deltaG mfe brainstorm

gistfile1.txt

class RNA_MFE_Calculator:

    Sequence seq
    BindSite[] bind_sites
    
    float base_MFE()
    
    float calcDeltaG(BindSite[])


##############

rna_calc = RNA_MFE_Calculator(rna_seq, bind_sites)

# For every combination in bind_sites

deldelGList = []

for site1 in rna_calc.bind_sites:
    for site2 in rna_calc.bind_sites:
        
        // logic to skip overlapping, the same, or whatever.
        
        delDelG = rna_calc.calcDeltaG([site1, site2]) \
                - rna_calc.calcDeltaG(site1) \
                - rna_calc.calcDeltaG(site2)
        
        deldelGList.append([site1, site2, delDelG])