bionetgen.core package


bionetgen.core.defaults module

class bionetgen.core.defaults.BNGDefaults[source]

Bases: object


bionetgen.core.exc module

exception bionetgen.core.exc.BioNetGenError[source]

Bases: Exception

Generic errors.

bionetgen.core.main module

bionetgen.core.main.graphDiff(config, args)[source]
bionetgen.core.main.plotDAT(inp, out='.', kw={})[source]

Convenience function to plot dat/scan files from the CLI

Usage: plotDAT(inp, out, kw)


input gdat/cdat/scan file to plot


(optional) output file path, can be used to define the output format as well. Default is the current folder, filename is the same as the input file and default format is PNG.


(optional) this is a set of keyword arguments you want to pass for certain matplotlib options. Check -h for details

bionetgen.core.main.printInfo(config, args)[source]

Uses BNGInfo class to print BioNetGen information using arguments and config from Cement framework.

bionetgen.core.main.runAtomizeTool(config, args)[source]
bionetgen.core.main.runCLI(config, args)[source]

Convenience function to run from the CLI app

Usage: runCLI(config, args)


configuration dictionary from BioNetGen cement app


arguments parsed from the command line with argparser.

bionetgen.core.main.visualizeModel(config, args)[source]

Uses BNGVisualize class to visualize BNGL models using arguments and configuration from Cement framework.

bionetgen.core.notebook module

class bionetgen.core.notebook.BNGNotebook(nb_template, **kwargs)[source]

Bases: object

This is a class for writing BNG notebook from a template and given arguments.

Initalize with keywords to replace values in the template. E.g. BNGNotebook(template_file, TEST=”CHANGE”).write(outfile) will write the template file to outfile while changing every instance of “TEST” to “CHANGE”


the notebook template to use


the dictionary built from keywords the class is initalized with


writes the template file to outfile, replacing keywords


This method will overwrite the given arguments

bionetgen.core.plot module

bionetgen.core.result module

bionetgen.core.version module

bionetgen.core.version.get_version(version=(0, 6, 0, 'alpha', 0))[source]

Module contents