bionetgen.network package

Submodules

bionetgen.network.blocks module

class bionetgen.network.blocks.NetworkBlock

Bases: object

Base block object that will be used for each block in the network.

Attributes

namestr

Name of the block which will be used to write the BNGL text

comment(str, str)

comment at the begin {block} or end {block} statements, tuple

itemsOrderedDict

all the model objects in the block

Methods

add_item((name,value))

sets self.item[name] = value to add a particular model object into a block

add_items(item_list)

loops over every element in the list and uses add_item on it

gen_string()

for every block this method generates the BNGL string of the block. it has to be overwritten for each block.

add_item(item_tpl) → None

add_items(item_list) → None

gen_string() → str

class bionetgen.network.blocks.NetworkCompartmentBlock

Bases: NetworkBlock

Compartment block object, subclass of ModelBlock.

Methods

add_compartment(name, dim, size, outside=None)

adds a compartment by making a new Compartment object and passing the args/kwargs to its initialization.

add_compartment(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkEnergyPatternBlock

Bases: NetworkBlock

Energy pattern block object, subclass of NetworkBlock.

Methods

add_energy_pattern(id, pattern, expression)

adds an energy pattern by making a new EnergyPattern object and passing the args/kwargs to its initialization.

add_energy_pattern(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkFunctionBlock

Bases: NetworkBlock

Function block object, subclass of NetworkBlock.

Methods

add_function(name, name, expr, args=None)

adds a function by making a new Function object and passing the args/kwargs to its initialization.

add_function(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkGroupBlock

Bases: NetworkBlock

Group block object, subclass of NetworkBlock.

Methods

add_group(name, otype, patterns=[])

adds an group by making a new NetworkGroup object and passing the args/kwargs to its initialization.

add_group(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkParameterBlock

Bases: NetworkBlock

Parameter block object, subclass of ModelBlock.

Methods

add_parameter(name, value, expr=None)

adds a parameter by making a new Parameter object and passing the args/kwargs to its initialization.

add_parameter(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkPopulationMapBlock

Bases: NetworkBlock

Population map block object, subclass of NetworkBlock.

Methods

add_population_map(id, struct_species, pop_species, rate)

adds a population map by making a new PopulationMap object and passing the args/kwargs to its initialization

add_population_map(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkReactionBlock

Bases: NetworkBlock

Rule block object, subclass of NetworkBlock.

Methods

add_rule(name, name, reactants=[], products=[], rate_constants=())

adds a rule by making a new Rule object and passing the args/kwargs to its initialization.

consolidate_rulesNone

XML loading makes it so that reversible rules are split into two unidirectional rules. This find them and combines them into a single rule to correctly represent the original model rule.

add_reaction(*args, **kwargs) → None

class bionetgen.network.blocks.NetworkSpeciesBlock

Bases: NetworkBlock

Species block object, subclass of NetworkBlock.

Methods

add_species(name, pattern=Pattern(), count=0)

adds a species by making a new Species object and passing the args/kwargs to its initialization.

add_species(*args, **kwargs) → None

bionetgen.network.network module

class bionetgen.network.network.Network(bngl_model, BNGPATH='/home/docs/checkouts/readthedocs.org/user_builds/pybionetgen/checkouts/latest/bionetgen/bng-linux')

Bases: object

Main model object and entry point for model API. The goal of this object is to generate and read the BNGXML of a given BNGL model and give the user a pythonic interface to the resulting model object.

Usage: bngmodel(bng_model)

bngmodel(bng_model, BNGPATH)

Attributes

active_blockslist[str]

a list of the blocks that have been parsed in the model

bngnetworkparserBNGNetworkParser

BNGParser object that’s responsible for .bngl file reading and model setup

network_namestr

name of the model, generally set from the given BNGL file

Methods

write_model(model_name)

write the model in BNGL format to the path given

setup_simulator(sim_type)

sets up a simulator in bngmodel.simulator where the only current supported type of simulator is libRR for libRoadRunner simulator.

add_block(block)

add_empty_block(block_name)

add_groups_block(block=None)

add_parameters_block(block=None)

add_reactions_block(block=None)

add_species_block(block=None)

write_model(file_name)

write the model to file

bionetgen.network.networkparser module

class bionetgen.network.networkparser.BNGNetworkParser(path)

