript_degradation_rate (float) – Deprecated. Unary binding rate constant for binding of RNases to internal RNase sites. (See the add_rnase_site() method below for details.)

add_rnase_site(name, start, stop, rate)¶

Define an Rnase cleavage site.

Parameters:	name (string) – A unique identifier for this RNase cleavage site. start (int) – Start position of RNase cleavage site. stop (int) – Stop position of RNase cleavage site. rate (float) – Binding rate constant between RNase and this cleavage site.

Note

The internal RNase binding rate constant can alternatively be supplied as an argument during Genome initialization (see Genome class description above). In this case, add_rnase_site() will only accept values for start and stop, and all rnase binding sites will be initialized with the same rate constant. Warning: This method is deprecated and may be removed in the future.

add_gene(self: pinetree.core.Genome, name: str, start: int, stop: int, rbs_start: int, rbs_stop: int, rbs_strength: float) → None¶

Define a gene. Genes may be defined in any order.

Note

Overlapping genes, or genes that overlap with ribosome binding sites, are supported as of release 0.3.0. If using an ealier version, specifing overlapping genes is not recommended, and could cause the program to crash.

Parameters:

name (str) – Name of gene. Name may be referenced by Genome.add_reaction.
start (int) – Start position of gene.
stop (int) – Stop position of gene.
rbs_start (int) – Start position of ribosome binding site. Generally positioned upstream of gene start.
rbs_stop (int) – Stop position of ribosome binding site.
rbs_strength (float) – Binding rate constant between ribosome and ribosome binding site.

add_mask(self: pinetree.core.Genome, start: int, interactions: List[str]) → None¶

Mask a portion of this Genome. This mask may correspond to a portion of the genome that has not yet entered the cell or is otherwise inaccessible. Also define which Polymerases are capabile of moving the Mask (e.g. an RNA polymerase that actively pulls the genome into the cell.)

Parameters:	start (int) – Start position of Mask. The Mask is assumed to extend to the end of the genome. interactions (list) – List of Polymerase names capable of shifting the Mask backwards and revealing more of the genome.

add_promoter(self: pinetree.core.Genome, name: str, start: int, stop: int, interactions: Dict[str, float]) → None¶

Define a promoter.

Parameters:	name (str) – Name of promoter. start (int) – Start position of promoter. stop (int) – Stop position of promoter. interactions (dict) – Dictionary of binding rate constants for different Polymerases that this promoter interacts with.

Example

>>> genome.add_promoter(name="phi1", start=1, stop=10,
>>>                     interactions={'rnapol': 1e7})

add_terminator(self: pinetree.core.Genome, name: str, start: int, stop: int, efficiency: Dict[str, float]) → None¶

Define a terminator.

Parameters:

name (str) – Name of terminator.
start (int) – Start position of terminator.
stop (int) – Stop position of terminator.
efficiency (dict) – Dictionary of termination efficiencies (between 0 and 1) for different Polymerases that this terminator interacts with. A value of 1.0 represents complete stop of transcription and removal of the Polymerase. A value of 0.0 means that the Polymerase will always read through the terminator and continue transcription.

Example

>>> genome.add_terminator(name="t1", start=50, stop=51,
>>>                       efficiency={'rnapol': 0.85})

add_weights(self: pinetree.core.Genome, weights: List[float]) → None¶

Define position-specific translation speed weights. These may correspond, for example, codon-specific translation rates.

Parameters:	weights (list) – List of weights of same length as Genome. These weights are multiplied by the ribosome speed to calculate a final translation rate at every position in the genome.