nuskell.ioutils

exception nuskell.ioutils.NuskellObjectError[source]
nuskell.ioutils.get_domains(complexes)[source]

Return a set of domains present in the TestTube.

nuskell.ioutils.get_strands(complexes)[source]

Return a set of strands present in the TestTube.

nuskell.ioutils.load_pil(data, is_file=False)[source]

Parses a string or file written in PIL notation!

nuskell.ioutils.write_pil(solution, reactions, fh=None, molarity='nM', crn=None, fsc=None, ts=None)[source]

Write the contents of solution into a PIL file (kernel notation).

Parameters:

  • solution (dict) – A dictionary containing all the complexes in solution.

  • fh (filehandle) – A filehandle that the output is written to or None.

  • molarity (str, optional) – Specify a molarity of concentrations (M, mM, uM, nM, pM).

  • crn (list[list], optional) – a nuskell-style CRN expression

  • fsc (dict, optional) – formal species and their concentrations.

  • ts (str, optional) – name of the translation scheme

Example

length d1 = 6 length d2 = 4 length h3 = 1 cplx1 = h3 d1( d2( + )) @ initial 10 nM

nuskell.ioutils.write_vdsd(solution, fh=None, molarity='nM', crn=None, fsc=None, ts=None)[source]

Write the contents of solution into VisualDSD *.dna format.

Parameters:

  • solution (dict) – A dictionary containing all the complexes in solution.

  • fh (filehandle) – A filehandle that the output is written to or None.

  • molarity (str, optional) – Specify a molarity of concentrations (M, mM, uM, nM, pM).

  • crn (list[list], optional) – a nuskell-style CRN expression

  • fsc (dict, optional) – formal species and their concentrations.

  • ts (str, optional) – name of the translation scheme

Note

This function assumes that toehold domains are named starting with a ‘t’, history domains start with a ‘h’ and anti-sense domains end with ‘*’.