from biocrnpyler import *
# let's build the following CRN
# A -->[k1] 2B
# B -->[k2] C+D
# Species
A = Species("A")
B = Species("B")
C = Species("C")
D = Species("D")

#Reaction Rates
k1 = 3.
k2 = 1.4

#Reaction Objects
R1 = Reaction.from_massaction([A], [B, B], k_forward = k1)
R2 = Reaction.from_massaction([B], [C, D], k_forward = k2)

#Make a CRN
CRN = ChemicalReactionNetwork(species = [A, B, C, D], reactions = [R1, R2])
print(CRN)

from biocrnpyler import *

#Define a set of DNA parts
ptet = RegulatedPromoter("ptet",["tetr"],leak=True) #this is a promoter repressed by tetR and has a leak reaction
pconst = Promoter("pconst") #constitutive promoter
pcomb = CombinatorialPromoter("pcomb",["arac","laci"], leak=False, tx_capable_list = [["arac"], ["laci"]]) #the Combinations A and B or just A or just B be transcribed
utr1 = RBS("UTR1") #regular RBS
utr2 = RBS("UTR1") #regular RBS
gfp = CDS("GFP","GFP") #a CDS has a name and a protein name. so this one is called GFP and the protein is also called GFP
fusrfp = CDS("fusRFP","RFP",no_stop_codons=["forward"]) #you can say that a protein has no stop codon. This is a little different from a fusion protein, because in this case you are saying that the ribosome reads through two proteins but still produces two distinct proteins, rather than one fused protein. This can happen in the case of the ta peptide which causes a peptide bond not to be formed while making a protein.
rfp = CDS("RFP","RFP") #regular RFP
cfp = CDS("CFP","CFP") #cfp
t16 = Terminator("t16") #a terminator stops transcription

#Combine the parts together in a DNA_construct with their directions
construct = DNA_construct([[ptet,"forward"],[utr1,"forward"],[gfp,"forward"],[t16,"forward"],[t16,"reverse"],[rfp,"reverse"],[utr1,"reverse"],[pconst,"reverse"]])

#some very basic parameters are defined - these are sufficient for the whole model to compile!
parameters={"cooperativity":2,"kb":100, "ku":10, "ktx":.05, "ktl":.2, "kdeg":2,"kint":.05}

#Place the construct in a context (TxTlExtract models a bacterial lysate with machinery like Ribosomes and Polymerases modelled explicitly)
myMixture = TxTlExtract(name = "txtl", parameters = parameters, components = [construct])

#Compile the CRN
myCRN = myMixture.compile_crn()

#plotting not shown - but BioCRNpyler automatically produces interactive reaction network graphs to help visualize and debug complex CRNs!