bionetgen package
Subpackages
- bionetgen.atomizer package
- Subpackages
- bionetgen.atomizer.atomizer package
- Submodules
- bionetgen.atomizer.atomizer.analyzeRDF module
- bionetgen.atomizer.atomizer.analyzeSBML module
- bionetgen.atomizer.atomizer.atomizationAux module
- bionetgen.atomizer.atomizer.atomizerUtils module
- bionetgen.atomizer.atomizer.detectOntology module
- bionetgen.atomizer.atomizer.moleculeCreation module
- bionetgen.atomizer.atomizer.resolveSCT module
- Module contents
- bionetgen.atomizer.merging package
- bionetgen.atomizer.rulifier package
- Submodules
- bionetgen.atomizer.rulifier.arial10 module
- bionetgen.atomizer.rulifier.compareModels module
- bionetgen.atomizer.rulifier.componentGroups module
- bionetgen.atomizer.rulifier.parameterExtraction module
- bionetgen.atomizer.rulifier.postAnalysis module
- bionetgen.atomizer.rulifier.stateTransitionDiagram module
- bionetgen.atomizer.rulifier.stdgraph module
- Module contents
- bionetgen.atomizer.utils package
- Submodules
- bionetgen.atomizer.utils.annotationComparison module
- bionetgen.atomizer.utils.annotationDeletion module
- bionetgen.atomizer.utils.annotationExtender module
- bionetgen.atomizer.utils.annotationExtractor module
- bionetgen.atomizer.utils.annotationResolver module
- bionetgen.atomizer.utils.consoleCommands module
- bionetgen.atomizer.utils.extractAtomic module
- bionetgen.atomizer.utils.modelComparison module
- bionetgen.atomizer.utils.nameNormalizer module
- bionetgen.atomizer.utils.pathwaycommons module
- bionetgen.atomizer.utils.readBNGXML module
- bionetgen.atomizer.utils.smallStructures module
- bionetgen.atomizer.utils.structures module
- bionetgen.atomizer.utils.util module
- Module contents
- bionetgen.atomizer.writer package
- bionetgen.atomizer.atomizer package
- Submodules
- bionetgen.atomizer.atomizeTool module
- bionetgen.atomizer.biogrid module
- bionetgen.atomizer.bngModel module
ARule
Compartment
Function
Molecule
Observable
Parameter
Rule
Species
bngModel
bngModel.add_arule()
bngModel.add_compartment()
bngModel.add_function()
bngModel.add_molecule()
bngModel.add_observable()
bngModel.add_parameter()
bngModel.add_rule()
bngModel.add_species()
bngModel.add_time_rule()
bngModel.adjust_concentrations()
bngModel.adjust_frate_functions()
bngModel.adjust_volume_corrections()
bngModel.check_for_time_function()
bngModel.consolidate()
bngModel.consolidate_arules()
bngModel.consolidate_compartments()
bngModel.consolidate_molecules()
bngModel.consolidate_observables()
bngModel.make_arule()
bngModel.make_compartment()
bngModel.make_function()
bngModel.make_molecule()
bngModel.make_observable()
bngModel.make_parameter()
bngModel.make_rule()
bngModel.make_species()
bngModel.print_obs_map()
bngModel.remove_sympy_symbols()
bngModel.reorder_functions()
- bionetgen.atomizer.contactMap module
- bionetgen.atomizer.contextAnalyzer module
- bionetgen.atomizer.libsbml2bngl module
AnalysisResults
BNGL2XML()
analyzeFile()
analyzeHelper()
bondPartners()
changeDefs()
changeNames()
changeRates()
correctRulesWithParenthesis()
detectCustomDefinitions()
evaluation()
extractAtoms()
extractCompartmentCoIncidence()
extractCompartmentStatistics()
flatStatusVector()
getAnnotations()
getAnnotationsDict()
getFiles()
getMoleculeByName()
getRelationshipDegree()
handler()
isActivated()
listFiles()
loadBioGrid()
main()
main2()
postAnalysisHelper()
