src.basics package

Submodules

src.basics.check_rules module

src.basics.check_rules.check_binding(graph)

check rule binding

Parameters

graph – a StrandGraph object

Returns

edges to be added

src.basics.check_rules.check_existence_4way(elist, edge)

prevent double check in four-way migration

Parameters

• elist – changeedge4

• edge – edge to be examined

Returns

src.basics.check_rules.check_migration(graph)

check rule migration

Parameters

graph – a StrandGraph object

Returns

changeedge3: edges to be changed in three-way migration changeedge4: edges to be changed in four-way migration

src.basics.check_rules.check_unbinding(graph)

check rule unbinding

Parameters

graph – a StrandGraph object

Returns

edges to be deleted

src.basics.generate_pysbmodel module

src.basics.generate_pysbmodel.generate_concentrations(initlen, concentrations)

generate concentrations of the initial species

Parameters

• initlen – number of the initial species

• concentrations – concentrations of the initial species

Returns

PySB parameters for concentrations

src.basics.generate_pysbmodel.generate_model(specieslist, reactionlist, initlen, initnames, concentrations, defobs=[])

generate a PySB model for the DSD reaction network

Parameters

• specieslist – list of species that can be synthesized in the DSD system

• reactionlist – list of reactions that can happen in the DSD system

• initlen – number of the initial species

• initnames – names of the initial species

• concentrations – concentrations of the initial species

• defobs – a debug argument for defining observables

Returns

a PySB model

src.basics.generate_pysbmodel.generate_monomer(species, monomerdict, initlen, initnames, tbobs)

generate a PySB monomer based on species

Parameters

• species – a Species object

• monomerdict – a dictionary with all monomers linked to their species id

• initlen – number of the initial species

• initnames – names of the initial species

Returns

monomer, observable, and updated monomerdict

src.basics.generate_pysbmodel.generate_rule(reaction, i, monomerdict, rate)

generate a PySB rule based on reaction

Parameters

• reaction – a Reaction object

• i – ordered position of reaction in reactionlist

• monomerdict – a dictionary with all monomers linked to their species id

• rate – reaction rate, a Parameter object

Returns

PySB rule

src.basics.initialize_system module

src.basics.initialize_system.get_additional_info(fp, line)

get additional info from input

Parameters

• fp – opened file

• line – current line

Returns

names of initial species, concentrations of initial species, a dictionary object of kinetics, output directory, simulation parameters

src.basics.initialize_system.get_kinetics(fp, line)

get the kinetics info from input

Parameters

• fp – opened file

• line – current line

Returns

a dictionary object of kinetics, output directory, simulation parameters

src.basics.initialize_system.get_outdir_simupara(fp, line)

get output directory and simulation parameters (in format: time steps)

Parameters

• fp – opened file

• line – current line

Returns

output directory and simulation parameters

Note: output directory is ‘’ if not specified and list of simulation parameters is empty if not specified

src.basics.initialize_system.initialize(filedir)

initialize the DSD system

Parameters

filedir – file directory of the input

Returns

specieslist, speciesidmap, kinetics, names, concentrations, output directory, simulation parameters

src.basics.lexical_analyzer module

src.basics.lexical_analyzer.lexer_site(string)

src.basics.lexical_analyzer.lexer_strand(str, cnt)

a lexer for transforming strand in any canonical form to a Strand object

Parameters

• str – string

• cnt – count

Returns

a Strand object

src.basics.output module

Module contents