Bases: object

Parser object that deals with reading in the BNGL file and setting up the model object

Usage: BNGParser(bngl_path)

BNGParser(bngl_path, BNGPATH)

Attributes

bngfileBNGFile

BNGFile object that’s responsible for .bngl file manipulations

Methods

parse_model(model_file)

parses the BNGL model at the given path and adds everything to a given model object

parse_xml(xml_str)

parses given xml string and adds everything to a given model object

parse_network(network_obj) → None

Will determine the parser route eventually and call the right parser

bionetgen.network.structs module

class bionetgen.network.structs.NetworkCompartment(name, dim, size, outside=None)

Bases: NetworkObj

Class for all compartments in the network, subclass of NetworkObj.

In BNGL the compartments are of the form

compartment_name dimensions size

Attributes

namestr

name of the compartment

dimstr

dimensionality of the compartment

sizestr

size/volume of the compartment

outsidestr

parent compartment, if exists

gen_string() → str

class bionetgen.network.structs.NetworkEnergyPattern(name, pattern, expression)

Bases: NetworkObj

Class for all energy patterns in the network, subclass of NetworkObj.

In BNGL the energy patterns are of the form

EP_pattern EP_expression

Attributes

namestr

id of the energy pattern

patternPattern

Pattern object representing the energy pattern

expressionstr

expression used for energy pattern

gen_string() → str

class bionetgen.network.structs.NetworkFunction(name, expr, args=None)

Bases: NetworkObj

Class for all functions in the network, subclass of NetworkObj.

In BNGL functions are of the form

function_name function_expression

Attributes

namestr

name of the function

exprstr

function expression

argslist

optional list of arguments for the function

gen_string() → str

class bionetgen.network.structs.NetworkGroup(gid, name, members=[], comment='')

Bases: NetworkObj

Class for all groups in the network, subclass of NetworkObj.

In BNGL networks the groups are of the form

group_ID group_name group_species

where species are separated by commas.

Attributes

idstr

id of the group

namestr

name of the group

specieslist[expr]

list of species expressions of the group

gen_string() → str

class bionetgen.network.structs.NetworkObj

Bases: object

The base class for all items in a network object (parameter, groups etc.).

Attributes

commentstr

comment at the end of the line/object

line_labelstr

line label at the beginning of the line/object

Methods

print_line()

generates the actual line string with line label and comments if applicable

gen_string()

generates the BNGL string of the object itself, separate from line attributes

property comment: None

property line_label: str

print_line() → str

class bionetgen.network.structs.NetworkParameter(pid, name, value, comment='')

Bases: NetworkObj

Class for all parameters in the network, subclass of NetworkObj.

In BNGL networks parameters are of the form

parameter_ID parameter_name parameter_value/expression # comment

Attributes

idint

ID/line label of the network parameter

namestr

name of the network parameter

valuestr

value of the network parameter

gen_string() → str

class bionetgen.network.structs.NetworkPopulationMap(name, struct_species, pop_species, rate)

Bases: NetworkObj

Class for all population maps in the model, subclass of ModelObj.

In BNGL the population maps are of the form

structured_species -> population_species lumping_parameter

Attributes

namestr

id of the population map

struct_speciesPattern

Pattern object representing the species to be mapped

pop_speciesPattern

Pattern object representing the population count

ratestr

lumping parameter used in population mapping

gen_string() → str

class bionetgen.network.structs.NetworkReaction(rid, reactants=[], products=[], rate_constant=None, comment=None)

Bases: NetworkObj

Class for all reactions in the network, subclass of NetworkObj.

Attributes

namestr

name of the rule, optional

reactantslist[Pattern]

list of patterns for reactants

productslist[Pattern]

list of patterns for products

rule_modRuleMod

modifier (moveConnected, TotalRate, etc.) used by a given rule

operationslist[Operation]

list of operations

gen_string()

class bionetgen.network.structs.NetworkSpecies(sid, name, count=0, comment='')

Bases: NetworkObj

Class for all species in the network, subclass of NetworkObj.

In BNGL the species/seed species are of the form

species count

where species is a single pattern and count is the starting value for that specific pattern

Attributes

patternPattern

pattern of the seed species

countstr

starting value of the seed species

gen_string() → str

Module contents