postAnalyzeFile()
postAnalyzeString()
processDir()
processFile()
processFile2()
processFile3()
processFunctions()
readFromString()
recursiveSearch()
reorderFunctions()
reorder_and_replace_arules()
resolveDependencies()
resource_path()
selectReactionDefinitions()
unrollFunctions()
validateReactionUsage()
- bionetgen.atomizer.parseAnnotation module
- bionetgen.atomizer.sbml2bngl module
SBML2BNGL
SBML2BNGL.adjustInitialConditions()
SBML2BNGL.analyzeReactionRate()
SBML2BNGL.calculate_factor()
SBML2BNGL.check_noCompartment()
SBML2BNGL.convertToName()
SBML2BNGL.convertToStandardUnitString()
SBML2BNGL.convertToStandardUnits()
SBML2BNGL.extractModelAnnotation()
SBML2BNGL.find_all_symbols()
SBML2BNGL.gather_terms()
SBML2BNGL.getAssignmentRules()
SBML2BNGL.getCompartments()
SBML2BNGL.getFullAnnotation()
SBML2BNGL.getInitialAssignments()
SBML2BNGL.getIsTreeNegative()
SBML2BNGL.getMetaInformation()
SBML2BNGL.getModelAnnotation()
SBML2BNGL.getParameters()
SBML2BNGL.getPrunnedTree()
SBML2BNGL.getRawSpecies()
SBML2BNGL.getReactionCenter()
SBML2BNGL.getReactions()
SBML2BNGL.getSBMLFunctions()
SBML2BNGL.getSpecies()
SBML2BNGL.getSpeciesAnnotation()
SBML2BNGL.getSpeciesInfo()
SBML2BNGL.getStandardName()
SBML2BNGL.getSymmetryFactors()
SBML2BNGL.getUnitDefinitions()
SBML2BNGL.isAmount()
SBML2BNGL.isSameNameDifferentCompartment()
SBML2BNGL.preProcessStoichiometry()
SBML2BNGL.reduceComponentSymmetryFactors()
SBML2BNGL.removeFactorFromMath()
SBML2BNGL.reset()
SBML2BNGL.setConversion()
SBML2BNGL.static_var()
SBML2BNGL.updateComponentCount()
SBML2BNGL.updateFunctionReference()
SBML2BNGL.writeLog()
comb()
factorial()
standardizeName()
sympyAnd
sympyGEQ
sympyGT
sympyIF
sympyLEQ
sympyLT
sympyNot
sympyOr
sympyPiece
unrollSBMLFunction()
- bionetgen.atomizer.sbml2json module
- bionetgen.atomizer.sbmlTranslator module
- Module contents
- Subpackages
- bionetgen.core package
- bionetgen.modelapi package
- Submodules
- bionetgen.modelapi.blocks module
- bionetgen.modelapi.bngfile module
- bionetgen.modelapi.bngparser module
- bionetgen.modelapi.model module
bngmodel
bngmodel.add_action()
bngmodel.add_actions_block()
bngmodel.add_block()
bngmodel.add_compartments_block()
bngmodel.add_empty_block()
bngmodel.add_energy_patterns_block()
bngmodel.add_functions_block()
bngmodel.add_molecule_types_block()
bngmodel.add_observables_block()
bngmodel.add_parameters_block()
bngmodel.add_population_maps_block()
bngmodel.add_rules_block()
bngmodel.add_species_block()
bngmodel.changes
bngmodel.recompile
bngmodel.reset_compilation_tags()
bngmodel.setup_simulator()
bngmodel.write_model()
- bionetgen.modelapi.pattern module
- bionetgen.modelapi.pattern_reader module
- bionetgen.modelapi.rulemod module
- bionetgen.modelapi.runner module
- bionetgen.modelapi.structs module
- bionetgen.modelapi.xmlparsers module
- Module contents
- bionetgen.network package
- Submodules
- bionetgen.network.blocks module
- bionetgen.network.network module
- bionetgen.network.networkparser module
- bionetgen.network.structs module
- Module contents
- bionetgen.simulator package
Submodules
bionetgen.main module
- class bionetgen.main.BNGBase(*args, **kw)[source]
Bases:
ArgparseController
Base cement controller for BioNetGen CLI
Used to set meta attributes like program name (label) as well as command line arguments. Each method is a subcommand in the command line with its own command line arguments.
