pep.pep

Functions

print_token_by_line(v)	Prints tokens separated by spaces on their original line (with line numbering)
processPostfixOperator(postfixStack, operator)	Compares the provided operator with a postfix stack to determine where to place a new operator (output list or stack)
process_tokens(tokens, parent, index)	Process tokens recurently and return a P system structure (or a subcomponent of the same type as parent)
readInputFile(filename[, printTokens])	parses the given input file and produces a P system object
tokenize(code)	generate a token list of input text

Classes

DistributionFunction()	Distribution function class (list of distribution rules)
DistributionRule()	Class for the distribution rules that make up a program, together with the production rules
Membrane([parentMembrane])	Membrane class, that can contain other membranes or be part of another membrane
MembraneStructure()	P system membrane structure (list of structural elements)
NumericalPsystem()	Numerical P systems class
OperatorType	Enumeration of operator types, ordered by precedence in calculus
Pobject([name, value])	Mutable objects that are needed in order to allow all membranes that use the P object to globally modify the object
ProductionFunction()	Production function class that stores expressions using the postfix (reversed polish) form
Program()	Program class
Token(type, value, line, column)

class pep.pep.DistributionFunction

Distribution function class (list of distribution rules)

Variables:

• proportionTotal (int) – the sum of all proportions
• expression (str) – string representation of the distribution function

distribute(newValue)

Update the variables referenced in the distribution rules according to the specified proportions :newValue: a value that has to be distributed to the variables based on the proportions specified in the distribution rules

class pep.pep.DistributionRule

Class for the distribution rules that make up a program, together with the production rules

Variables:

• proportion (int) –
• variable (Pobject) –

print(indentSpaces=2, toString=False)

Print a distribution rule with a given indentation level

IndentSpaces:number of spaces used for indentation ToString:write to a string instead of stdout Returns:string print of the rule if toString = True otherwise returns None

class pep.pep.Membrane(parentMembrane=None)

Membrane class, that can contain other membranes or be part of another membrane

Variables:

• variables (list(Pobject)) – array of P objects
• programs (list(Program)) – list of Program objects
• chosenProgramNr (int|list) – the program nr that was chosen for execution OR array of chosen program numbers when enzymes are used
• newValue (double|list(double)) – the value that was produced during the previous production phase OR array of values when using enzymes
• enzymes (list(Pobject)) – array of enzyme P objects
• parent (Membrane) – parent membrane (Membrane object)
• children (dict) – map (dictioanry) between String membrane_name: Membrane object

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

Print a membrane 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

class pep.pep.MembraneStructure

P system membrane structure (list of structural elements)

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

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

class pep.pep.OperatorType

Enumeration of operator types, ordered by precedence in calculus

class pep.pep.Pobject(name='', value=0)

Mutable objects that are needed in order to allow all membranes that use the P object to globally modify the object

Variables:

• name (str) –
• value (double) –
• wasConsumed (boolean) – was consumed in production function

class pep.pep.ProductionFunction

Production function class that stores expressions using the postfix (reversed polish) form

Variables:

• infixExpression (str) – string representation of the original expression from the input file (written in infix form)
• postfixStack (list) – stack of operands and operators (auxiliary for postfix form)
• items (list) – list of operands and operators written in postfix (reverse polish) form

evaluate()

Evaluates the postfix form of a production function and returns the computed value. During the evaluation, Pobject references are replaced with their value. :returns: the computed value of the production function, as a numeric value

class pep.pep.Program

Program class

Variables:

• prodFunction (ProductionFunction) – ProductionFunction object
• distribFunction (DistributionFunction) – DistributionFunction object
• enzyme (Pobject) – Pobject if an enzyme is used for this program

isActivatedByEnzyme()

Checks whether the production function activation condition Enzyme > min(PROD_FUNCTION_VARIABLES) is true :returns: True / False

print(indentSpaces=2, toString=False)

Print a program with a given indentation level

IndentSpaces:number of spaces used for indentation ToString:write to a string instead of stdout Returns:string print of the rule if toString = True otherwise returns None

class pep.pep.Token(type, value, line, column)

column

Alias for field number 3

line

Alias for field number 2

type

Alias for field number 0

value

Alias for field number 1

pep.pep.print_token_by_line(v)

Prints tokens separated by spaces on their original line (with line numbering)

pep.pep.processPostfixOperator(postfixStack, operator)

Compares the provided operator with a postfix stack to determine where to place a new operator (output list or stack)

PostfixStack:stack used for operators Operator:OperatorType variable Returns:postfixStack, outputList - outputList == array of OperatorType elements that have been popped from the stack

pep.pep.process_tokens(tokens, parent, index)

Process tokens recurently and return a P system structure (or a subcomponent of the same type as parent)

Tokens:the list of tokens to be processed Parent:an object that represents the type of the result Index:the start index in the list of tokens Returns:index - the current index in the token list (after finishing this component) Returns:result - an object that is the result of processing the input parent and tokens

pep.pep.readInputFile(filename, printTokens=False)

parses the given input file and produces a P system object

Filename:string path to the file that will be parsed Returns:P system object

pep.pep.tokenize(code)

generate a token list of input text adapted from https://docs.python.org/3/library/re.html#writing-a-tokenizer