nuskell.framework

class nuskell.framework.ColorFormatter(msg, use_color=True)

format(record)

Format the specified record as text.

The record’s attribute dictionary is used as the operand to a string formatting operation which yields the returned string. Before formatting the dictionary, a couple of preparatory steps are carried out. The message attribute of the record is computed using LogRecord.getMessage(). If the formatting string uses the time (as determined by a call to usesTime(), formatTime() is called to format the event time. If there is exception information, it is formatted using formatException() and appended to the message.

nuskell.framework.assign_species(complexes)

The nuskell naming standard for all types of species.

nuskell.framework.get_nuskell_args(parser)

A collection of arguments for Nuskell

nuskell.framework.get_peppercorn_args(parser)

Selected arguments for the peppercorn interface.

nuskell.framework.main()

The nuskell command line interface.

Translates formal chemical reaction networks (CRNs) into domain-level strand displacement (DSD) systems. Enumerates DSD systems using the domain-level reaction enumerator “peppercorn”. Verifies the correctness of the traslation using the notions of “pathway decomposition”, “crn bisimulation”, or hybrid notions thereof using the Python package “crnverifier”. Use nuskell –help for options.

Nuskell can report every stage of the compilation by printing the corresponding *.pil file. After initial translation, this file only contains signal and fuel species. After enumeration it contains also the (potentially processed) enumerated reaction network.