now write_pil can be used to write to a string instead of a filehandle.
0.6.1
Previous versions of peppercorn may break, if the latest version of the dsdobjects changes.
Now this should work just fine.
0.6
* The max-helix notion is now consistent with explanations of the upcoming manuscript. * Reject-remote 4-way mode requires now both sides to be remote. * reactions.py: separated the max-helix function (zipper) from the find_on_loop function
**peppercorn (executable)** * can specify composite-domains in PIL input * Sequence information of domains and concentrations of complexes will be present in the output, if they were specified in the input. * more commandline options Added "pilsimulator" (executable) for convenient ODE simulations of peppercorn results.
0.5
- new max helix semantics including 4-way branch migration - corrected calculation of condensed rates - new input standard are PIL files in kernel notation - using dsdobjects to define Domains, Complexes, Reactions and RestingSets