pep.pep.NumericalPsystem

class pep.pep.NumericalPsystem

Numerical P systems class

Variables:

• H (array(str)) – array of strings (names of membranes)
• membranes (dict) – map (dictioanry) between String membrane_name: Membrane object
• structure (MembraneStructure) – MembraneStructure object (list of structural elements) [1 [2 ]2 ]1
• variables (list(Pobject)) – list of Pobjects that appear throughtout the P system
• enzymes (list(Pobject)) – list of enzyme Pobjects that appear throughtout the P system
• csvFile (file) – file used for Comma Separated Value output

__init__()

Methods

__init__()
openCsvFile()	Opens a .csv (Comma Separated Value) file where the values of all variables and enzymes are printed at each simulation step
print([indentSpaces, toString, withPrograms])	Print the entire Numerical P system with a given indentation level
runSimulationStep()	Runs 1 simulation step consisting of executing one program (production & dispersion functions) for all membranes that have programs
simulate([stepByStepConfirm, …])	Simulates the numericP system until one of the imposed limits is reached

openCsvFile()

Opens a .csv (Comma Separated Value) file where the values of all variables and enzymes are printed at each simulation step The output file is named using the pattern pep_DAY-MONTH-YEAR_HOUR-MINUTE-SECOND.csv

print(indentSpaces=2, toString=False, withPrograms=False)

Print the entire Numerical P system with a given indentation level

IndentSpaces:number of spaces used for indentation ToString:write to a string instead of stdout WithPrograms:print out the programs from each membrane, along with the membrane variables Returns:string print of the membrane if toString = True otherwise returns None

runSimulationStep()

Runs 1 simulation step consisting of executing one program (production & dispersion functions) for all membranes that have programs If a membrane has more than one program, one is chosen randomly for execution

simulate(stepByStepConfirm=False, printEachSystemState=True, maxSteps=-1, maxTime=-1)

Simulates the numericP system until one of the imposed limits is reached

StepByStepConfirm:  True / False - whether or not to wait for confirmation before starting the next simulation step PrintEachSystemState:  True / False - whether or not to print the P system state after the execution ofeach simulation step MaxSteps:The maximmum number of simulation steps to run MaxTime:The maximum time span that the entire simulation can last