Subcommands
- run
runs a model given by -i in folder given by -o
- notebook
generates and opens a notebook for a model given by -i, optional
- plot
plots a gdat/cdat/scan file given by -i into file supplied by -o
- info
provides version and path information about the BNG installation and dependencies
- visualize
provides various visualization options for BNG models
- class Meta[source]
Bases:
object
- arguments = [(['-v', '--version'], {'action': 'version', 'version': 'BioNetGen simple command line interface 0.8.0\nBioNetGen version: BioNetGen-2.8.5\nCement Framework 3.0.8\nPython 3.7.9\nPlatform Linux-5.15.0-1004-aws-x86_64-with-debian-buster-sid\n '}), (['-req', '--require'], {'action': <class 'bionetgen.main.requireAction'>, 'type': <class 'str'>, 'default': None}), (['-ll', '--log-level'], {'help': 'This option allows you to select a logging level, from quietest to loudest options are: "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG". Default is set to INFO', 'default': None, 'type': <class 'str'>})]
- description = 'A simple CLI to bionetgen <https://bionetgen.org>. Note that you need Perl installed.'
- help = 'bionetgen'
- label = 'bionetgen'
- info()[source]
Information subcommand to provide installation versions and paths.
Currently provides version information for BioNetGen, the BNG CLI, Perl, numpy, pandas, and libroadrunner. Also provides BNG2.pl and pyBNG paths.
- notebook()[source]
Notebook subcommand that boots up a Jupyter notebook using the nbopen library. It uses a BNGNotebook class defined in core/notebook.
The default template can be found under assets and in the future will likely be replaced by a standard templating tool (e.g. Jinja).
The default base template is agnostic to the model and if -i is given the template then will be adjusted to load in the model supplied.
- plot()[source]
Plotting subcommand for very basic plotting using a convenience function defined in core/main.
Currently we support gdat/cdat/scan file plotting, in a very basic manner. This command expects a space separated file where each column is a series. The first column is used for the x-axis and the rest is used as y-axis and every series is plotted.
See bionetgen plot -h for all the allowed options.
- run()[source]
This is the main run functionality of the CLI.
It uses a convenience function defined in core/main to run BNG2.pl using subprocess, given the set of arguments in the command line and the configuraions set by the defaults as well as the end-user.
- visualize()[source]
Subcommand to generate visualizations. Currently only supports visualize action from BioNetGen.
Types of visualizations and their options - Rule pattern visualization: Visualization of each rule as a bipartite graph - Rule operation visualization: Visualization of each rule showing explicit graph operations - Contact map: Visualize the contact map of the model - Regulatory graph: Visualize the regulatory graph of the model, also called atom rule graph
- class bionetgen.main.BioNetGen(label=None, **kw)[source]
Bases:
App
Cement app for BioNetGen CLI
Used to set configuration options like config default, exiting on close and setting log handler. Currently set attributes are below.
Attributes
- labelstr
name of the application
- config_defaultsstr
the default set of configuration options, set in BNGDefaults object
- config_handler: str
the name of the config handler, determines the syntax of the config files
- config_file_suffix: str
the suffix to be used for config files
- config_files: list of str
additional list of config files to enable
- exit_on_closeboolean
determine if the app should exit when the key function is ran
- extensionslist of str
extensions to be used with cement framework
- log_handler: str
name of the log handler
- handlers: list of obj
list of objects derived from cement.Controller that handles the actual CLI
- class Meta[source]
Bases:
object
- config_defaults = {'bionetgen': {'bngpath': '/home/docs/checkouts/readthedocs.org/user_builds/pybionetgen/checkouts/latest/bionetgen/bng-linux', 'cvode_include': None, 'cvode_lib': None, 'notebook': {'name': 'bng-notebook.ipynb', 'path': '/home/docs/checkouts/readthedocs.org/user_builds/pybionetgen/checkouts/latest/bionetgen/assets/bionetgen.ipynb', 'template': '/home/docs/checkouts/readthedocs.org/user_builds/pybionetgen/checkouts/latest/bionetgen/assets/bionetgen-temp.ipynb'}, 'stderr': 'STDOUT', 'stdout': 'PIPE'}}
- config_file_suffix = '.conf'
- config_files = ['./.bionetgen.conf']
- config_handler = 'configparser'
- exit_on_close = True
- extensions = ['colorlog']
- handlers = [<class 'bionetgen.main.BNGBase'>]
- label = 'bionetgen'
- log_handler = 'colorlog'